Microorganisms doi: 10.3390/microorganisms12030606
Authors: Qingwei Jiang Feng Geng Juan Shen Ping Zhu Zhaoxin Lu Libang Zhou Fengxia Lu
Knock-out of genes of metabolic pathways is conventionally used in the metabolic engineering of microorganisms, but it is not applicable for genes of essential pathways. In order to avoid undesirable effects caused by gene deletion, it is attractive to develop riboswitches to dynamically control the metabolic pathways of microbial cell factories. In this regard, the aim of this study is to utilize the lysine riboswitch to control gene expressions of the biosynthetic pathways and by-pathways and thus improve lysine production in Corynebacterium glutamicum. To achieve this, a natural lysine riboswitch from Lactobacillus plantarum (LPRS) was first detected and then fused with RFP to test its functionality. After that, engineered lysine-activated (Lys-A) and lysine-repressed (Lys-R) riboswitches were successfully screened by dual genetic selection. Furthermore, the optimized A263 and R152 were applied to control the expression of aspartate kinase III and homoserine dehydrogenase in the lysine-producing strain C. glutamicum QW45, respectively. In contrast with QW45, the growth of the resulting A263-lysC mutant QW48 was similar to that of QW45; however, the growth of the resulting R357-hom mutant QW54 was slightly inhibited, indicating an inhibition of threonine biosynthesis caused by the riboswitch upon binding of intracellular lysine. Importantly, the lysine production of QW48 and QW54 was, respectively, 35% and 43% higher than that of the parent strain QW45, implying more metabolic flux directed into the lysine synthesis pathway. Finally, the engineered A263 and R357 were simultaneously applied to the same mutant QW55, which greatly improved lysine production. Thus, the approach demonstrated in this work could be principally used as a powerful tool to dynamically control any other undesired metabolic pathways.
]]>Microorganisms doi: 10.3390/microorganisms12030605
Authors: Raminta Antanynienė Vidmantas Stanys Birutė Frercks
A freely available Monilinia spp. marker database was created, containing microsatellite (SSR) data of the three most essential European fungal pathogens: M. fructigena, M. laxa, and M. fructicola. These pathogens cause brown rot blossom blight. Microsatellites were identified using the bioinformatics tool Genome-wide Microsatellite Analyzing Toward Application (GMATA). The database provides information about SSR markers: forward and reverse sequences of the primers, fragment sizes, SSR motifs (and repeats), and the exact locations with the coordinates in the reference genome. This database currently contains information about 39,216 SSR motifs and 26,366 markers. In total, eight primers generated in silico were validated experimentally and they are marked in the database. All scientists can join this collaboration by adding their experimental data. This database is the initial start of organizing Monilinia spp. molecular data worldwide and, in the future, it could be extended by adding more molecular and genomic information.
]]>Microorganisms doi: 10.3390/microorganisms12030604
Authors: Lea Ouaknin Hirsch Bharath Gandu Abhishiktha Chiliveru Irina Amar Dubrovin Shmuel Rozenfeld Alex Schechter Rivka Cahan
The bacterial anode in microbial fuel cells was modified by increasing the biofilm’s adhesion to the anode material using kaolin and graphite nanoparticles. The MFCs were inoculated with G. sulfurreducens, kaolin (12.5 g·L−1), and three different concentrations of graphite (0.25, 1.25, and 2.5 g·L−1). The modified anode with the graphite nanoparticles (1.25 g·L−1) showed the highest electroactivity and biofilm viability. A potential of 0.59, 0.45, and 0.23 V and a power density of 0.54 W·m−2, 0.3 W·m−2, and 0.2 W·m−2 were obtained by the MFCs based on kaolin–graphite nanoparticles, kaolin, and bare anodes, respectively. The kaolin–graphite anode exhibited the highest Coulombic efficiency (21%) compared with the kaolin (17%) and the bare (14%) anodes. Scanning electron microscopy and confocal laser scanning microscopy revealed a large amount of biofilm on the kaolin–graphite anode. We assume that the graphite nanoparticles increased the charge transfer between the bacteria that are in the biofilm and are far from the anode material. The addition of kaolin and graphite nanoparticles increased the attachment of several bacteria. Thus, for MFCs that are fed with wastewater, the modified anode should be prepared with a pure culture of G. sulfurreducens before adding wastewater that includes non-exoelectrogenic bacteria.
]]>Microorganisms doi: 10.3390/microorganisms12030603
Authors: Saanu Victoria Otite Bhushan P. Gandhi Esther Agyabeng Fofie Alfonso José Lag-Brotons Lawrence I. Ezemonye Alastair D. Martin Roger W. Pickup Kirk T. Semple
The effects of the inoculum (anaerobic digestion effluent) to substrate (simulated food waste) ratio (ISR) 4.00 to 0.25 on putative pathogens and microbial kinetics during batch mesophilic anaerobic digestion were investigated. Red fluorescent protein labelled (RFPAKN132) Escherichia coli JM105 was introduced as a marker species, and together with the indigenous Clostridium sp., Enterococcus sp., Escherichia coli, and total coliforms were used to monitor pathogen death kinetics. Quantitative polymerase chain reaction was also used to estimate the bacterial, fungal, and methanogenic gene copies. All the ISRs eliminated E. coli and other coliforms (4 log10 CFU/mL), but ISR 0.25 achieved this within the shortest time (≤2 days), while ISR 1.00 initially supported pathogen proliferation. Up to 1.5 log10 CFU/mL of Clostridium was reduced by acidogenic conditions (ISR 0.25 and 0.50), while Enterococcus species were resistant to the digestion conditions. Fungal DNA was reduced (≥5 log10 copies/mL) and was undetectable in ISRs 4.00, 2.00, and 0.50 at the end of the incubation period. This study has demonstrated that ISR influenced the pH of the digesters during batch mesophilic anaerobic digestion, and that acidic and alkaline conditions achieved by the lower (0.50 and 0.25) and higher (4.00 and 2.00) ISRs, respectively, were critical to the sanitisation of waste.
]]>Microorganisms doi: 10.3390/microorganisms12030602
Authors: Yue Zheng Xue Pan Jialei Hou Wenchong Shi Shuhong Sun Mengze Song Zheng Gao
Salmonella infection causes serious economic losses, threatens food safety, and is one of the most important diseases threatening meat duck farming. The gut microbiome is critical in providing resistance against colonization by exogenous microorganisms. Studying the relationship between Salmonella and gut microbiota can help us better understand the threat of the pathogenic mechanism of Salmonella and provide a more scientific theoretical basis for its prevention and treatment. This study uses Salmonella Typhimurium as the research object and Cherry Valley meat duck as the model with which to study the impact of Salmonella infection on ducks. In this field trial, 2 × 108 CFUs Salmonella Typhimurium were administered to 3-day-old ducks. After infection, duck viscera were collected to detect the colonization of Salmonella, and cecal contents were collected to analyze the changes in gut microbiota. The results show that Salmonella Typhimurium can colonize ducks three days after infection and alter the gut microbiota composition, mainly by increasing the abundance of Ruminococcaceae and Lachnospiraceae. In conclusion, Salmonella Typhimurium infection significantly alters the intestinal microbiota of ducks and poses a serious public health risk.
]]>Microorganisms doi: 10.3390/microorganisms12030601
Authors: Yue Hou Bo Han Zehua Lin Qizheng Liu Zhenhe Liu Hongbin Si Dandan Hu
Chicken coccidiosis costs the poultry industry over GBP 10 billion per year. The main method of preventing and controlling coccidiosis in chickens continues to be the use of drugs. Unfortunately, the prevalence of drug resistance in the field reduces or even eliminates the effectiveness of drugs, and drug residues in the food supply chain can also can be harmful to humans. Therefore, safe and effective anticoccidial drugs are urgently needed. Natural products have many advantages such as being safe, effective and inexpensive and are a sustainable way to control coccidiosis. In this study, the anticoccidial effects of six natural compounds were tested by Eimeria tenella infection. Oocyst production, cecum lesion, body weight gain, feed conversion ratio, and intestinal microbiota were measured. The results showed that nerolidol had a moderate effect on maintaining both body weight gain and feed conversion ratio. Silymarin and dihydroartemisinin showed significant anticoccidial effects by reducing total oocyst output. Dihydroartemisinin also significantly reduced the cecum lesion caused by Eimeria infection, but this compound may be toxic to the host at such informed doses because it decreases growth and survival rates. In addition, both silymarin and dihydroartemisinin partly restored the microbiota after challenge. This indicates that silymarin, dihydroartemisinin, and nerolidol are effective in the control of chicken coccidiosis. Our data provide basic knowledge about the anticoccidial effects of such natural compounds/derivates.
]]>Microorganisms doi: 10.3390/microorganisms12030600
Authors: Jun Wang Qinghe Zhu Xiaoxu Xing Dongbo Sun
Coronaviruses in general are a zoonotic pathogen with significant cross-species transmission. They are widely distributed in nature and have recently become a major threat to global public health. Vaccines are the preferred strategy for the prevention of coronaviruses. However, the rapid rate of virus mutation, large number of prevalent strains, and lag in vaccine development contribute to the continuing frequent occurrence of coronavirus diseases. There is an urgent need for new antiviral strategies to address coronavirus infections effectively. Antiviral drugs are important in the prevention and control of viral diseases. Members of the genus coronavirus are highly similar in life-cycle processes such as viral invasion and replication. These, together with the high degree of similarity in the protein sequences and structures of viruses in the same genus, provide common targets for antiviral drug screening of coronaviruses and have led to important advances in recent years. In this review, we summarize the pathogenic mechanisms of coronavirus, common drugs targeting coronavirus entry into host cells, and common drug targets against coronaviruses based on biosynthesis and on viral assembly and release. We also describe the common targets of antiviral drugs against coronaviruses and the progress of antiviral drug research. Our aim is to provide a theoretical basis for the development of antiviral drugs and to accelerate the development and utilization of commonly used antiviral drugs in China.
]]>Microorganisms doi: 10.3390/microorganisms12030599
Authors: Laura Sneller Christine Lin Angie Price Shyam Kottilil Joel V. Chua
Chronic hepatitis B (CHB) is a global health challenge that can result in significant liver-related morbidity and mortality. Despite a prophylactic vaccine being available, patients already living with CHB often must engage in lifelong therapy with nucleoside analogues. However, the potential of RNA interference (RNAi) therapeutics as a promising avenue for CHB treatment is being explored. RNAi, particularly using small interfering RNA (siRNA), targets viral RNA that can be used to inhibit hepatitis B virus (HBV) replication. Several candidates are currently being studied and have exhibited varying success in reducing hepatitis B surface antigen (HBsAg) levels, with some showing sustained HBsAg loss after cessation of therapy. The dynamic evolution of RNAi therapy presents a promising trajectory for the development of effective and sustained treatments for CHB. This review highlights recent findings on RNAi therapeutics, including modifications for stability, various delivery vectors, and specific candidates currently in development.
]]>Microorganisms doi: 10.3390/microorganisms12030598
Authors: Olga Gavrilova Aleksandra Orina Ilya Trubin Tatiana Gagkaeva
Dry rot of potato tubers is a harmful disease caused by species of the Fusarium genus. Studies on the composition and features of Fusarium spp. that cause the disease in Russia are limited. Thirty-one Fusarium strains belonging to the F. sambucinum species complex (FSAMSC) and F. solani species complex (FSSC) were accurately identified using multilocus phylogenetic analysis of the tef and rpb2 loci, and their physiological characteristics were studied in detail. As a result, 21 strains of F. sambucinum s. str. and 1 strain of F. venenatum within the FSAMSC were identified. Among the analyzed strains within the FSSC, one strain of F. mori, four strains of F. noneumartii, and two strains of both F. stercicola and F. vanettenii species were identified. This is the first record of F. mori on potato as a novel host plant, and the first detection of F. noneumartii and F. stercicola species in Russia. The clear optimal temperature for the growth of the strains belonging to FSAMSC was noted to be 25 °C, with a growth rate of 11.6–15.0 mm/day, whereas, for the strains belonging to FSSC, the optimal temperature range was between 25 and 30 °C, with a growth rate of 5.5–14.1 mm/day. The distinctive ability of F. sambucinum strains to grow at 5 °C has been demonstrated. All analyzed Fusarium strains were pathogenic to potato cv. Gala and caused extensive damage of the tuber tissue at an incubation temperature of 23 °C for one month. Among the fungi belonging to the FSAMSC, the F. sambucinum strains were more aggressive and caused 23.9 ± 2.2 mm of necrosis in the tubers on average compared to the F. venenatum strain—17.7 ± 1.2 mm. Among the fungi belonging to the FSSC, the F. noneumartii strains were the most aggressive and caused 32.2 ± 0.8 mm of necrosis on average. The aggressiveness of the F. mori, F. stercicola, and especially the F. vanettenii strains was significantly lower: the average sizes of damage were 17.5 ± 0.5 mm, 17.2 ± 0.2 mm, and 12.5 ± 1.7 mm, respectively. At an incubation temperature of 5 °C, only the F. sambucinum strains caused tuber necroses in the range of 6.7 ± 0.5–15.9 ± 0.8 mm.
]]>Microorganisms doi: 10.3390/microorganisms12030595
Authors: Pilar Blanco Isaac Rodríguez Victoria Fernández-Fernández María Ramil David Castrillo Marta Acín-Albiac Irene Adamo Clara Fernández-Trujillo Beatriz García-Jiménez Alberto Acedo Noemi Calvo-Portela Andrea Parente-Sendín Lara Acemel-Míguez Flora Alonso-Vega
Agricultural management influences the soil ecosystem by affecting its physicochemical properties, residues of pesticides and microbiome. As vineyards grow crops with the highest incidence of pesticides, the aim of this study was to evaluate the impact of conventional and sustainable management systems of vineyards from DOP Ribeiro on the soil’s condition. Samples from soils under three different management systems were collected, and the main soil physicochemical properties were evaluated. A selection of 50 pesticides were investigated by liquid chromatography with tandem mass spectrometry. The bacterial and fungal microbiomes were characterized through amplicon sequencing. The results show that organic agriculture positively influences soil pH and the concentration of some nutrients compared to conventional management. Our microbiome analysis demonstrated that transitioning from conventional to organic management significantly improves several BeCrop® indexes related to key microbial metabolism and soil bio-sustainability. Such a transition does not affect soil alpha diversity, but leads to a higher interconnected microbial network structure. Moreover, differential core genera and species for each management system are observed. In addition, the correlation of the microbiome with geographical distance is evidence of the existence of different microbial terroirs within DOP Ribeiro. Indeed, sustainable management leads to higher nutrient availability and enhances soil health in the short term, while lowering pesticide usage.
]]>Microorganisms doi: 10.3390/microorganisms12030597
Authors: Natalia S. Egozarian Elena V. Emelyanova Nataliya E. Suzina Olesya I. Sazonova Valentina N. Polivtseva Tatiana O. Anokhina Yonghong Wu Inna P. Solyanikova
Biodegradation of phenol is an effective method for removing this toxicant from contaminated sites. Phenol is a toxic compound for living cells, so many bacteria degrade phenol in relatively low concentrations, up to 0.75 g L−1. The Rhodococcus opacus strain 1CP is an effective destructor of a wide range of pollutants. In the absence of a carbon source in the medium, cells of the R. opacus 1CP strain easily form cyst-like resting cells (CLC). The purpose of this work was to evaluate the viability of cells during long-term storage and the efficiency of the process of phenol destruction by R. opacus 1CP cells germinating after dormancy. Resting cells were obtained by simple cultivation in a rich medium followed by storage under static conditions. This is a simple approach to obtain a large amount of biomass. Decomposition of phenol proceeded via catechol followed by ortho-cleavage of aromatic ring. The induction of three phenol hydroxylases was detected by RT-PCR in cells germinated in a mineral medium with phenol as the carbon source. The stability of the genome of cells germinating after dormancy is shown by box-PCR. Dormant R. opacus 1CP cells, both suspended and immobilized, can be directly used for the decomposition of phenol after 4–12 months storage. In addition to phenol, after 9 months of storage, immobilized germinating cells easily metabolized 4-chlorophenol and 2,4,6-trichlorophenol. The results demonstrate a potential and simple approach toward achieving long-term storage of cells for further use in bioremediation.
]]>Microorganisms doi: 10.3390/microorganisms12030596
Authors: Lubna Osman Christopher Lopez Yoichiro Natori Shweta Anjan Julia Bini Viotti Jacques Simkins
Mycobacterium abscessus complex (MABC), a rapidly growing Mycobacterium, is one of the most common causes of non-tuberculous mycobacteria (NTM) infections in the United States of America, and it has been associated with a wide spectrum of infections in immunocompetent and immunosuppressed individuals. Eradicating MABC is very challenging, even with prolonged combination therapies. The management of MABC infections in solid organ transplant (SOT) patients is usually complex given their net state of immunosuppression, associated comorbidities, and potential drug–drug interactions, among other things. In this manuscript, we discussed the antimicrobial management of pulmonary and extrapulmonary MABC infections. In addition, we reviewed promising novel therapies such as clofazimine, omadacycline, bedaquiline, and inhaled tigecycline that could join the existing antimicrobial armamentarium to fight this infection associated with significant morbidity and mortality. However, further studies are needed, especially among the immunocompromised host.
]]>Microorganisms doi: 10.3390/microorganisms12030594
Authors: Lis Alvarez Baranowski Helver Gonçalves Dias Débora Familiar-Macedo Gilberto Sabino-Santos Heitor Miraglia Herrera Renata Dezengrini Slhessarenko Flávia Barreto dos Santos Alex Pauvolid-Corrêa
Following the first report of zika virus in March 2015, Brazil experienced its largest sylvatic yellow fever outbreak between 2016 and 2019. This study aimed to investigate the circulation of yellow fever virus (YFV) in non-human primates (NHPs) and mosquitoes collected in urban parks and other metropolitan areas of midwest Brazil between 2017 and 2018. Whole blood samples from 80 NHPs, including 48 black-tailed marmosets (Mico melanurus) and 2332 mosquitoes from six different genera, were collected in the states of Mato Grosso (MT) and Mato Grosso do Sul (MS) and then tested for YFV by RT-qPCR. Additionally, 23 plasma samples of NHPs were tested for neutralizing antibodies for YFV by a plaque reduction neutralization test (PRNT). No YFV RNA or neutralizing antibodies for YFV were detected in NHPs and mosquitoes from MT and MS. The continuous monitoring of YFV circulation in different species of NHPs and vectors in urban areas is instrumental to quickly assess potentially unknown maintenance cycles of yellow fever at the human–animal interface in Brazil.
]]>Microorganisms doi: 10.3390/microorganisms12030593
Authors: Lucas Rafael Santana Pinheiro Érika Dayane Leal Rodrigues Francisco Amilton dos Santos Paiva Ana Cecília Ribeiro Cruz Daniele Barbosa de Almeida Medeiros Alexandre do Rosário Casseb Sandro Patroca da Silva Livia Medeiros Neves Casseb
Bats are widely distributed in Brazil, including the Amazon region, and their association with viral pathogens is well-known. This work aimed to evaluate the metavirome in samples of Molossus sp. bats captured in the Brazilian Amazon from 2019 to 2021. Lung samples from 58 bats were divided into 13 pools for RNA isolation and sequencing followed by bioinformatic analysis. The Retroviridae family showed the highest abundance of viral reads. Although no complete genome could be recovered, the Paramyxoviridae and Dicistroviridae families showed the formation of contigs with satisfactory identity and size characteristics for further analysis. One contig of the Paramyxoviridae family was characterized as belonging to the genus Morbillivirus, being grouped most closely phylogenetically to Porcine morbillivirus. The contig related to the Dicistroviridae family was identified within the Cripavirus genus, with 94%, 91%, and 42% amino acid identity with Culex dicistrovirus 2, Rhopalosiphum padi, and Aphid lethal paralysis, respectively. The presence of viruses in bats needs constant updating since the study was able to identify viral sequences related to families or genera still poorly described in the literature in association with bats.
]]>Microorganisms doi: 10.3390/microorganisms12030592
Authors: La Lai Shuqi Li Shaoping Zhang Manchun Liu Lianwei Xia Yuan Ren Tangbing Cui
We investigated biostimulation as an effective strategy for enhancing the degradation efficiency of recalcitrant organic compounds, with MSC14 (a novel polycyclic aromatic hydrocarbon degrading bacterium Pantoea dispersa MSC14) as the study material. Here, we investigated the impact of sodium gluconate on MSC14-mediated degradation of B[a]p. This study focused on the application of sodium gluconate, a biostimulant, on MSC14, targeting Benzo[a]pyrene (B[a]p) as the model pollutant. In this study, the novel PAHs-degrading bacterium P. dispersa MSC14 demonstrated the capability to degrade 24.41% of B[a]p after 4 days. The addition of the selected sodium gluconate stimulant at a concentration of 4 g/L stimulated MSC14 to degrade 54.85% of B[a]p after 16 h. Intermediate metabolites were analyzed using gas chromatography-mass spectrometry to infer the degradation pathway. The findings indicated that sodium gluconate promoted the intracellular transport of B[a]p by MSC14, along with the secretion of biosurfactants, enhancing emulsification and solubilization capabilities for improved B[a]p dissolution and degradation. Further analysis through transmission electron microscopy (TEM) and scanning electron microscopy (SEM) revealed the formation of a biofilm by MSC14 and an increase in flagella as a response to B[a]p stress. Transcriptome profiling elucidated the interplay of quorum sensing systems, chemotaxis systems, and flagellar systems in the degradation mechanism. Additionally, the study uncovered the molecular basis of B[a]p transport, degradation pathways, metabolic changes, and genetic regulation. In summary, the addition of sodium gluconate promotes the degradation of B[a]p by P. dispersa MSC14, offering the advantages of being rapid, efficient, and cost-effective. This research provides an economically viable approach for the remediation of petroleum hydrocarbon pollution, with broad potential applications.
]]>Microorganisms doi: 10.3390/microorganisms12030591
Authors: Sarah Dräger Flavio Bruni Melina Bernasconi Anya Hammann-Hänni Vlastimil Jirasko Alexander Tanno Yves Blickenstorfer Karoline Leuzinger Hans H. Hirsch Michael Osthoff
This study compared SARS-CoV-2 RNA loads at different anatomical sites, and the impact of self-swabbing and food intake. Adult symptomatic patients with SARS-CoV-2 or non-SARS-CoV-2 respiratory tract infection were included between 2021 and 2022. Patients performed a nasal and buccal swab before a professionally collected nasopharyngeal/oropharyngeal swab (NOPS). Buccal swabs were collected fasting and after breakfast in a subgroup of patients. SARS-CoV-2 RNA loads were determined by nucleic acid testing. Swabbing convenience was evaluated using a survey. The median age of 199 patients was 54 years (interquartile range 38–68); 42% were female and 52% tested positive for SARS-CoV-2. The majority of patients (70%) were hospitalized. The mean SARS-CoV-2 RNA load was 6.6 log10 copies/mL (standard deviation (SD), ±1.5), 5.6 log10 copies/mL (SD ± 1.9), and 3.4 log10 copies/mL (SD ± 1.9) in the professionally collected NOPS, and self-collected nasal and buccal swabs, respectively (p < 0.0001). Sensitivity was 96.1% (95% CI 90.4–98.9) and 75.3% (95% CI 63.9–81.8) for the nasal and buccal swabs, respectively. After food intake, SARS-CoV-2 RNA load decreased (p = 0.0006). Buccal swabbing was the preferred sampling procedure for the patients. In conclusion, NOPS yielded the highest SARS-CoV-2 RNA loads. Nasal self-swabbing emerged as a reliable alternative in contrast to buccal swabs. If buccal swabs are used, they should be performed before food intake.
]]>Microorganisms doi: 10.3390/microorganisms12030590
Authors: Quansheng Wang Haijun Long Huiqi Wang Maggie C. Y. Lau Vetter
Acidophiles are capable of surviving in extreme environments with low pH. Acidithiobacillus ferrooxidans is a typical acidophilic bacterium that has been extensively studied when grown chemoautotrophically, i.e., when it derives energy from oxidation of Fe2+ or reduced inorganic sulfur compounds (RISCs). Although it is also known to grow with electrons supplied by solid electrodes serving as the sole source of energy, the understanding of its electroautotrophic growth is still limited. This study aimed to compare the growth characteristics of A. ferrooxidans under electroautotrophic (ea) and chemoautotrophic (ca) conditions, with an attempt to elucidate the possible mechanism(s) of extracellular electron flow into the cells. Jarosite was identified by Raman spectroscopy, and it accumulated when A. ferrooxidans used Fe2+ as the electron donor, but negligible mineral deposition occurred during electroautotrophic growth. Scanning electron microscopy (SEM) showed that A. ferrooxidans possesses more pili and extracellular polymeric substances (EPSs) under electroautotrophic conditions. A total of 493 differentially expressed genes (DEGs) were identified, with 297 genes being down-regulated and 196 genes being up-regulated in ea versus ca conditions. The genes known to be essential for chemoautotrophic growth showed a decreased expression in the electroautotrophic condition; meanwhile, there was an increased expression of genes related to direct electron transfer across the cell’s outer/inner membranes and transmembrane proteins such as pilin and porin. Joint analysis of DEGs and differentially expressed metabolites (DEMs) showed that galactose metabolism is enhanced during electroautotrophic growth, inducing A. ferrooxidans to produce more EPSs, which aids the cells in adhering to the solid electrode during their growth. These results suggested that electroautotrophy and chemoautotrophy of A. ferrooxidans have different extracellular electron uptake (EEU) pathways, and a model of EEU during electroautotrophic growth is proposed. The use of extracellular electrons as the sole energy source triggers A. ferrooxidans to adopt metabolic and subsequently phenotypic modifications.
]]>Microorganisms doi: 10.3390/microorganisms12030589
Authors: Lei Wang Ying Hua Xiangning Bai Ji Zhang Sara Mernelius Milan Chromek Anne Frykman Sverker Hansson Andreas Matussek
Shiga toxin-producing Escherichia coli (STEC) infection can cause a broad spectrum of symptoms spanning from asymptomatic shedding to mild and bloody diarrhea (BD) and even life-threatening hemolytic-uremic syndrome (HUS). As a member of the serine protease autotransporters of Enterobacteriaceae (SPATE) family, EspP has the ability to degrade human coagulation factor V, leading to mucosal bleeding, and also plays a role in bacteria adhesion to the surface of host cells. Here, we investigated the prevalence and genetic diversity of espP among clinical STEC isolates from patients with mild diarrhea, BD, and HUS, as well as from asymptomatic individuals, and assessed the presence of espP and its subtypes in correlation to disease severity. We found that 130 out of 239 (54.4%) clinical STEC strains were espP positive, and the presence of espP was significantly associated with BD, HUS, and O157:H7 serotype. Eighteen unique espP genotypes (GTs) were identified and categorized into four espP subtypes, i.e., espPα (119, 91.5%), espPγ (5, 3.8%), espPδ (4, 3.1%), and espPε (2, 1.5%). espPα was widely distributed, especially in strains from patients with BD and HUS, and correlated with serotype O157:H7. Serogroup O26, O145, O121, and O103 strains carried espPα only. Ten GTs were identified in espPα, and espPα/GT2 was significantly associated with severe disease, i.e., BD and HUS. Additionally, espP was strongly linked to the presence of eae gene, and the coexistence of espPα and stx2/stx2a + stx2c was closely related to HUS status. To sum up, our data demonstrated a high prevalence and genetic diversity of the espP gene in clinical STEC strains in Sweden and revealed an association between the presence of espP, espP subtypes, and disease severity. espP, particularly the espPα subtype, was prone to be present in more virulent STEC strains, e.g., “top-six” serotypes strains.
]]>Microorganisms doi: 10.3390/microorganisms12030588
Authors: Yuta Chiba Yasuhiro Takenaka Nobuyuki Haga
The process of sexual reproduction in eukaryotes starts when gametes from two different sexes encounter each other. Paramecium, a unicellular eukaryote, undergoes conjugation and uses a gametic nucleus to enter the sexual reproductive process. The molecules responsible for recognizing mating partners, hypothetically called mating-type substances, are still unclear. We have identified an O3-type mating substance polypeptide and its gene sequence using protein chemistry, molecular genetics, immunofluorescence, RNA interference, and microinjection. The O3-type substance is a polypeptide found in the ciliary membranes, located from the head to the ventral side of cells. The O3-type substance has a kinase-like domain in its N-terminal part located outside the cell and four EF-hand motifs that bind calcium ions in its C-terminal part located inside the cell. RNA interference and immunofluorescence revealed that this polypeptide positively correlated with the expression of mating reactivity. Microinjection of an expression vector incorporating the O3Pc-MSP gene (Oms3) induced additional O3 mating type in the recipient clones of different mating types or syngen. Phylogenetic analysis indicates that this gene is widely present in eukaryotes and exhibits high homology among closely related species. The O3Pc-MSP (Oms3) gene had nine silent mutations compared to the complementary mating type of the E3 homologue gene.
]]>Microorganisms doi: 10.3390/microorganisms12030587
Authors: Karina Andrea Büttner Andrea Carolina Entrocassi María Lucía Gallo Vaulet Deysi López Aquino Dolores Caffarena Luciana La Rosa Laura Svidler López Osvaldo Degregorio Björn Herrmann Marcelo Rodríguez Fermepin
Since the Lymphogranuloma venereum (LGV) outbreak was first described in Buenos Aires in 2017, the detected strains presented peculiar characteristics. Our goal was to increase the understanding of the strains involved in the LGV outbreak in Argentina. We characterized the ompA gene sequences, using Sanger sequencing, of 88 LGV strains from 239 symptomatic patients in Buenos Aires enrolled between 2017 and 2019, and selected 20 C. trachomatis strains for further characterization using Multilocus Sequence Typing (MLST). Following the ompA gene analysis of the 88 LGV strains, we detected 43% L2b, 31% L1-like, and 26% L2. Among the 38 L2b samples analyzed, there were 7 distinct sequences, 3 of them not previously reported (L2bv12, L2bv13, and L2bv14). Additionally, we detected a strain with a new mutation (AM884176.1:g.59122A>T) found in the position defining L2 or L2b, proposed as L2i. Using MLST, five different sequence types (STs) were detected, including the ST2 (corresponding to the L1-like strains) and a new one (ST60). ST58 was associated with the concomitant presence of another STI and HIV. A high genetic diversity in C. trachomatis LGV strains in Argentina was observed in a short period of time, with a relatively low number of samples from a limited geographical area.
]]>Microorganisms doi: 10.3390/microorganisms12030586
Authors: María Fernández-Álvarez Pilar Horcajo Alejandro Jiménez-Meléndez Pablo Angulo Lara Ana Huertas-López Francisco Huertas-López Ignacio Ferre Luis Miguel Ortega-Mora Gema Álvarez-García
Endothelial injury, inflammatory infiltrate and fibrosis are the predominant lesions in the testis of bulls with besnoitiosis that may result in sterility. Moreover, fibroblasts, which are key players in fibrosis, are parasite target cells in a Besnoitia besnoiti chronic infection. This study aimed to decipher the molecular basis that underlies a drift toward fibrosis during the disease progression. Transcriptomic analysis was developed at two times post-infection (p.i.), representative of invasion (12 h p.i.) and intracellular proliferation (32 h p.i.), in primary bovine aorta fibroblasts infected with B. besnoiti tachyzoites. Once the enriched host pathways were identified, we studied the expression of selected differentially expressed genes (DEGs) in the scrotal skin of sterile infected bulls. Functional enrichment analyses of DEGs revealed shared hallmarks of cancer and early fibrosis. Biomarkers of inflammation, angiogenesis, cancer, and MAPK signaling stood out at 12 h p.i. At 32 h p.i., again MAPK and cancer pathways were enriched together with the PI3K–AKT pathway related to cell proliferation. Some DEGs were also regulated in the skin samples of naturally infected bulls (PLAUR, TGFβ1, FOSB). We have identified potential biomarkers and host pathways regulated during fibrosis that may hold prognostic significance and could emerge as potential therapeutic targets.
]]>Microorganisms doi: 10.3390/microorganisms12030585
Authors: Zhaojing Yu Bin Wang Xiaoyan Wu Runlan Yu Li Shen Xueling Wu Jiaokun Li Yuandong Liu Weimin Zeng
Vermiculite is a clay mineral with unique physical properties that plays a significant role in plant cultivation, soil remediation, and solid waste management. In this research, we first explored how vermiculite-to-microbe interactions evolved during sludge–waste mushroom residue co-composting. Vermiculite’s addition had a substantial impact on the microbial α and β diversities, significantly changed the microbial community pattern, and strengthened the composting nutrient circulation through the formation of more specialist and generalist species. The microbial community characteristics exhibited common co-networks for resisting composting environment stresses. Vermiculite contributed to enhancing the keystone taxa Proteobacteria and Actinobacteriota and caused the ecological function network to diversify in the warming and maturation phases, with more complexity and tightness in the thermophilic phase (with super-generalist species existing). The enhanced microbial interactions induced by vermiculite possessed a greater capacity to facilitate the metabolisms of carbohydrates and amino acids and cellulolysis, thereby promoting composting humification, and nitrogen retention in the final compost and composting maturity. These findings are helpful for us to understand the biological process mechanisms of the effect of vermiculite additives on composting and contribute to the establishment of a theoretical framework for enhancing the microbial interactions in composting systems by adding vermiculite in practical applications.
]]>Microorganisms doi: 10.3390/microorganisms12030583
Authors: Marco Prato Natalia Tiberti Cristina Mazzi Federico Gobbi Chiara Piubelli Silvia Stefania Longoni
The RAS is a hormonal system playing a pivotal role in the control of blood pressure and electrolyte homeostasis, the alteration of which is associated with different pathologies, including acute respiratory distress syndrome (ARDS). As such, it is not surprising that a number of studies have attempted to elucidate the role and balance of the renin–angiotensin system (RAS) in COVID-19. In this review article, we will describe the evidence collected regarding the two main enzymes of the RAS (i.e., ACE and ACE2) and their principal molecular products (i.e., AngII and Ang1-7) in SARS-CoV-2 infection, with the overarching goal of drawing conclusions on their possible role as clinical markers in association with disease severity, progression, and outcome. Moreover, we will bring into the picture new experimental data regarding the systemic activity of ACE and ACE2 as well as the concentration of AngII and Ang1-7 in a cohort of 47 COVID-19 patients hospitalized at the IRCCS Sacro Cuore-Don Calabria Hospital (Negrar, Italy) between March and April 2020. Finally, we will discuss the possibility of considering this systemic pathway as a clinical marker for COVID-19.
]]>Microorganisms doi: 10.3390/microorganisms12030584
Authors: Kan Yan Yanni Ma Songming Bao Wandi Li Yunjiao Wang Chao Sun Xin Lu Juan Ran
Soilless cultivation of potatoes often utilizes organic coconut peat and inorganic vermiculite as growing substrates. The unique microbial communities and physicochemical characteristics inherent to each substrate significantly influence the microecological environment crucial for potato growth and breeding. This study analyzed environmental factors within each substrate and employed Illumina sequencing alongside bioinformatics tools to examine microbial community structures, their correlation with environmental factors, core microbial functions, and the dynamics of microbial networks across various samples. These included pure coconut peat (CP1) and pure vermiculite (V1), substrates mixed with organic fertilizer for three days (CP2 and V2), and three combinations cultivated with potatoes for 50 days (CP3, V3, and CV3—a 1:1 mix of coconut peat and vermiculite with organic fertilizer). Vermiculite naturally hosts a more diverse microbial community. After mixing with fertilizer and composting for 3 days, and 50 days of potato cultivation, fungal diversity decreased in both substrates. Coconut peat maintains higher bacterial diversity and richness compared to vermiculite, harboring more beneficial bacteria and fungi, resulting in a more complex microbial network. However, vermiculite shows lower bacterial diversity and richness, with an accumulation of pathogenic microorganisms. Among the 11 environmental factors tested, water-soluble nitrogen (WSN), total nitrogen (TN), available potassium (AK), total organic carbon (TOC) and air-filled porosity (AFP) were significantly associated with microbial succession in the substrate.The nutritional type composition and interaction patterns of indigenous microorganisms differ between vermiculite and coconut peat. Adding abundant nutrients significantly affects the stability and interaction of the entire microbial community, even post-potato cultivation. When using vermiculite for soilless cultivation, precise control and adjustment of nutrient addition quantity and frequency are essential.
]]>Microorganisms doi: 10.3390/microorganisms12030582
Authors: Katty Ogata-Gutiérrez Carolina Chumpitaz-Segovia Jesus Lirio-Paredes Doris Zúñiga-Dávila
Peru is one of the leading countries that produce and export specialty coffees, favorably positioned in the international markets for its physical and organoleptic cup qualities. In recent years, yellow coffee rust caused by the phytopathogenic fungus Hemileia vastatrix stands out as one of the main phytosanitary diseases that affect coffee culture yields. Many studies have demonstrated bacteria antagonistic activity against a number of phytopathogen fungi. In this context, the aim of this work was to select and characterize phyllospheric bacteria isolated from Coffea arabica with antagonistic features against coffee rust to obtain biocontrollers. For that purpose, a total of 82 phyllospheric bacteria were isolated from two coffee leaf rust-susceptible varieties, typica and caturra roja, and one tolerant variety, catimor. Of all the isolates, 15% were endophytic and 85% were epiphytes. Among all the isolates, 14 were capable of inhibiting the mycelial radial growth of Mycena citricolor, and Colletotrichum sp. 16S rRNA gene sequence-based analysis showed that 9 isolates were related to Achromobacter insuavis, 2 were related to Luteibacter anthropi and 1 was related to Rodococcus ceridiohylli, Achromobacter marplatensis and Pseudomonas parafulva. A total of 7 representative bacteria of each group were selected based on their antagonistic activity and tested in germination inhibition assays of coffee rust uredinospores. The CRRFLT7 and TRFLT8 isolates showed a high inhibition percentage of urediniospores germination (81% and 82%, respectively), similar to that obtained with the chemical control (91%). An experimental field assay showed a good performance of both strains against rust damage too, making them a promising alternative for coffee leaf rust biocontrol.
]]>Microorganisms doi: 10.3390/microorganisms12030580
Authors: Stoycho D. Stoev
The purpose of this review is to elucidate the actual threat of the most prevalent mycotoxins in agricultural commodities and human/animal food/feed for the induction of foodborne diseases or ailments. The underestimated hazard of combined mycotoxin uptake by animals or humans is critically discussed with regard to synergistic or additive interaction between some target mycotoxins. The real toxicity of target mycotoxin combinations as it happens in practice is evaluated and possible lower limit values or control measures are suggested in such cases. Some critical points on adequate risk assessment, hygiene control, and regulation of mycotoxins are discussed. The efficiency of current mycotoxin regulations and control measures is evaluated in regard to human/animal health hazards. The risk assessment in the case of multiple mycotoxin exposure of humans/animals via food/feed or agricultural commodities is evaluated and some suggestions are proposed in such cases. Appropriate control measures and food safety issues throughout the food supply chain are proposed in order to prevent the target foodborne diseases. Some preventive measures and possible veterinary hygiene controls or risk evaluations are proposed in some natural cases of foodborne diseases for preventing mycotoxin contamination of animal products designed for human consumption and to avoid possible public health issues.
]]>Microorganisms doi: 10.3390/microorganisms12030581
Authors: Lidia Chomicz Jacek P. Szaflik Wanda Baltaza
Acanthamoeba spp [...]
]]>Microorganisms doi: 10.3390/microorganisms12030579
Authors: Xin Zhang Hengjie Wang Tinglu Yan Yuhan Chen Qi Peng Fuping Song
Bacillus thuringiensis produces insecticidal crystal proteins encoded by cry or cyt genes and targets a variety of insect pests. We previously found that a strong promoter of a DeoR family transcriptional regulator (HD73_5014) can efficiently drive cry1Ac expression in B. thuringiensis HD73. Here, we investigated the regulation of neighbor genes by HD73_5014. The HD73_5014 homologs are widely distributed in Gram-positive bacterial species. Its neighbor genes include pepV, rsuA, and ytgP, which encode dipeptidase, rRNA pseudouridine synthase and polysaccharide biosynthesis protein, respectively. The four open reading frames (ORFs) are organized to be a pepR gene cluster in HD73. RT-PCR analysis revealed that the rsuA and ytgP genes formed a transcriptional unit (rsuA-ytgP operon), while pepV formed a transcriptional unit in HD73. Promoter-lacZ fusion assays showed that the pepV and rsuA-ytgP promoters are regulated by HD73_5014. EMSA experiments showed that HD73_5014 directly binds to the pepV promoter region but not to the rusA-ytgP promoter region. Thus, the HD73_5014 transcriptional regulator, which controls the expression of the dipeptidase pepV, was named PepR (dipeptidase regulator). We also confirmed the direct regulation between PepR and PepV by the increased sensitivity to vancomycin in ΔpepV and ΔpepR mutants compared to HD73.
]]>Microorganisms doi: 10.3390/microorganisms12030578
Authors: Vartika Srivastava Ravinder Kumar Aijaz Ahmad
Viruses are minuscule infectious agents that reproduce exclusively within the living cells of an organism and are present in almost every ecosystem. Their continuous interaction with humans poses a significant threat to the survival and well-being of everyone. Apart from the common cold or seasonal influenza, viruses are also responsible for several important diseases such as polio, rabies, smallpox, and most recently COVID-19. Besides the loss of life and long-term health-related issues, clinical viral infections have significant economic and social impacts. Viral enzymes, especially proteases which are essential for viral multiplication, represent attractive drug targets. As a result, screening of viral protease inhibitors has gained a lot of interest in the development of anti-viral drugs. Despite the availability of anti-viral therapeutics, there is a clear need to develop novel curative agents that can be used against a given virus or group of related viruses. This review highlights the importance of yeasts as an in vivo model for screening viral enzyme inhibitors. We also discuss the advantages of yeast-based screening platforms over traditional assays. Therefore, in the present article, we discuss why yeast is emerging as a model of choice for in vivo screening of anti-viral molecules and why yeast-based screening will become more relevant in the future for screening anti-viral and other molecules of clinical importance.
]]>Microorganisms doi: 10.3390/microorganisms12030577
Authors: Konstantinos Tegopoulos Theodora Tsirka Christos Stekas Eleni Gerasimidi George Skavdis Petros Kolovos Maria E. Grigoriou
Vitis vinifera, an economically significant grapevine species, is known for wine, juice, and table grape production. The berries of wine grapes host a diverse range of microorganisms influencing both grapevine health and the winemaking process. Indigenous to Greece, the emblematic variety Assyrtiko, renowned for high-quality white wines, originated from Santorini and spread to various Greek regions. Despite existing studies on the microbiota of several varieties, the carposphere microbiota of Assyrtiko grapes remains unexplored. Thus, we conducted a spatiotemporal metagenomic study to identify the epiphytic microbial community composition of Assyrtiko grapes. The study was conducted in two consecutive vintage years (2019 and 2020) across three different and distinct viticulture regions in Greece (Attica, Thessaloniki, Evros). We performed amplicon sequencing, targeting the 16S rRNA gene for bacteria and the ITS region for fungi, with subsequent comprehensive bioinformatic analysis. Our data indicate that the distribution and relative abundance of the epiphytic carposphere microbial communities of the Assyrtiko variety are shaped both by vintage and biogeography.
]]>Microorganisms doi: 10.3390/microorganisms12030576
Authors: Alexander Hammerhøj John Mark Gubatan Ole Haagen Nielsen
The protective intestinal epithelial barrier is constantly exposed to more than 100 trillion commensal microorganisms (bacteria, archaea, viruses, and fungi), i [...]
]]>Microorganisms doi: 10.3390/microorganisms12030575
Authors: Zugang Li Chaoying Jia Zizhe Hu Yancheng Jin Tianzhi Li Xiaoxue Zhang Zhong Peng Ruicheng Yang Huanchun Chen Xiangru Wang
Escherichia coli (E. coli) is an important foodborne pathogen and a biomarker for monitoring antimicrobial resistance. Investigating the prevalence of E. coli in the poultry industry holds great importance, particularly in Henan province, a major poultry-producing region in China. Here, we investigated the antimicrobial resistance (AMR) phenotypes of E. coli strains obtained from the poultry industry in Henan, China. A total of 344 E. coli strains were isolated from 638 samples collected from seven farms, three slaughterhouses, and ten terminal markets. Approximately 96.4%, 81.7%, and 52.5% of the isolates from the farms, slaughterhouses, and terminal markets exhibited multidrug resistance. Whole-genome sequencing was performed on 169 strains to reveal their genomic characteristics. The sequence type (ST) analysis revealed that ST10 and ST156 were the most frequent types within the poultry supply chain, whereas ST10 and ST162 were commonly found across the farms, slaughterhouses, and terminal markets. Fourteen ST10 E. coli strains belonged to phylogenetic group A, while fifteen ST165 and six ST162 E. coli strains belonged to phylogenetic group B1. In addition, several antimicrobial resistance genes and virulence factor genes were identified. The blaNDM-5 gene mediated carbapenem resistance in two E. coli strains, while mcr-1-mediated colistin resistance was detected in nine E. coli strains. Phylogenetic group A exhibited fewer virulence genes compared to other groups of E. coli. Plasmid replicons, such as IncFIB (AP001918), IncX1, IncFIC (FII), and IncFII (pHN7A8), were frequently observed. These findings provide valuable insights into the current AMR profiles of E. coli strains isolated from the poultry industry in Central China and highlight the need to implement good manufacturing practices and reduce antibiotic usage to mitigate potential risks associated with E. coli.
]]>Microorganisms doi: 10.3390/microorganisms12030574
Authors: Yuanzheng Zhao Shiyu Wang Meiling Zhang Li Zeng Liyu Zhang Shuyu Huang Rong Zhang Wei Zhou Chao Ai
Crop residue decomposition is an important part of the carbon cycle in agricultural ecosystems, and microorganisms are widely recognized as key drivers during this process. However, we still know little about how nitrogen (N) input and rhizosphere effects from the next planting season impact key straw-decomposing microbial communities. Here, we combined amplicon sequencing and DNA-Stable Isotope Probing (DNA-SIP) to explore these effects through a time-series wheat pot experiment with four treatments: 13C-labeled maize straw addition with or without N application (S1N1 and S1N0), and no straw addition with or without N application (S0N1 and S0N0). The results showed that straw addition significantly reduced soil microbial alpha diversity in the early stages. Straw addition changed microbial beta diversity and increased absolute abundance in all stages. Growing plants in straw-amended soil further reduced bacterial alpha diversity, weakened straw-induced changes in beta diversity, and reduced bacterial and fungal absolute abundance in later stages. In contrast, N application could only increase the absolute abundance of soil bacteria and fungi while having little effect on alpha and beta diversity. The SIP-based taxonomic analysis of key straw-decomposing bacteria further indicated that the dominant phyla were Actinobacteria and Proteobacteria, with overrepresented genera belonging to Vicinamibacteraceae and Streptomyces. Key straw-decomposing fungi were dominated by Ascomycota, with overrepresented genera belonging to Penicillium and Aspergillus. N application significantly increased the absolute abundance of key straw-decomposing microorganisms; however, this increase was reduced by the rhizosphere effect. Overall, our study identified key straw-decomposing microorganisms in straw-amended soil and demonstrated that they exhibited opposite responses to N application and the rhizosphere effect.
]]>Microorganisms doi: 10.3390/microorganisms12030573
Authors: Jessica E. Beetch Amanda Janitz Laura A. Beebe Mary Gowin Chao Xu Shari Clifton Katrin Gaardbo Kuhn
The COVID-19 pandemic halted progress in global vaccine coverage and disrupted routine childhood vaccination practices worldwide. While there is ample evidence of the vaccination decline experienced during the pandemic, it is less clear how low-income countries were affected. We executed a systematic review to synthesize the current literature on the impacts of routine childhood vaccinations in low-income countries from 1 January 2020 to 8 February 2023. We collected data using an extraction form on Covidence and assessed the quality of studies included in the review using the Risk of Bias in Non-Randomized Studies of Interventions (ROBINS-I) tool. Effect estimates for changes in vaccination during the pandemic were reported and summarized. Factors that influenced changes were grouped into descriptive themes. Thirteen studies, encompassing 18 low-income countries and evaluating 15 vaccines at varying doses, were included in the final review. We found that routine childhood vaccinations during the COVID-19 pandemic varied considerably by vaccine type, location, and phase of the pandemic. Nine different themes were identified as factors that influenced changes in vaccination. Documenting past experiences and lessons learned is crucial for informing preparedness efforts in anticipation of future public health emergencies. Failure to effectively address these things in the next public health emergency could result in a recurrence of declining routine childhood vaccinations.
]]>Microorganisms doi: 10.3390/microorganisms12030572
Authors: Baodi Shang Xiaoyi Li Xiaoping Zhang Meiyan Zhang Jie Kong Jinle Wang Aiping Tan Feng Zhao Defeng Zhang
Pathogenic Aeromonas spp. are the etiological agents of Motile Aeromonas Septicemia (MAS). This study aimed to identify the pathogen of diseased tadpoles (Quasipaa spinosa) and the antibiotic-resistance characteristics of this bacterium. A Gram-negative bacterium, named strain QST31, was isolated from the ascites of diseased tadpoles and was identified as Aeromonas media based on physiological and biochemical tests, as well as molecular identification. Artificial infection experiments showed that strain QST31 was highly virulent to tadpoles, with an LC50 of 2.56 × 107 CFU/mL. The antimicrobial susceptibility of strain QST31 was evaluated using the disk diffusion method, and the results indicated that strain QST31 was resistant to 28 antibacterial agents. In addition, the whole genome of strain QST31 was sequenced, and the presence of antimicrobial resistance genes, integron, and transposon was investigated. Genes involved in adherence, hemolysis, type II secretion system (T2SS), T6SS, iron uptake system, and quorum sensing were identified in the genome of strain QST31. More than 12 antimicrobial resistance genes were predicted in the genome of strain QST31. Interestingly, a novel Tn7709 transposon harboring sul1, aadA16, catB3, blaOXA-21, aac(6′)-IIa, and tet(A) genes was identified. In conclusion, this is the first report on the isolation and identification of pathogenic A. media with multidrug resistance genes from diseased tadpoles. The results revealed that preventing and controlling aquatic animal diseases caused by multidrug resistance A. media will be a huge challenge in the future.
]]>Microorganisms doi: 10.3390/microorganisms12030571
Authors: Rahul Bhandary Geethu Venugopalan Amitha Ramesh Guilia Tartaglia Ishita Singhal Shahnawaz Khijmatgar
This comprehensive review delves into the forefront of research on the human oral microbiome, exploring recent advancements that span microbial colonization, state-of-the-art detection methodologies, and the complex interplay involved in disease progression. Through an exhaustive analysis of the contemporary literature, we illuminate the dynamic orchestration of microbial communities within the oral cavity, underscoring their pivotal role in health and disease. Cutting-edge detection techniques, including metagenomics and high-throughput sequencing, are discussed regarding their transformative impact on understanding the intricacies of oral microbial ecosystems. As we stand on the cusp of a new decade, this review anticipates a paradigm shift in the field, emphasizing the potential for rapid identification and targeted management of detrimental oral microorganisms. Insights gained from this exploration not only contribute to our fundamental understanding of the oral microbiome but also hold promise for the development of innovative therapeutic strategies to maintain oral health. This article aims to serve as a valuable resource for researchers, clinicians, and public health professionals engaged in unraveling the mysteries of the microbial symphony within the human oral cavity.
]]>Microorganisms doi: 10.3390/microorganisms12030570
Authors: Sibongile Mtimka Priyen Pillay Lusisizwe Kwezi Ofentse Jacob Pooe Tsepo Lebiletsa Tsekoa
Tuberculosis (TB) is a highly prevalent infectious disease that causes more than 1.5 million deaths a year. More than 25% of TB deaths occur in Africa, and TB is South Africa’s leading cause of death, with about 89,000 people dying of it yearly. The emergence of multidrug-resistant TB (MDR-TB) poses a significant threat to health security and could reverse the positive gains already made in the fight against TB. Antibiotic treatments are available, but side effects and the alarming increase in the prevalence of drug-resistant strains of Mycobacterium tuberculosis (Mtb) will compromise the control of the spread and treatment of the disease. A promising option is to employ specialized enzymes encoded by bacteriophages, which destroy bacterial cell membranes and walls to treat tuberculosis. Phage therapy against bacteria is a known treatment that is now reemerging with lytic proteins. These proteins provide an alternative means to treat infectious diseases where conventional antibiotic regimens do not meet the requirements. This review explores and discusses the potential of lytic protein therapy as an antimicrobial strategy against M. tuberculosis and multidrug-resistant tuberculosis.
]]>Microorganisms doi: 10.3390/microorganisms12030569
Authors: Jie Tao Benqiang Li Ying Shi Jinghua Cheng Pan Tang Jiajie Jiao Huili Liu
Porcine sapovirus (PoSaV) is one of the most significant pathogens causing piglet diarrhea, and one with limited genetic characterization. In this study, the prevalence, infection pattern, and genetic evolution of porcine sapovirus were elucidated in detail. The positive rate of PoSaV was 10.1% (20/198), with dual, triple, and quadruple infections of 45%, 40%, and 5%, respectively. To further explore the viral composition in the PoSaV-positive diarrhea feces, metagenomic sequencing was carried out. The results confirmed that RNA viruses accounted for a higher proportion (55.47%), including the two primary viruses of PoSaV (21.78%) and porcine astrovirus (PAstV) (24.54%) in the tested diarrhea feces samples. Afterward, a full-length sequence of the PoSaV isolate was amplified and named SHCM/Mega2023, and also given the identifier of GenBank No. PP388958. Phylogenetic analysis identified the prevalent PoSaV strain SHCM/Mega2023 in the GIII genogroup, involving a recombinant event with MK962338 and KT922089, with the breakpoint at 2969–5132 nucleotides (nt). The time tree revealed that the GIII genogroup exhibits the widest divergence time span, indicating a high likelihood of viral recombination. Moreover, SHCM/Mega2023 had three nucleotide “RPL” insertions at the 151–153 nt site in the VP2 gene, compared to the other GIII strains. Further selective pressure calculations demonstrate that the whole genome of the SHCM/Mega2023 strain was under purifying selection (dN/dS < 1), with seven positively selected sites in the VP1 protein, which might be related to antigenicity. In conclusion, this study presents a novel genomic evolution of PoSaV, offering valuable insights into antigenicity and for vaccine research.
]]>Microorganisms doi: 10.3390/microorganisms12030568
Authors: Norman Arthur Ratcliffe Cicero Brasileiro Mello Helena Carla Castro Paul Dyson Marcela Figueiredo
This overview initially describes insect immune reactions and then brings together present knowledge of the interactions of vector insects with their invading parasites and pathogens. It is a way of introducing this Special Issue with subsequent papers presenting the latest details of these interactions in each particular group of vectors. Hopefully, this paper will fill a void in the literature since brief descriptions of vector immunity have now been brought together in one publication and could form a starting point for those interested and new to this important area. Descriptions are given on the immune reactions of mosquitoes, blackflies, sandflies, tsetse flies, lice, fleas and triatomine bugs. Cellular and humoral defences are described separately but emphasis is made on the co-operation of these processes in the completed immune response. The paper also emphasises the need for great care in extracting haemocytes for subsequent study as appreciation of their fragile nature is often overlooked with the non-sterile media, smearing techniques and excessive centrifugation sometimes used. The potential vital role of eicosanoids in the instigation of many of the immune reactions described is also discussed. Finally, the priming of the immune system, mainly in mosquitoes, is considered and one possible mechanism is presented.
]]>Microorganisms doi: 10.3390/microorganisms12030567
Authors: Chenchen Zhang Zheng Qu Jie Hou Yanpo Yao
Mycotoxins are carcinogenic, teratogenic and mutagenic toxic compounds produced by some filamentous fungi, which are extremely harmful to corn, rice, wheat, peanut, soybean, rapeseed and other grain and oil crops, and seriously threaten environmental safety, food safety and human health. With the rapid increase in the global population and the expansion of the main crop planting area, mycotoxin contamination has increased year by year in agricultural products. The current review aimed to summarize the contamination status and harmful effects of major mycotoxins of grain and oil crops and the environmental factors that impact mycotoxin contamination. Further, control measures of mycotoxin contamination, especially the biological control strategies, were discussed.
]]>Microorganisms doi: 10.3390/microorganisms12030566
Authors: Roxana Mihaela Chiorescu Sandor Botond Buksa Alexandru Botan Mihaela Mocan Carmen Costache Dan Alexandru Toc
Streptococcus thoraltensis is a rare species, part of the viridans streptococcus group, found initially in rabbits and pigs, which can be vancomycin-resistant. We present the case of a 65-year-old patient, a smoker and chronic alcohol consumer with chronic obstructive pulmonary disease (COPD) and multiple dental foci who had been diagnosed with bacterial endocarditis caused by Streptococcus thoraltensis. The particular elements of the case consisted of an atypical clinical presentation with diarrheal stools, abdominal pain, concomitant damage to the aortic and tricuspid valves, the presence of large vegetations (>2 cm), and a vancomycin-resistant strain of Streptococcus thoraltensis. The evolution of the patient was unfavorable due to septic embolisms, respiratory failure requiring orotracheal intubation, and septic and cardiogenic shock. Infections with Streptococcus thoraltensis are challenging to treat because of the severity of the clinical form it causes and the pattern of antibiotic resistance in this germ. Based on our brief review, Streptococcus thoraltensis is an extremely rare human pathogen previously described as the etiologic agent of infectious endocarditis in only one case.
]]>Microorganisms doi: 10.3390/microorganisms12030565
Authors: Yuhong Zhang Yuxin Nie Luyou Wang Jian Wu
Viroids represent distinctive infectious agents composed solely of short, single-stranded, circular RNA molecules. In contrast to viruses, viroids do not encode for proteins and lack a protective coat protein. Despite their apparent simplicity, viroids have the capacity to induce diseases in plants. Currently, extensive research is being conducted on the replication cycle of viroids within both the Pospiviroidae and Avsunviroidae families, shedding light on the intricacies of the associated host factors. Utilizing the potato spindle tuber viroid as a model, investigations into the RNA structural motifs involved in viroid trafficking between different cell types have been thorough. Nevertheless, our understanding of the host factors responsible for the intra- and inter-cellular movement of viroids remains highly incomplete. This review consolidates our current knowledge of viroid replication and movement within both families, emphasizing the structural basis required and the identified host factors involved. Additionally, we explore potential host factors that may mediate the intra- and inter-cellular movement of viroids, addressing gaps in our understanding. Moreover, the potential application of viroids and the emergence of novel viroid-like cellular parasites are also discussed.
]]>Microorganisms doi: 10.3390/microorganisms12030564
Authors: Yucheng Liu Xueying Zai Guangying Weng Xianyong Ma Dun Deng
Brevibacillus laterosporus (B. laterosporus) is widely distributed in nature and demonstrates significant potential for applications in biological control, environmental protection, agricultural production, and clinical medicine. This review provides a comprehensive overview of the applications of B. laterosporus in crop cultivation and animal feeding, as well as an examination of the antimicrobial peptides produced by B. laterosporus and their antibacterial mechanisms. B. laterosporus enhances crop cultivation by secreting hydrolases to improve nutrient absorption capabilities, synthesizing hormones to promote crop growth, and producing proteins to inhibit the reproduction of harmful organisms. B. laterosporus has been used to improve animal production by regulating the structure of the intestinal microbiota and inhibiting the growth of pathogenic bacteria through the secretion of various antimicrobial peptides. The bactericidal activity of Brevilaterins secreted by B. laterosporus is attributed to their ability to bind to lipopolysaccharide/lipid II molecules on the cell membrane, thereby altering permeability. Brevilaterins also inhibit bacterial reproduction by affecting relevant gene pathways in the cell membranes of pathogenic bacteria. These pathways include ATP synthesis, peptidoglycan biosynthesis, membrane transport, and cellular metabolism. In conclusion, B. laterosporus exhibits substantial potential as a probiotic activity in crop and animal production. However, applications of B. laterosporus in animal production could be improved, necessitating further research to elucidate the underlying probiotic mechanisms.
]]>Microorganisms doi: 10.3390/microorganisms12030563
Authors: Bo Jiang Lu Li Yu Wu Xiaoying Wang Ning Gao Zhichao Xu Chunhe Guo Sheng He Guihong Zhang Yaosheng Chen Xiaohong Liu Zhengcao Li
African swine fever virus (ASFV) and porcine reproductive and respiratory syndrome virus (PRRSV) infections lead to severe respiratory diseases in pigs, resulting in significant economic losses for the global swine industry. While numerous studies have focused on specific gene functions or pathway activities during infection, an investigation of shared immune responses in porcine alveolar macrophages (PAMs) after ASFV and PRRSV infections was lacking. In this study, we conducted a comparison using two single-cell transcriptomic datasets generated from PAMs under ASFV and PRRSV infection. Pattern recognition receptors (PRRs) RIG-I (DDX58), MDA5 (IFIH1), and LGP2 (DHX58) were identified as particularly recognizing ASFV and PRRSV, triggering cellular defense responses, including the upregulation of four cytokine families (CCL, CXCL, IL, and TNF) and the induction of pyroptosis. Through weighted gene co-expression network analysis and protein–protein interaction analysis, we identified thirteen gene and protein interactions shared by both scRNA-seq analyses, suggesting the ability to inhibit both ASFV and PRRSV viral replication. We discovered six proteins (PARP12, PARP14, HERC5, DDX60, RSAD2, and MNDA) in PAMs as inhibitors of ASFV and PRRSV replication. Collectively, our findings showed detailed characterizations of the immune responses in PAMs during ASFV and PRRSV infections, which may facilitate the treatments of these viral diseases.
]]>Microorganisms doi: 10.3390/microorganisms12030562
Authors: Li Mei Yang Song Xiao Liu Kun Li Xu Guo Li Liu Yang Liu Zisis Kozlakidis Io Hong Cheong Duochun Wang Qiang Wei
Bacterial antimicrobial resistance (AMR) poses a significant global public health challenge. The escalation of AMR is primarily attributed to the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs), often facilitated by plasmids. This underscores the critical need for a comprehensive understanding of the resistance mechanisms and transmission dynamics of these plasmids. In this study, we utilized in vitro drug sensitivity testing, conjugation transfer assays, and whole-genome sequencing to investigate the resistance mechanism of an extensively drug-resistant (XDR) Pseudomonas aeruginosa clinical isolate, MAS152. We specifically focused on analyzing the drug-resistant plasmid pMAS152 it harbors and its potential for widespread dissemination. Bioinformatics analysis revealed that MAS152 carries a distinct IncpP-2A plasmid, pMAS152, characterized by a 44.8 kb multidrug resistance (MDR) region. This region houses a 16S rRNA methyltransferase (16S-RMTase) gene, rmtB, conferring high-level resistance to aminoglycoside antibiotics. Notably, this region also contains an extended-spectrum β-Lactamase (ESBL) gene, blaPER-1, and an efflux pump operon, tmexCD-oprJ, which mediate resistance to β-Lactams and quinolone antibiotics, respectively. Such a combination of ARGs, unprecedented in reported plasmids, could significantly undermine the effectiveness of first-line antibiotics in treating P. aeruginosa infections. Investigation into the genetic environment of the MDR region suggests that Tn2 and IS91 elements may be instrumental in the horizontal transfer of rmtB. Additionally, a complex Class I integron with an ISCR1 structure, along with TnAs1, seems to facilitate the horizontal transfer of blaPER-1. The conjugation transfer assay, coupled with the annotation of conjugation-related genes and phylogenetic analysis, indicates that the plasmid pMAS152 functions as a conjugative plasmid, with other genus Pseudomonas species as potential hosts. Our findings provide vital insights into the resistance mechanisms and transmission potential of the XDR P. aeruginosa isolate MAS152, underlining the urgent need for novel strategies to combat the spread of AMR. This study highlights the complex interplay of genetic elements contributing to antibiotic resistance and underscores the importance of continuous surveillance of emerging ARGs in clinical isolates.
]]>Microorganisms doi: 10.3390/microorganisms12030561
Authors: Chenchen Qiu Nanbing Liu Xiaogao Diao Liwen He Hanlin Zhou Wei Zhang
This study was to investigate the effects of cellulase and xylanase on fermentation characteristics, nutrient composition and the bacterial community of the mixed silage of king grass and rice straw. Lab-scale bag silage was produced and seven groups were studied: blank control (CK); added 1%, 2% cellulase (CE1, CE2); added 1%, 2% xylanase (XY1, XY2); and added 0.5% cellulase +0.5% xylanase, 1% cellulase +1% xylanase (CX1, CX2). The results showed that the application of additives in six treated groups exerted a positive effect on lactic acid (LA) content and their pH values decreased significantly (p < 0.05). The addition of cellulase and xylanase decreased (p < 0.05) the content of neutral detergent fiber (NDF) and acid detergent fiber (ADF) significantly and increased (p < 0.01) the crude protein (CP) and water-soluble carbohydrate (WSC) content. Filter paper enzyme activity (FPA) declined and xylanase activity (XA) intensified (p < 0.05) as ensiling was prolonged, where most of the enzymatic treatments (especially XY2, CX2) resulted in increased enzyme activities. Moreover, the addition of cellulase and xylanase reduced the abundance of harmful bacteria such as Acinetobacter and Klebsiella and increased the abundance of lactic acid bacteria such as Lacticaseseibacillus, Lactiplantibacillus. In conclusion, the addition of cellulase and xylanase would improve fermentation quality and nutrient preservation via altering the bacterial community, with 1% cellulase or complex enzyme best.
]]>Microorganisms doi: 10.3390/microorganisms12030560
Authors: Wenlei Xue Hao Wu Xinyu Wu Nannan Li Ximei Nie Tianheng Gao
As an enduring Chinese freshwater aquaculture product, the Eriocheir sinensis has a high economic value and is characterized by a catadromous life style that undergoes seawater–freshwater migration. However, little is known about their gut microbial status as they move from saltwater to freshwater acclimatization. Here, we sampled and cultivated Eriocheir sinensis megalopa from three aquaculture desalination ponds and investigated their gut microbiota diversity, community structures and biotic interactions from megalopa stage to the first juvenile stage after desalination for 9 days. Our results revealed that during the transition from megalopa to the first juvenile in Eriocheir sinensis, a significant change in gut microbial composition was observed (for instance, changes in relative abundance of dominant phyla), which was, however, not influenced by different sampling sites. The species diversity (such as the richness) of the gut microbiota showed a hump-shaped pattern along the succession. However, the compositional differences of the gut microbes showed constantly increasing patterns during the succession after freshwater adaption for all three sampling sites. Further co-occurrence analysis also showed that the complexity of the ecological networks in gut microbes was significantly enhanced during the development, such as increasing numbers of network links, connectivity and modularity, and was confirmed by decreasing average path length and proportions of negative links. Taken together, the differences in community structures and biological interactions of gut microorganisms were more pronounced in Eriocheir sinensis megalopa during desalination than in diversity and species compositions. This implies that the gut microbes of Eriocheir sinensis megalopa would become more robust and adaptive during the developmental process.
]]>Microorganisms doi: 10.3390/microorganisms12030558
Authors: Wannaporn Thepbandit Dusit Athinuwat
Plant health is necessary for food security, which is a key determinant of secure and sustainable food production systems. Deficiency of soil nutrients and invasion of plant pathogens or insects are the main destroyers of the world’s food production. Synthetic fertilizers and chemical-based pesticides are frequently employed to combat the problems. However, these have negative impacts on microbial ecosystems and ecosystem functioning. Rhizosphere microorganisms have demonstrated their potency to improve or manage plant nutrients to encourage plant growth, resulting in increased yield and quality by converting organic and inorganic substances around the rhizosphere zone into available plant nutrients. Besides regulating nutrient availability and plant growth enhancement, rhizobacteria or fungi can restrict plant pathogens that cause disease by secreting inhibitory chemicals and boosting plant immunity to combat pests or pathogens. Thus, rhizosphere microorganisms are viewed as viable, alluring economic approaches for sustainable agriculture as biofertilizers and biopesticides. This review provides an overview of the role of rhizosphere microorganisms in soil nutrients and inducing of plant defenses. Moreover, a discussion is presented surrounding the recent consequences of employing these microorganisms and a sustainable strategy towards improving fertilization effectiveness, and encouraging stronger, more pest-resistant plants.
]]>Microorganisms doi: 10.3390/microorganisms12030559
Authors: Mengyi Wang Jinyan Wu Xiaoan Cao Long Xu Junhuang Wu Haiyan Ding Youjun Shang
Many epidemics are caused by negative-stranded RNA viruses, leading to serious disease outbreaks that threaten human life and health. These viruses also have a significant impact on animal husbandry, resulting in substantial economic losses and jeopardizing global food security and the sustainable livelihoods of farmers. However, the pathogenic and infection mechanism of most negative-stranded RNA viruses remain unclear. Reverse genetics systems are the most powerful tools for studying viral protein function, viral gene expression regulation, viral pathogenesis, and the generation of engineered vaccines. The reverse genetics of some negative-strand viruses have been successfully constructed, while others have not. In this review, we focus on representative viruses from the Orthomyxoviridae family (IAV), the Filoviridae family (EBOV), and the Paramyxoviridae family (PPRV) to compile and summarize the existing knowledge on reverse genetics techniques for negative-strand viruses. This will provide a theoretical foundation for developing reverse genetics techniques for some negative-strand viruses.
]]>Microorganisms doi: 10.3390/microorganisms12030556
Authors: Ayaka Harui Saki Maruyama Yukiko Segawa Nobutaka Kurihara
It was reported that the consumption of Saccharina japonica (SJ) lowers blood pressure (BP) in hypertensive rats. Hypertension is related to gut microbiota, and hypertensive patients develop dysbiosis. It was reported that the intake of dietary fiber and polysaccharides contained in SJ changes gut microbiota and increases short-chain fatty acids (SCFAs). The present study examined the effect of BP lowering by SJ in spontaneously hypertensive rats (SHRs) and observed changes in gut microbiota composition and SCFAs concentration. Male SHRs and Wistar Kyoto rats (WKYs) were fed a diet containing 5% SJ or a control diet for six weeks. We measured systolic BP (SBP) weekly, as well as mean arterial BP (MAP), the 16S rRNA gene, and SCFAs in the cecal contents at the end of the period. As a result, the intake of SJ significantly decreased SBP and MAP in SHRs. As well, it significantly changed the microbial diversity by altering the gut microbiota composition. Particularly, it increased the abundance of Bacteroides acidifaciens, which may be associated with the antihypertensive effect of SJ. Thus, SJ intake suppressed the increase in BP and altered the gut microbiota composition, although it did not significantly change the SCFAs concentration in the cecal contents.
]]>Microorganisms doi: 10.3390/microorganisms12030557
Authors: Francesco Montemagno Chiara Romano Deborah Bastoni Angelina Cordone Olga De Castro Sergio Stefanni Emilio Sperone Donato Giovannelli
Our knowledge regarding the role of the microbiome in fish health has been steadily increasing in the last decade, especially for species of commercial interest. Conversely, relatively few studies focus on the microbiomes of wild fish, especially apex predators like sharks, due to lower economic interest and greater difficulty in obtaining samples. Studies investigating microbiome differences between diverse anatomical locations of sharks are limited, and the majority of the available studies are focused on the microbial diversity present on shark teeth, with the aim of preventing infections due to bites of these animals or evaluating the presence of certain pathogens in healthy or diseased specimens. Here, we investigated the skin, mouth, gills, and cloaca microbiomes of five individuals of two phylogenetically distant species of sharks (Prionace glauca and Somniosus rostratus) to obtain a better understanding of the diversity regarding the microbiomes of these animals, how they change throughout different body parts, and how much they are influenced and determined by the ecology and evolutionary relationship between host and microbiome. To confirm the taxonomy of the sharks under study, we barcoded the specimens by sequencing the mtDNA COI from a biopsy of their skin. Microbial diversity based on the 16S rRNA gene reveals that partially overlapping microbiomes inhabit different body parts of each shark species, while the communities are distinct between the two species. Our results suggest that sharks’ microbiome species-specific differences are controlled by the ecology of the shark species. This is the first study comparatively analyzing the microbiome diversity of different anatomical locations in two shark species of the Mediterranean Sea.
]]>Microorganisms doi: 10.3390/microorganisms12030555
Authors: Catherine Jia-Yun Tsai Risa Takahashi Jacelyn Mei-San Loh Thomas Proft
The Gram-positive human pathogen Group A Streptococcus (GAS, Streptococcus pyogenes) employs an arsenal of virulence factors that contribute to its pathogenesis. The pilus is an important factor that enables the pathogen to adhere to and colonize host tissues. Emerging research in pilus function shows that pili’s involvement in establishing infection extends beyond host adhesion. The diversity of GAS pilus types reflect the varying characteristics identified in different pili. With the development of new experimental systems and animal models, a wider range of biological functions have been explored. This brief review summarizes recent reports of new functions in different GAS pilus types and the methodologies that contributed to the findings. The established importance of the pilus in GAS pathogenesis makes this surface structure a promising vaccine target. This article also reviews recent advancements in pilus-based vaccine strategies and discusses certain aspects that should be considered in vaccine development according to the newly defined properties of pili.
]]>Microorganisms doi: 10.3390/microorganisms12030552
Authors: Juan Francisco Gutiérrez-Bautista María Tarriño Adrián González María José Olivares Durán Fernando Cobo Juan Antonio Reguera Javier Rodríguez-Granger Antonio Sampedro
In this study, we have compared the detection of IgM and IgG against C. burnetii phase II of an enzyme-linked immunosorbent assay (ELISA) (Euroimmun) and a chemiluminescent immunoassay (CLIA) (VIRCLIA, Vircell). In addition, an indirect immunofluorescence assay (IFA) was used as a reference test. One hundred forty-eight sera were used for IgG evaluation, and eighty-eight for IgM. The sensitivity of ELISA and CLIA in detecting phase II IgM was excellent. On the other hand, the CLIA IgM showed better specificity than the ELISA IgM. As for phase II IgG, the specificity of ELISA and CLIA was similar, while the ELISA technique showed a higher sensitivity. In conclusion, the best system to detect phase II IgM antibodies against C. burnetii is the CLIA from Vircell, which is characterized by high sensitivity and specificity. For the detection of phase II IgG, the Euroimmun ELISA and Vircell CLIA assays are suitable for the determination of this marker in the laboratory, although the IgG ELISA has greater sensitivity.
]]>Microorganisms doi: 10.3390/microorganisms12030554
Authors: Victor Garcia-Bustos Begoña Acosta-Hernández Marta Dafne Cabañero-Navalón Alba Cecilia Ruiz-Gaitán Javier Pemán Inmaculada Rosario Medina
Over 60% of emerging infectious diseases in humans are zoonotic, often originating from wild animals. This long-standing ecological phenomenon has accelerated due to human-induced environmental changes. Recent data show a significant increase in fungal infections, with 6.5 million cases annually leading to 3.7 million deaths, indicating their growing impact on global health. Despite the vast diversity of fungal species, only a few are known to infect humans and marine mammals. Fungal zoonoses, especially those involving marine mammals like cetaceans, are of global public health concern. Increased human–cetacean interactions, in both professional and recreational settings, pose risks for zoonotic disease transmission. This review focuses on the epidemiology, clinical manifestations, and zoonotic potential of major fungal pathogens shared in humans and cetaceans, highlighting their interspecies transmission capability and the challenges posed by antifungal resistance and environmental changes. It underscores the need for enhanced awareness and preventative measures in high-risk settings to protect public health and marine ecosystems.
]]>Microorganisms doi: 10.3390/microorganisms12030553
Authors: Gan Li Yajie Zheng Qin Luo Yaohua Liang Hang Zhang Huiyang Sha Ruining Wang Weili Kong Mengmeng Zhao
Porcine reproductive and respiratory syndrome (PRRS) is a highly contagious and pathogenic infectious disease caused by the porcine reproductive and respiratory syndrome virus (PRRSV). It manifests as reproductive disorders in sows and respiratory disorders in piglets. PRRSV infects swine herds with symptoms such as abortions, stillbirths, and mummified fetuses in gestating sows. Piglets mainly experience abdominal respiration and respiratory symptoms. To date, the prevention of PRRS relies primarily on vaccination and the implementation of various preventive and control measures. Swine deaths caused by PRRS have resulted in significant economic losses to the pig industry worldwide. Non-structural protein 10 (NSP10) has helicase and adenosine triphosphatase (ATPase) activities that unwind DNA and RNA and play important roles in viral replication and transcription. Hence, it can be potentially used to develop novel reagents for the detection of PPRSV. This article reviews genetic variations, interaction with viral and host proteins, effects on PRRSV replication, immunomodulation, apoptosis, and viral virulence of NSP10, with the aim of providing a theoretical basis for the prevention and control of PRRS and drug development in the future.
]]>Microorganisms doi: 10.3390/microorganisms12030551
Authors: Raquel Cossio-Bayugar Cesar A. Arreguin-Perez Hugo Aguilar-Diaz Estefan Miranda-Miranda
Rhipicephalus microplus is a persistent ectoparasite of cattle that causes bovine anaplasmosis and babesiosis, causing economic losses worldwide. Chemical treatment is the primary method for tick control, but the emergence of pesticide-resistant ticks is a major challenge. Alternative biocontrol strategies utilizing entomopathogenic microorganisms are being explored. This study aimed to validate the species identification and assess the efficacy of four strains of Staphylococcus bacteria (S. shinii S1 and S-2, S. succinus, and S. xylosus) previously reported as being entomopathogenic to R. microplus ticks. According to the bioassays, S. shinii S-1 exhibited the greatest degree of reproductive inhibition (47%), followed by S. succinus (44.3%) at a concentration of 1 × 108 cfu/mL. S. xylosus displayed decreased reproductive inhibition (6.3%). In an additional bioassay, S. shinii S-1 exhibited a significant larval mortality of 67.63%, followed by S. succinus with 66.75%, S. shinni S-2 with 64.61%, and S. xylosus with 28.18% mortality. The common signs of infection observed on these ticks included swelling, yellowish exudate on the hypostome, and reduced limb mobility and color change, except for S. succinus, which did not cause color changes. These bacteria were naturally found on bovine skin. However, further studies are needed to confirm their potential as promising alternatives or complementary agents to existing acaricidal compounds.
]]>Microorganisms doi: 10.3390/microorganisms12030550
Authors: Silvia Valisena Giacomo De Marco Oscar Vazquez Blaise Cochard Christina Steiger Romain Dayer Dimitri Ceroni
Pediatric septic arthritis of the hip (SAH) in children is a severe pathology, requiring prompt diagnosis and treatment to avoid destructive sequelae of the joint. Its diagnosis can be challenging, however, due to its spectrum of manifestations and differential diagnosis. Last century, multiple research teams studied the curves of systemic inflammation markers to aid the differential diagnosis. Kocher showed that a history of fever >38.5 °C, non-weight bearing, an erythrocyte sedimentation rate >40 mm/h, and serum white blood cells >12,000/mm3 were highly suggestive of SAH, with a predicted probability of 99.6% when all these predictors manifested in pediatric patients. Caird validated these criteria, also adding a C-reactive protein >20 mg/L, reaching a 98% probability of SAH when these five criteria were present. The Kocher and the Caird criteria were then applied in multiple settings, but were never clearly validated. Moreover, they were studied and validated in the years when Kingella kingae was just emerging, and this was probably responsible for false-negative cases in multiple centers. For this reason, the Kocher and the Caird criteria are still at the center of a debate on the diagnostic tools for pediatric SAH. We provide a historical overview of the development of clinical and laboratory test algorithms for pediatric SAH. Further, new perspectives for future research on the prediction rules of pediatric SAH are here proposed.
]]>Microorganisms doi: 10.3390/microorganisms12030549
Authors: Magdalena Olson Samantha Toffoli Kiley B. Vander Wyst Fang Zhou Elizabeth Reifsnider Megan E. Petrov Corrie M. Whisner
This study examines how feeding, sleep, and growth during infancy impact the gut microbiome (GM) in toddlers. The research was conducted on toddlers (n = 36), born to Latina women of low-income with obesity. Their mothers completed retrospective feeding and sleeping questionnaires at 1, 6, and 12 months; at 36 months, fecal samples were collected. Sequencing of the 16S rRNA gene (V4 region) revealed that breastfeeding for at least 1 month and the introduction of solids before 6 months differentiated the GM in toddlerhood (Bray–Curtis, pseudo-F = 1.805, p = 0.018, and pseudo-F = 1.651, p = 0.044, respectively). Sleep had an effect across time; at 1 and 6 months of age, a lower proportion of nighttime sleep (relative to 24 h total sleep) was associated with a richer GM at three years of age (Shannon H = 4.395, p = 0.036 and OTU H = 5.559, p = 0.018, respectively). Toddlers experiencing rapid weight gain from birth to 6 months had lower phylogenetic diversity (Faith PD H = 3.633, p = 0.057). These findings suggest that early life nutrition, sleeping patterns, and growth rate in infancy may influence the GM composition. Further verification of these results with objective sleep data and a larger sample is needed.
]]>Microorganisms doi: 10.3390/microorganisms12030548
Authors: Prabin Tamang Arjun Upadhaya Pradeep Paudel Kumudini Meepagala Charles L. Cantrell
Natural product (NP)-based pesticides have emerged as a compelling alternative to traditional chemical fungicides, attracting substantial attention within the agrochemical industry as the world is pushing toward sustainable and environmentally friendly approaches to safeguard crops. Microbes, both bacteria and fungi, are a huge source of diverse secondary metabolites with versatile applications across pharmaceuticals, agriculture, and the food industry. Microbial genome mining has been accelerated for pesticide/drug discovery and development in recent years, driven by advancements in genome sequencing, bioinformatics, metabolomics/metabologenomics, and synthetic biology. Here, we isolated and identified Pseudomonas vancouverensis that had shown antifungal activities against crop fungal pathogens Colletotrichum fragariae, Botrytis cinerea, and Phomopsis obscurans in a dual-plate culture and bioautography assay. Further, we sequenced the whole bacterial genome and mined the genome of this bacterium to identify secondary metabolite biosynthetic gene clusters (BGCs) using antiSMASH 7.0, PRISM 4, and BAGEL 4. An in-silico analysis suggests that P. vancouverensis possesses a rich repertoire of BGCs with the potential to produce diverse and novel NPs, including non-ribosomal peptides (NRPs), polyketides (PKs), acyl homoserine lactone, cyclodipeptide, bacteriocins, and ribosomally synthesized and post-transcriptionally modified peptides (RiPPs). Bovienimide-A, an NRP, and putidacin L1, a lectin-like bacteriocin, were among the previously known predicted metabolites produced by this bacterium, suggesting that the NPs produced by this bacterium could have biological activities and be novel as well. Future studies on the antifungal activity of these compounds will elucidate the full biotechnological potential of P. vancouverensis.
]]>Microorganisms doi: 10.3390/microorganisms12030547
Authors: Svetla Blazheva Svetlana Pachkova Tatyana Bodurska Petar Ivanov Alexander Blazhev Tzvetan Lukanov Emiliana Konova
The uterine microbiota has been the subject of increasing study, but its interaction with the local immune system remains unclear. Successful embryo implantation relies on endometrial receptivity, which is pivotal for immunological tolerance to fetal antigens and precise regulation of inflammatory mediators. Emerging data suggest a dynamic interplay between endometrial microflora and the immune system, making dysbiosis a potential determinant of pregnancy outcomes. Imbalances in the regulation of immune cells in the endometrium and decidua have been associated with infertility, miscarriage, and obstetric complications. A thorough comprehension of the immune system in the female reproductive tract shows potential for improving women’s health and pregnancy outcomes. The objective of this study was to evaluate the patterns of endometrial microbiota in patients with recurrent implantation failure (RIF) and recurrent pregnancy loss (RPL) and to explore their implications for endometrial immune cells and chronic endometritis (CE). Immune cells in biopsies from 107 RIF and 93 RPL patients were examined using flow cytometry. The endometrial microbial composition was analyzed using real-time polymerase chain reaction (RT-PCR). The research uncovered disrupted endometrial microbiota in most women with RIF and RPL, which was often associated with significant effects on lymphocytes, T cells, and uNK cells.
]]>Microorganisms doi: 10.3390/microorganisms12030546
Authors: Pavlo Petakh Valentyn Oksenych Oleksandr Kamyshnyi
Leptospira, which are known to be important disease-causing agents transmitted between animals and humans, result in significant illness and, in some cases, significant death in human populations. This purpose of this study was to examine the genomic structure of Leptospira interrogans serovar Copenhageni strain FDAARGOS_203 to identify the specific genetic factors that contribute to antimicrobial resistance (AMR) and defense against phages. The genome, consisting of two contigs totaling 4,630,574 base pairs, underwent thorough examination for protein-coding sequences, transfer RNA genes, and ribosomal RNA genes. A total of twenty-two antibiotic resistance genes that specifically target essential cellular processes such as cell wall synthesis, DNA replication, and protein synthesis have been identified. Significant among these were gidB, gdpD, and ggsA, each involved in separate aspects of antibiotic resistance. In addition, the investigation explored the defense mechanisms of bacteriophages, revealing the presence of defense islands that contain a range of anti-phage systems, including RM_Type_IV, PrrC, Borvo, CAS_Class1-Subtype-IC, and CAS_Class1-Subtype-IB. This comprehensive genomic analysis enhances our understanding of the molecular mechanisms that determine Leptospira’s ability to adapt to various environments. The identified genetic factors linked to AMR and defense against phages not only enhance our scientific comprehension, but also provide a basis for focused interventions to reduce the impact of leptospirosis.
]]>Microorganisms doi: 10.3390/microorganisms12030545
Authors: Mahdokht Ilbeigi Khamseh Nejad Alessia Cappelli Claudia Damiani Monica Falcinelli Paolo Luigi Catapano Ferdinand Nanfack-Minkeu Marie Paul Audrey Mayi Chiara Currà Irene Ricci Guido Favia
Microbial communities play an important role in the fitness of mosquito hosts. However, the factors shaping microbial communities in wild populations, with regard to interactions among microbial species, are still largely unknown. Previous research has demonstrated that two of the most studied mosquito symbionts, the bacteria Wolbachia and Asaia, seem to compete or not compete, depending on the genetic background of the reference mosquito host. The large diversity of Wolbachia–Asaia strain combinations that infect natural populations of mosquitoes may offer a relevant opportunity to select suitable phenotypes for the suppression of pathogen transmission and for the manipulation of host reproduction. We surveyed Wolbachia and Asaia in 44 mosquito populations belonging to 11 different species of the genera Anopheles, Aedes, and Culex using qualitative PCR. Through quantitative PCR, the amounts of both bacteria were assessed in different mosquito organs, and through metagenomics, we determined the microbiota compositions in some selected mosquito populations. We show that variation in microbial community structure is likely associated with the species/strain of mosquito, its geographical position, and tissue localization. Together, our results shed light on the interactions among different bacterial species in the microbial communities of mosquito vectors, and this can aid the development and/or improvement of methods for symbiotic control of insect vectors.
]]>Microorganisms doi: 10.3390/microorganisms12030544
Authors: Federica Berrilli Margherita Montalbano Di Filippo Isabel Guadano-Procesi Marta Ciavurro David Di Cave
The genus Acanthamoeba comprises free-living amoebae distributed in a wide variety of environments. These amoebae are clinically significant, causing opportunistic infections in humans and other animals. Despite this, limited data on Acanthamoeba sequence types and alleles are available in Italy. In the present study, we analyzed all Acanthamoeba sequences deposited from Italy with new positive Acanthamoeba clinical samples from symptomatic AK cases, to provide an overview of the genetic variants’ spatial patterns from different sources within the Italian context. A total of 137 Acanthamoeba sequences were obtained. Six sequence types were identified: T2/6, T3, T4, T11, T13, and T15. Only T4 and T15 were found in both sources. The Acanthamoeba T4 sequence type was found to be the most prevalent in all regions, accounting for 73% (100/137) of the Italian samples analyzed. The T4 sequence type demonstrated significant allelic diversity, with 30 distinct alleles from clinical and/or environmental samples. These outcomes enabled a better understanding of the distribution of Acanthamoeba isolates throughout Italy, reaffirming its well-recognized ubiquity. Acanthamoeba isolates analysis from keratitis, together with the environmental strains monitoring, might provide important information on different genotypes spreading. This might be useful to define the transmission pathways of human keratitis across different epidemiological scales.
]]>Microorganisms doi: 10.3390/microorganisms12030543
Authors: Weihao Ou Zihe Guo Ying Pan Kai Huang Yanqun Ma Zhibiao Qin
The homeostasis of the intestinal microbiota of fish is beneficial to fish health, while food can affect the intestinal microbiota. Tilapia (Oreochromis spp.) has great economic value and is a good model to use in studying the digestion and absorption of nutrients. Furthermore, at present, due to a high demand and high price of high-quality feed raw materials, the nutritional composition of aquafeeds has been changing dynamically. There has yet to be a comprehensive review of research conducted on the influences of dietary macronutrients (proteins, lipids, and carbohydrates) on the tilapia intestinal microbiota. Therefore, this review focuses on the effects of dietary macronutrients on the gut microbiota of tilapia. Interestingly, we found that the best growth performance might not represent the best composition or functions of the gut microbiota. Overall, the unscientific addition of macronutrients to feed is harmful to the intestinal microbiota. Therefore, both growth performance and gut microbiota should be considered when evaluating certain macronutrients. It is our hope that this review will aid in regulating the intestinal microbiota of fish through nutritional means, thereby promoting tilapia farming.
]]>Microorganisms doi: 10.3390/microorganisms12030542
Authors: Karina Svanberga Jelena Avsejenko Juris Jansons Davids Fridmanis Tatjana Kazaka Aivars Berzins Andris Dislers Andris Kazaks Nikita Zrelovs
Representatives of the bacterial genus Aeromonas are some of the most notorious aquaculture pathogens associated with a range of diseases in different fish species. As the world forges toward the post-antibiotic era, alternative options for combating bacterial pathogens are needed. One such alternative option is phage biocontrol. In this study, a novel podophage—JELG-KS1—infecting Aeromonas salmonicida was retrieved from wastewater along with its host strain. The genome of the JELG-KS1 phage is a 40,505 bp dsDNA molecule with a GC% of 53.42% and 185 bp direct terminal repeats and encodes 53 predicted proteins. Genomic analysis indicates that JELG-KS1 might represent a novel genus within the subfamily Studiervirinae. Podophage JELG-KS1 is a strictly lytic phage without any identifiable virulence or AMR genes that quickly adsorbs onto the surface of host cells to initiate a 48 min long infectious cycle, resulting in the release of 71 ± 12 JELG-KS1 progeny virions per infected cell. JELG-KS1 effectively lyses its host population in vitro, even at very low multiplicities of infection. However, when challenged against a panel of Aeromonas spp. strains associated with diseases in aquaculture, JELG-KS1 shows host-specificity that is confined only to its isolation strain, immediately compromising its potential for Aeromonas spp. biocontrol in aquaculture.
]]>Microorganisms doi: 10.3390/microorganisms12030541
Authors: Sai Shiva Krishna Prasad Vurukonda Vasileios Fotopoulos Agnieszka Saeid
This review explores different methods of sustainably introducing nutrients from agro-industrial waste into the soil. The focus is on sustainable agriculture and how the soil system can be modified by introducing secondary raw materials and beneficial microorganisms. Soil is a nexus between plants and microorganisms that must be balanced. The article emphasizes the importance of maintaining the microbiological balance when supplying nutrients. This review is focused on the possible techniques involved in the production of biofertilizers and their mode of application into the soil system and on plants. We addressed several advantages concerning the use of beneficial microorganisms in waste management by microbial formulation techniques. Not only the advantages but several limitations and challenges were also discussed in regard to the large scale production of microbial products. Therefore, the proper treatment of industrial waste is essential so that we can preserve the environment and human safety and also achieve sustainable agriculture.
]]>Microorganisms doi: 10.3390/microorganisms12030540
Authors: Serigne Fallou Wade Abou Abdallah Malick Diouara Babacar Ngom Fatou Thiam Ndongo Dia
Acute respiratory viruses (ARVs) are the leading cause of diseases in humans worldwide. High-risk individuals, including children and the elderly, could potentially develop severe illnesses that could result in hospitalization or death in the worst case. The most common ARVs are the Human respiratory syncytial virus, Human Metapneumovirus, Human Parainfluenza Virus, rhinovirus, coronaviruses (including SARS and MERS CoV), adenoviruses, Human Bocavirus, enterovirus (-D68 and 71), and influenza viruses. The olfactory deficits due to ARV infection are a common symptom among patients. This review provides an overview of the role of SARS-CoV-2 and other common ARVs in the development of human olfactory pathophysiology. We highlight the critical need to understand the signaling underlying the olfactory dysfunction and the development of therapeutics for this wide-ranging category of AVRs to restore the altered or loss of smell in affected patients.
]]>Microorganisms doi: 10.3390/microorganisms12030539
Authors: Jia-Jie Ding Guo-Jun Zhou Xiao-Jie Chen Wei Xu Xing-Mei Gao Yong-Zeng Zhang Bei Jiang Hai-Feng Li Kai-Ling Wang
Astragalus is a medicinal plant with obvious rhizosphere effects. At present, there are many Astragalus plants with high application value but low recognition and resource reserves in the northwestern area of Yunnan province, China. In this study, metagenomics was used to analyze the microbial diversity and community structure of rhizosphere soil of A. forrestii, A. acaulis, and A. ernestii plants grown in a special high-cold environment of northwestern Yunnan, China, at different altitudes ranging from 3225 to 4353 m. These microbes were taxonomically annotated to obtain 24 phyla and 501 genera for A. forrestii, 30 phyla and 504 genera for A. acaulis, as well as 39 phyla and 533 genera for A. ernestii. Overall, the dominant bacterial phyla included Proteobacteria, Actinobacteria, and Acidobacteria, while the dominant fungal ones were Ascomycota and Basidiomycota. At the genus level, Bradyrhizobium, Afipia, and Paraburkholderia were the most prevalent bacteria, and Hyaloscypha, Pseudogymnoascus, and Russula were the dominant fungal genera. Some of them are considered biocontrol microbes that could sustain the growth and health of host Astragalus plants. Redundancy analysis revealed that pH, TN, and SOM had a significant impact on the microbial community structures (p < 0.05). Finally, triterpene, flavonoid, polysaccharide, and amino acid metabolisms accounted for a high proportion of the enriched KEGG pathways, which possibly contributed to the synthesis of bioactive constituents in the Astragalus plants.
]]>Microorganisms doi: 10.3390/microorganisms12030538
Authors: Naoki Kawahara Shoichiro Yamanaka Kyohei Nishikawa Motoki Matsuoka Tomoka Maehana Ryuji Kawaguchi Naoki Ozu Tomomi Fujii Aya Sugimoto Akihiko Yoshizawa Fuminori Kimura
Among epithelial ovarian cancer, clear cell carcinoma is common for chemo-resistance and high mortality. This cancer arises from benign ovarian endometrioma (OE), which is a high oxidative stress environment due to the cystic retention of menstrual blood produced during menstruation and the “iron” liberated from the cyst. There has been strong evidence that the iron concentration in OE decreases when they become cancerous. A decrease in iron concentration is a necessary condition for the formation of cancer. However, the mechanism of carcinogenesis is not yet clear. In the current study, the bacterial flora in endometriosis-associated ovarian cancer (EAOC), including clear cell carcinoma, and their origin, OE, were investigated using next-generation sequencing. The Shannon index in the genus level was significantly higher in EAOC than in OE fluids. Among several bacterial flora that were more abundant than benign chocolate cysts, a number of bacterial species that correlate very well with iron concentrations in the cysts were identified. These bacterial species are likely to be associated with decreased iron concentrations and cancer development.
]]>Microorganisms doi: 10.3390/microorganisms12030537
Authors: Encarnación Gutiérrez-Carretero Eduardo Arana-Rueda Antonio Ortiz-Carrellán Alonso Pedrote-Martínez Mariano García-de-la-Borbolla Arístides De Alarcón
Background: Cardiac device infections are serious adverse events associated with considerable morbidity and mortality, significant costs, and increased healthcare utilization. The aim of this study is to calculate the costs of treatment of cardiac implantable electrostimulation device (CIED)-related infections for different types of infection (local or systemic) and therapeutic approaches. Patients and Methods: Single-center cohort (1985–2018). The costs of the CIED-related infections were analyzed according to initial treatment (antimicrobial treatment exclusively, local approach, or transvenous lead extraction (TLE)). Total costs (including those for hospitalization stay, drugs, extraction material, and newly implanted devices) were assigned to each case until its final resolution. Results: A total of 380 cases (233 local and 147 systemic infections) were analyzed. The average cost of systemic infection was EUR 34,086, mainly due to hospitalization (78.5%; mean: 24 ± 14 days), with a mortality rate of 10.8%. Local infection had a mortality rate of 2.5% (mainly related to the extraction procedure) and an average cost of EUR 21,790, which was higher in patients with resynchronization therapy devices and defibrillators (46% of total costs). Surgical procedures limited to the pocket for local infections resulted in a high rate of recurrence (87%), evolved to systemic infections in 48 patients, and had a higher cost compared to TLE (EUR 42,978 vs. EUR 24,699; p < 0.01). Conclusions: The costs of treating CIED-related infections are high and mainly related to the type of treatment and length of hospitalization. Complete device removal is always the most effective approach and is a cost-saving strategy.
]]>Microorganisms doi: 10.3390/microorganisms12030536
Authors: Mia N. Carmichael Madison M. Dycus Jeferson M. Lourenco Christina B. Welch Dylan B. Davis Taylor R. Krause Michael J. Rothrock Francis L. Fluharty Timothy D. Pringle Todd R. Callaway
The catabolic activity of the ruminal microbial community of cattle enables the conversion of low-quality feedstuffs into meat and milk. The rate at which this conversion occurs is termed feed efficiency, which is of crucial importance given that feed expenses account for up to 70% of the cost of animal production. The present study assessed the relationship between cattle feed efficiency and the composition of their ruminal microbial communities during the feedlot finishing period. Angus steers (n = 65) were fed a feedlot finishing diet for 82 days and their growth performance metrics were evaluated. These included the dry matter intake (DMI), average daily gain (ADG), and residual feed intake (RFI). Steers were rank-ordered based upon their RFI, and the five lowest RFI (most efficient) and five highest RFI (least efficient) steers were selected for evaluations. Ruminal fluid samples were collected on days 0 and 82 of the finishing period. Volatile fatty acids (VFA) were quantified, and microbial DNA was extracted and the 16S rRNA gene was sequenced. The results showed that the ADG was not different (p = 0.82) between efficiency groups during the 82-day feedlot period; however, the efficient steers had lower (p = 0.03) DMI and RFI (p = 0.003). Less-efficient (high RFI) steers developed higher (p = 0.01) ruminal Methanobrevibacter relative abundances (p = 0.01) and tended (p = 0.09) to have more Methanosphaera. In high-efficiency steers (low RFI), the relative abundances of Ruminococcaceae increased (p = 0.04) over the 82-day period. The molar proportions of VFA were not different between the two efficiency groups, but some changes in the concentration of specific VFA were observed over time. The results indicated that the ruminal microbial populations of the less-efficient steers contained a greater relative abundance of methanogens compared to the high-efficiency steers during the feedlot phase, likely resulting in more energetic waste in the form or methane and less dietary energy being harvested by the less-efficient animals.
]]>Microorganisms doi: 10.3390/microorganisms12030535
Authors: Tanya Kapes Charles Quinn Andrew Eli Cragun Taylor House Raymond W. Nims S. Steve Zhou
Three lipid-enveloped viruses (bovine viral diarrhea virus [BVDV], vaccinia virus, and severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) were evaluated in side-by-side liquid inactivation efficacy studies of low pH (3.0 to 3.1) treatment and of the non-formulated microbicidal actives sodium hypochlorite (100 ppm), ethanol (70%), quaternary ammonium compound BTC® 835 (100 ppm), and peracetic acid (100 ppm). Low pH was evaluated at 10 and 60 min contact times, and the microbicides were evaluated at 1 min contact time at room temperature per the ASTM E1052 standard. In each case, 5% animal serum was included in the viral inoculum as a challenge soil load. The three viruses displayed similar susceptibility to sodium hypochlorite and ethanol, with complete inactivation resulting. Significant differences in susceptibility to BTC® 835 and peracetic acid were identified, with the ordering of the three viruses for susceptibility to BTC® 835 being SARS-CoV-2 > vaccinia virus = BVDV, and the ordering for peracetic acid being vaccinia virus > SARS-CoV-2 > BVDV. The ordering for susceptibility to low pH treatment (60 min contact time) was vaccinia virus > SARS-CoV-2 > BVDV. Not all enveloped viruses display equivalent susceptibilities to inactivation approaches. For the chemistries evaluated here, BVDV appears to represent a worst-case enveloped virus.
]]>Microorganisms doi: 10.3390/microorganisms12030534
Authors: María-Isabel González-Siso Manuel Becerra
Yeasts, both Saccharomyces and non-conventional strains, are currently the focus of active research due to their impressive applications in biotechnological bioprocesses, such as being hosts to produce recombinant proteins or main actors of the fermentation industries [...]
]]>Microorganisms doi: 10.3390/microorganisms12030533
Authors: Jinjian He Yuying Li Xihang Sun Dinghui Zuo Mansheng Wang Xia Zheng Pinglian Yu Pengjun Shi
A putative β-glucosidase gene, BglAc, was amplified from Acidilobus sp. through metagenome database sampling from a hot spring in Yellowstone National Park. BglAc is composed of 485 amino acid residues and bioinformatics analysis showed that it belongs to the GH1 family of β-glucosidases. The gene was successfully expressed in Escherichia coli with a molecular weight of approximately 55.3 kDa. The purified recombinant enzyme showed the maximum activity using p-nitrophenyl-β-D-glucopyranoside (pNPG) as the substrate at optimal pH 5.0 and 100 °C. BglAc exhibited extraordinary thermostability, and its half-life at 90 °C was 6 h. The specific activity, Km, Vmax, and Kcat/Km of BglAc toward pNPG were 357.62 U mg−1, 3.41 mM, 474.0 μmol min−1·mg−1, and 122.7 s−1mM−1. BglAc exhibited the characteristic of glucose tolerance, and the inhibition constant Ki was 180.0 mM. Furthermore, a significant ethanol tolerance was observed, retaining 96% relative activity at 10% ethanol, and even 78% at 20% ethanol, suggesting BglAc as a promising enzyme for cellulose saccharification. BglAc also had a strong ability to convert the major soybean isoflavone glycosides (daidzin, genistin, and glycitin) into their corresponding aglycones. Overall, BglAc was actually a new β-glucosidase with excellent thermostability, ethanol tolerance, and glycoside hydrolysis ability, indicating its wide prospects for applications in the food industry, animal feed, and lignocellulosic biomass degradation.
]]>Microorganisms doi: 10.3390/microorganisms12030532
Authors: Sarita Pandey Anaïs Blache Wafa Achouak
Plant–microbe interactions play a crucial role in shaping plant health and survival. In recent years, the role of extracellular vesicles (EVs) in mediating intercellular communication between plants and microbes has emerged as an intriguing area of research. EVs serve as important carriers of bioactive molecules and genetic information, facilitating communication between cells and even between different organisms. Pathogenic bacteria leverage extracellular vesicles (EVs) to amplify their virulence, exploiting their cargo rich in toxins and virulence factors. Conversely, beneficial microbes initiate EV secretion to stimulate plant immune responses and nurture symbiotic relationships. The transfer of EV-packed small RNAs (sRNAs) has been demonstrated to facilitate the modulation of immune responses. Furthermore, harnessing the potential of EVs holds promise for the development of innovative diagnostic tools and sustainable crop protection strategies. This review highlights the biogenesis and functions of EVs in bacteria and their importance in plant defense, and paves the way for future research in this exciting field.
]]>Microorganisms doi: 10.3390/microorganisms12030531
Authors: Marina Passos Torrealba Fabio Seiti Yamada Yoshikawa Valeria Aoki Maria Notomi Sato Raquel Leão Orfali
Atopic dermatitis (AD) is a chronic and relapsing inflammatory cutaneous disease. The role of host defense and microbial virulence factors in Staphylococcus aureus skin colonization, infection, and inflammation perpetuation in AD remains an area of current research focus. Extracellular vesicles (EV) mediate cell-to-cell communication by transporting and delivering bioactive molecules, such as nucleic acids, proteins, and enzymes, to recipient cells. Staphylococcus aureus spontaneously secretes extracellular vesicles (SA-derived EVs), which spread throughout the skin layers. Previous research has shown that SA-derived EVs from AD patients can trigger cytokine secretion in keratinocytes, shape the recruitment of neutrophils and monocytes, and induce inflammatory AD-type lesions in mouse models, in addition to their role as exogenous worsening factors for the disease. In this review article, we aim to examine the role of SA-derived EVs in AD physiopathology and its progression, highlighting the recent research in the field and exploring the potential crosstalk between the host and the microbiota.
]]>Microorganisms doi: 10.3390/microorganisms12030530
Authors: Nancy Calisto Laura Navarro Cristian Iribarren Paz Orellana Claudio Gómez Lorena Salazar Ana Gutiérrez Carlos Aranda Alex R. González Mario Tello Piedad Cortés-Cortés Manuel Gidekel Gino Corsini
In this study, bacterial isolates C1-4-7, D2-4-6, and M1-4-11 from Antarctic soil were phenotypically and genotypically characterized, and their antibacterial spectrum and that of cell-free culture supernatant were investigated. Finally, the effect of temperature and culture medium on the production of antimicrobial compounds was investigated. The three bacteria were identified as different strains of the genus Pseudomonas. The three bacteria were multi-drug resistant to antibiotics. They exhibited different patterns of growth inhibition of pathogenic bacteria. M1-4-11 was remarkable for inhibiting the entire set of pathogenic bacteria tested. All three bacteria demonstrated optimal production of antimicrobial compounds at 15 °C and 18 °C. Among the culture media studied, Nutrient broth would be the most suitable to promote the production of antimicrobial compounds. The thermostability exhibited by the antimicrobial molecules secreted, their size of less than 10 kDa, and their protein nature would indicate that these molecules are bacteriocin-like compounds.
]]>Microorganisms doi: 10.3390/microorganisms12030529
Authors: Jonas Widberger Andreas Wittgens Sebastian Klaunig Markus Krämer Ann-Kathrin Kissmann Franziska Höfele Tina Baur Tanja Weil Marius Henkel Rudolf Hausmann Frank R. Bengelsdorf Bernhard J. Eikmanns Peter Dürre Frank Rosenau
The establishment of sustainable processes for the production of commodity chemicals is one of today’s central challenges for biotechnological industries. The chemo-autotrophic fixation of CO2 and the subsequent production of acetate by acetogenic bacteria via anaerobic gas fermentation represents a promising platform for the ecologically sustainable production of high-value biocommodities via sequential fermentation processes. In this study, the applicability of acetate-containing cell-free spent medium of the gas-fermenting acetogenic bacterium A. woodii WP1 as the feeder strain for growth and the recombinant production of P. aeruginosa PAO1 mono-rhamnolipids in the well-established nonpathogenic producer strain P. putida KT2440 were investigated. Additionally, the potential possibility of a simplified production process without the necessary separation of feeder strain cells was elucidated via the cultivation of P. putida in cell-containing A. woodii culture broth. For these cultures, the content of both strains was investigated by examining the relative quantification of strain-exclusive genes via qPCR. The recombinant production of mono-rhamnolipids was successfully achieved with maximum titers of approximately 360–400 mg/L for both cell-free and cell-containing A. woodii spent medium. The reported processes therefore represent a successful proof of principle for gas fermentation-derived acetate as a potential sustainable carbon source for future recombinant rhamnolipid production processes by P. putida KT2440.
]]>Microorganisms doi: 10.3390/microorganisms12030528
Authors: Nneka Vivian Iduu Donna Raiford Austin Conley Joy Scaria Julie Nelson Laura Ruesch Stuart Price Min Yue Jiansen Gong Lanjing Wei Chengming Wang
Antimicrobial resistance (AMR) in non-typhoidal Salmonella is a pressing public health concern in the United States, necessitating continuous surveillance. We conducted a retrospective analysis of 251 Salmonella isolates from 11 animal species recovered between 1982 and 1999, utilizing serotyping, antimicrobial susceptibility testing, and whole-genome sequencing (WGS). Phenotypic resistance was observed in 101 isolates, with S. Typhimurium, S. Dublin, S. Agona, and S. Muenster prevailing among 36 identified serovars. Notably, resistance to 12 of 17 antibiotics was detected, with ampicillin being most prevalent (79/251). We identified 38 resistance genes, primarily mediating aminoglycoside (n = 13) and β-lactamase (n = 6) resistance. Plasmid analysis unveiled nine distinct plasmids associated with AMR genes in these isolates. Chromosomally encoded blaSCO-1 was present in three S. Typhimurium and two S. Muenster isolates from equine samples, conferring resistance to amoxicillin/clavulanic acid. Phylogenetic analysis revealed three distinct clusters for these five isolates, indicating evolutionary divergence. This study represents the first report of blaSCO-1 in the USA, and our recovered isolates harboring this gene as early as 1989 precede those of all other reports. The enigmatic nature of blaSCO-1 prompts further research into its function. Our findings highlight the urgency of addressing antimicrobial resistance in Salmonella for effective public health interventions.
]]>Microorganisms doi: 10.3390/microorganisms12030527
Authors: Dan-Cornel Popovici Gheorghe Dărăbuș Ana-Maria Marin Ovidiu Ionescu Maria Monica Florina Moraru Mirela Imre Emil Tîrziu Narcisa Mederle
Fascioloidosis is a parasitic disease of primary wild and domestic ruminants, caused by giant liver fluke, Fascioloides magna. The definitive host of the liver fluke in its area of origin (North America) is the white-tailed deer (Odocoileus virginianus). In Europe, the red deer (Cervus elaphus) and European fallow deer (Dama dama) are definitive hosts and the most sensitive hosts to F. magna infection, on which the parasite exerts serious pathogenic effects. In this study, we analyzed fecal samples and livers of 72 D. dama from 11 hunting grounds in Arad County, Romania. Of the 72 fecal samples and livers from D. dama, trematodes of the genus Fascioloides were identified in four (5.56%). Sequencing revealed that the trematodes identified in the samples were similar to the sequence of F. magna (GenBank no. EF534992.1, DQ683545.1, KU232369.1). The sequence obtained from the molecular analysis has been deposited in GenBank® under accession number OQ689976.1. This study describes the first report of giant liver fluke (F. magna) infection in D. dama in Romania.
]]>Microorganisms doi: 10.3390/microorganisms12030526
Authors: Vanessa Fernandes de Abreu Costa Thaize Quiroga Chometon Katherine Kelda Gomes de Castro Melissa Silva Gonçalves Ponte Maria Inês Fernandes Pimentel Marcelo Rosandiski Lyra Alvaro Luiz Bertho
Cutaneous leishmaniasis is a neglected tropical disease caused, in Brazil, mainly by Leishmania braziliensis, which is a protozoan transmitted during the blood feeding of infected female sandflies. To control leishmaniasis, the participation of CD4+ Th1 cells together with macrophages, neutrophils, and other peripheral blood cells, including platelets, is necessary. These anuclear fragments, when activated, produce microvesicles (MVs) that can reach locations outside the blood, carrying molecules responsible for activating pro-inflammatory responses and antigen presentation. Using flow cytometry, this current study evaluated the frequency and concentration of platelet-derived MVs (pMVs) in plasma samples obtained from patients in the acute phase and undergoing treatment, as well as from healthy volunteers. Our results revealed a higher frequency and concentration of pMVs in the plasma of patients with acute CL when compared to all other groups studied. These results highlight the impact of pMVs in modulating the immune response of CL patients, correlating their higher concentrations and frequencies in CL-patient plasmas, with the acute inflammatory status of the disease and their reduction with beneficial results of systemic treatment with antimony. This knowledge is essential to define potential treatment protocols, as well as highlight pMVs as biomarkers for the different clinical stages of CL.
]]>Microorganisms doi: 10.3390/microorganisms12030524
Authors: Chahrazed Yousfi Saoussen Oueslati Dina Daaboul Delphine Girlich Alexis Proust Chafia Bentchouala Thierry Naas
Abscesses represent the most prominent emerging problem in the red meat industry, leading to great economic constraints and public health hazards. Data on etiological agents present in these purulent lesions in Algeria are very scarce. The aim of this study was to identify the bacteria responsible for these abscesses and to determine their antibiotic susceptibility profiles. A total of 123 samples of abscesses from 100 slaughtered sheep and 23 slaughtered cattle were cultured in several media. A total of 114 bacterial isolates were cultured from 103 abscesses. Bacteria were identified using MALDI–TOF, and antibiotic susceptibility was determined by the disk diffusion method on Mueller–Hinton agar. A total of 73.6% (n = 84) corresponded to Enterobacterales, of which four were multidrug-resistant (MDR). These isolates, together with Staphylococcus aureus, coagulase negative Staphylococci, and seven randomly chosen susceptible Escherichia coli isolates, were further characterized using WGS. Resistome analysis of the four MDR Enterobacterales isolates revealed the presence of OXA-48 carbapenemase in two Klebsiella pneumoniae ST985 and one E. coli ST10 isolates and a CTX-M-15 ESBL in one E. coli isolate ST1706. Two coagulase-negative Staphylococci isolates were found to carry the mecA gene. WGS showed the presence of different resistance genes and virulence genes. Our study revealed 5% of MDR Enterobacterales (including ESBLs and carbapenemases) identified from abscesses, thus urging the need for abscess monitoring in slaughterhouses.
]]>Microorganisms doi: 10.3390/microorganisms12030525
Authors: Tomoko Ohshima Yoko Mukai Hitoshi Watanabe Keijiro Ohshima Koichi Makimura Takashi Komabayashi Chul Ahn Karen Meyer Nobuko Maeda
Introduction: Candida dubliniensis was reclassified from the C. albicans genotype D, and reports show its frequent detection in HIV-positive individuals and easy acquisition of antifungal drug resistance. However, the oral carriage rate in healthy people and contribution to candidiasis in Japan is unclear. Methods: We conducted a cross-sectional survey of the C. dubliniensis carriage rate, performed genotyping and tested antifungal drug susceptibility and protease productivity. Specimens from 2432 Japanese subjects in six regions (1902 healthy individuals, 423 with candidiasis individuals, 107 HIV-positive individuals) were cultured using CHROMagarTMCandida, and the species was confirmed via 25S rDNA amplification and ITS sequences analyzed for genotyping. Results: The C. dubliniensis carriage rate in healthy Japanese was low in the central mainland (0–15%) but high in the most northerly and southerly areas (30–40%). The distribution of these frequencies did not differ depending on age or disease (HIV-infection, candidiasis). Genotype I, previously identified in other countries, was most frequent in Japan, but novel genotypes were also observed. Six antifungal drugs showed higher susceptibility against C. albicans, but protease productivity was low. Conclusions: Oral C. dubliniensis has low pathogenicity with distribution properties attributed to geography and not dependent on age or disease status.
]]>Microorganisms doi: 10.3390/microorganisms12030523
Authors: Ji-Young Kwon Jong-Hoon Choi Hee-Il Lee Jung-Won Ju Myoung-Ro Lee
Blastocystis sp. is the most common intestinal protozoan affecting human health worldwide. Several studies have reported the prevalence of Blastocystis sp. in various regions of the Republic of Korea. However, limited data are available on the prevalence and subtype (ST) distribution of this parasite among regions. Therefore, we investigated the prevalence and ST distributions of this parasite in the Republic of Korea. For this purpose, 894 stool specimens were collected from patients with diarrhea and tested for the presence of Blastocystis sp. using PCR analysis. The isolates were subsequently subtyped. The overall prevalence was 11.6%. Of the 104 isolates, ST3 was the most prevalent, followed by ST1. Additionally, a single case of the rare subtype ST8 was identified, representing the first reported case in the Republic of Korea. The results suggested that the predominance of ST3 observed in this study reflects human-to-human transmission with low genetic diversity within the ST, while ST1 transmission is likely correlated with animals. In the future, to better understand Blastocystis sp. transmission dynamics, human, animal, and environmental factors should be studied from a “One Health” perspective.
]]>Microorganisms doi: 10.3390/microorganisms12030522
Authors: Guizong Xu Zengyi Zhang Qianjin Zhou Mingyan Song Guanjun Yang Jinwei Kang Zhongjie Xu Fangjie Chen Jiong Chen
Glugea plecoglossi is an obligate intracellular microsporidium, which poses a significant threat to ayu (Plecoglossus altivelis). In vitro cultivation models are invaluable tools for investigating intracellular microorganisms, including G. plecoglossil. In this study, we attempted to in vitro cultivate G. plecoglossi using primary cultures derived from ayu monocytes/macrophages (MO/MΦ), a murine-derived macrophage cell line RAW264.7, and the epithelioma papulosum cyprini (EPC) cell line. The results demonstrated that MO/MΦ infected with spores exhibited a pronounced immune response which was presented by rapidly high expression levels of inflammatory cytokines, such as PaIL-1β, PaTNF-α, PaIL-10, and PaTGF-β, and detached within 96 h post-infection (hpi). Infected RAW264.7 cells remained capable of stable passage yet exhibited cellular deformation with a decrease in intracellular spores occurring around 8 days post-infection (dpi). In contrast, EPC cells promised a substantial parasite population, and the cytokine expression levels returned to normal by 8 dpi. In addition, G. plecoglossi spores recovered from EPC cells could infect young ayu, suggesting that EPC cells might be used as an in vitro cultivation system for G. plecoglossi.
]]>Microorganisms doi: 10.3390/microorganisms12030520
Authors: Wei Zhou Xiangyang Sun Suyan Li Bingpeng Qu Jianbing Zhang
Urban forest soil is often disturbed by frequent human activity. Organic mulching is effective for improving soil quality; however, the effects of organic mulching on soil bacterial communities in urban forests are still largely unexplored. This study evaluated how organic mulching changed the urban forest soil bacterial community through an incubation experiment. Four treatments were applied: (1) no organic mulch (CK); (2) wood chips alone (5 g, Mw); (3) wood compost alone (5 g, Mc); and (4) wood chips + wood compost (This mulch was divided into two layers, i.e., the upper layer of wood chips (2.5 g) and the lower layer wood compost (2.5 g, Mw+c).) We found significant differences in the soil physicochemical properties under organic mulching after incubation. Overall, organic mulching can alter soil bacterial community structure. Soil alkali-hydrolyzable nitrogen, soil organic carbon, soil total nitrogen, and carbon-nitrogen ratio were the main factors affecting soil microbial community structures. Soil bacterial groups under organic mulching treatments mainly acted on the C and N cycling of functional pathways in soil. This study suggests that organic mulching could maintain the development of soil bacteria, which establishes a theoretical foundation for enhancing the microbiological environment of urban forest soils.
]]>Microorganisms doi: 10.3390/microorganisms12030521
Authors: Isabella Chi John A. Blaho
HSV-1 major tegument protein VP22 is present in multiple subcellular locations in the late stages of productive viral infection. We initially performed a detailed time course experiment and observed that VP22 was detected in nuclear and nuclear matrix fractions as early as 4 hpi. The goal was to determine the fate of virion-derived incoming VP22, and we report the following: (i) VP22 was detected in nuclear matrix fractions 1 hpi. (ii) In the presence of cycloheximide (CHX), VP22 was present in the nuclear matrix 1–6 hpi, demonstrating the stability of the protein. (iii) The nuclear matrix targeting of VP22 occurred in infected Vero, HEp-2, and human mammary epithelial (HME) cells and following synchronized infection. Based on these results, we conclude that (iv) VP22 targets the nuclear matrix and chromatin upon entry into cells during productive HSV-1 infection.
]]>Microorganisms doi: 10.3390/microorganisms12030519
Authors: Jiansen Gong Di Zhang Lixia Fu Yongyi Dong Kun Wu Xinhong Dou Chengming Wang
Salmonella enterica serovar Indiana (S. Indiana) is among the most prevalent serovars of Salmonella and is closely associated with foodborne diseases worldwide. In this study, we combined a recombinase polymerase amplification (RPA) technique with clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated (Cas) protein Cas12b (CRISPR/Cas12b)-based biosensing in a one-pot platform to develop a novel one-step identification method for S. Indiana infection diagnosis. The entire RPA-CRISPR/Cas12b reaction can be completed at 41 °C within 1 h without the need for specific instruments. The optimal concentrations of Cas12b and single-guide RNA (sgRNA) for the reaction were the same at 250 nM. The single-stranded DNA (ssDNA) reporter 8C-FQ (5′-/6-FAM/CCCCCCCC/BHQ1/-3′) presented the best performance in the reaction compared with the other reporters. The limit of detection (LoD) of the RPA-CRISPR/Cas12b assay was 14.4 copies per reaction. As for specificity, we successfully identified four S. Indiana strains among twenty-two Salmonella strains without any false-positive results, presenting 100% accuracy for S. Indiana, and no cross-reactions were observed in eight other pathogens. Moreover, a total of 109 chicken carcasses were classified by the S. Indiana RPA-CRISPR assay and PCR methods from three processing points, including 43 post-shedding, 35 post-evisceration, and 31 post-chilling. There were 17 S. Indiana-positive samples identified during the whole processing step, consisting of nine post-shedding, five post-evisceration, and three post-chilling. The corresponding S. Indiana-positive rates of post-shedding, post-evisceration, and post-chilling were 20.93% (9/43), 14.29% (5/35), and 9.68% (3/31), respectively. Results from the S. Indiana one-step RPA-CRISPR/Cas12b assay were totally in agreement with those obtained using a traditional culture method, demonstrating 100% agreement with no false-positive or false-negative results observed. Altogether, the RPA-CRISPR/Cas12b assay developed in this study represents a promising, accurate, and simple diagnostic tool for S. Indiana detection.
]]>Microorganisms doi: 10.3390/microorganisms12030518
Authors: Qin Zhang Junbin Lin Junjie Yan Renyun Miao Rencai Feng Ying Gan Bingcheng Gan
This study focuses on optimizing the mutagenesis process for Morchella eximia (Mel-7) mycelia through atmospheric and room temperature plasma (ARTP) mutation and explores the resultant thermal adaptability and physiological responses of mutant strains. This research demonstrated a clear relationship between ARTP mutagenesis exposure duration and lethality rate, indicating that an exposure time of 40 s resulted in the optimal balance of inducing mutations without causing excessive mortality. Additionally, this study established 43 °C as the ideal screening temperature for identifying mutant strains with enhanced heat resistance, as this temperature significantly challenges the mycelia while allowing thermotolerant strains to be distinguishable. Among the screened mutants, strains L21, L23, L44, and L47 exhibited superior growth and high-temperature tolerance, with notable resilience at 30 °C, highlighting their enhanced adaptability to above-optimal temperatures. Furthermore, this research delved into biochemical responses, including lipid peroxidation and non-enzymatic antioxidant content, highlighting the diverse mechanisms, such as enhanced lipid peroxidation resistance and increased antioxidant content, employed by mutant strains to adapt to temperature fluctuations. The activities of antioxidant enzymes, including peroxidase (POD) and superoxide dismutase (SOD), were shown to be significantly influenced by temperature elevations, illustrating their critical roles in the thermal adaptation of mutant strains. These findings shed light on the importance of considering mutation duration and temperature screening in the development of thermotolerant fungal strains with potential applications in various industries. This study’s breakthrough lies in its comprehensive understanding of the thermal adaptability of Mel-7 mycelia and the identification of promising mutant strains, offering valuable insights for both academic and industrial purposes.
]]>Microorganisms doi: 10.3390/microorganisms12030517
Authors: Jiake Li Haojin Cheng Fu Yin Jiwen Liu Xiao-Hua Zhang Min Yu
Deep-sea hydrothermal vents have been extensively explored around the globe in the past decades, and the diversity of microbial communities and their ecological functions related to hydrothermal vents have become hotspots in the study of microbial biogeochemistry. However, knowledge of dominant microbial communities and their unique metabolic characteristics adapting to hydrothermal vents is still limited. In our study, the sediment sample near the Tangyin hydrothermal vent in the southern part of the Okinawa Trough was collected, and the most abundant phyla are Proteobacteria and Desulfobacterota based on the 16S rRNA genes and metagenome sequencing. Metagenomic analysis revealed that methane metabolism, sulfur reduction, and Fe2+ uptake were abundantly distributed in hydrothermal sediment. In addition, most of the metagenomic assembly genomes (MAGs), belonging to Chloroflexota, Desulfobacterota, and Gammaproteobacteria, were found to be involved in methanogenesis, sulfur oxidation/reduction, and ferrous/ferric iron metabolisms. Among these MAGs, the two representative groups (Bathyarchaeia and Thioglobaceae) also showed distinct metabolic characteristics related to carbon, sulfur, and iron to adapt to hydrothermal environments. Our results reveal the dominant microbial populations and their metabolic features in the sediment near the Tangyin hydrothermal fields, providing a better understanding of microbial survival strategies in the extreme environment.
]]>Microorganisms doi: 10.3390/microorganisms12030516
Authors: Da Hee Kang Song Yeol Yun SoYoung Eum Kyung Eun Yoon Seung-Rel Ryu Chulhyun Lee Hye-Ryeon Heo Kwang Moon Lee
Gram-negative bacterial endotoxins can cause pathophysiological effects such as high fever when introduced into the bloodstream. Therefore, endotoxin testing is necessary when producing injectable pharmaceuticals. The pharmaceutical industry has widely used Limulus amebocyte lysate (LAL) to certify product quality. However, ethical concerns have been raised and the increasing scarcity of Limulus polyphemus necessitates the development of novel testing techniques. Recombinant factor C (rFC) was developed using genetic engineering techniques. The aim of this study was to investigate the validity of rFC testing and compare it with the LAL method. The specificity, linearity, accuracy, precision, and robustness of the rFC assay were evaluated. After validation, the rFC assay was found to be suitable for endotoxin detection. We compared the accuracy of the rFC and LAL assays using reference standard endotoxin. The rFC assay was as accurate as the LAL assay. We also compared the two assays using biopharmaceuticals. Greater interference occurred in some samples when the rFC assay was used than when the LAL assay was used. However, the rFC assay overcame the interference when the samples were diluted. Overall, we suggest that rFC can be applied to test biopharmaceuticals.
]]>Microorganisms doi: 10.3390/microorganisms12030515
Authors: LaShelle Spencer Blake Costine Tesia Irwin Anirudha Dixit Cory Spern Angie Diaz Brittney Lozzi Wenyan Li Christina Khodadad Trent Smith Raymond Wheeler Aubrie O’Rourke
Ionic silver (Ag+) is being investigated as a residual biocide for use in NASA spacecraft potable water systems on future crewed missions. This water will be used to irrigate future spaceflight crop production systems. We have evaluated the impact of three concentrations (31 ppb, 125 ppb, and 500 ppb) of ionic silver biocide solutions on lettuce in an arcillite (calcinated clay particle substrate) and hydroponic (substrate-less) growth setup after 28 days. Lettuce plant growth was reduced in the hydroponic samples treated with 31 ppb silver and severely stunted for samples treated at 125 ppb and 500 ppb silver. No growth defects were observed in arcillite-grown lettuce. Silver was detectable in the hydroponic-grown lettuce leaves at each concentration but was not detected in the arcillite-grown lettuce leaves. Specifically, when 125 ppb silver water was applied to a hydroponics tray, Ag+ was detected at an average amount of 7 μg/g (dry weight) in lettuce leaves. The increase in Ag+ corresponded with a decrease in several essential elements in the lettuce tissue (Ca, K, P, S). In the arcillite growth setup, silver did not impact the plant root zone microbiome in terms of alpha diversity and relative abundance between treatments and control. However, with increasing silver concentration, the alpha diversity increased in lettuce root samples and in the water from the hydroponics tray samples. The genera in the hydroponic root and water samples were similar across the silver concentrations but displayed different relative abundances. This suggests that ionic silver was acting as a selective pressure for the microbes that colonize the hydroponic water. The surviving microbes likely utilized exudates from the stunted plant roots as a carbon source. Analysis of the root-associated microbiomes in response to silver showed enrichment of metagenomic pathways associated with alternate carbon source utilization, fatty-acid synthesis, and the ppGpp (guanosine 3′-diphosphate 5′-diphosphate) stringent response global regulatory system that operates under conditions of environmental stress. Nutrient solutions containing Ag+ in concentrations greater than 31 ppb in hydroponic systems lacking cation-exchange capacity can severely impact crop production due to stunting of plant growth.
]]>Microorganisms doi: 10.3390/microorganisms12030514
Authors: Ji-Yang Zheng He-Liang Shi Dun Wang
Monochamus alternatus is a serious trunk-boring pest. The isolation and utilization of entomopathogenic fungi to manage M. alternatus is important. Here, a new strain GQH6 of Metarhizium robertsii, isolated from the Loess Plateau, was identified morphologically and molecularly. The virulence of the strain GQH6 against the third-instar larvae of M. alternatus was studied. Then, the pathological process, including symptom observation and histopathological observation, was also researched. The corrected mortality was 100% at 109 and 108 conidia/mL, and 88.89 ± 5.88% at 107 conidia/mL. The LC50 was 1.93 × 106 conidia/mL and the LC90 was 1.35 × 107 conidia/mL. And the LT50 of the strain GQH6 was 3.96 days at 109 conidia/mL, and 4.99 days at 108 conidia/mL. These virulence indices showed high virulence against M. alternatus larvae. In addition, the symptoms of the infected M. alternatus larvae were obvious. After one day, dark spots appeared and increased in number. By four days, white mycelia appeared. Finally, the larvae body became green. Similarly, the histopathological changes after infection were obvious, mainly manifested in muscle tissue rupture, adipose tissue fracture and midgut disintegration. These results demonstrated that the M. robertsii strain GQH6 isolated from the Loess Plateau was highly virulent against M. alternatus larvae of the third instar.
]]>Microorganisms doi: 10.3390/microorganisms12030513
Authors: Ting Huang Daniel Carrizo Laura Sánchez-García Qitao Hu Angélica Anglés David Gómez-Ortiz Liang-Liang Yu David C. Fernández-Remolar
The process of soil genesis unfolds as pioneering microbial communities colonize mineral substrates, enriching them with biomolecules released from bedrock. The resultant intricate surface units emerge from a complex interplay among microbiota and plant communities. Under these conditions, host rocks undergo initial weathering through microbial activity, rendering them far from pristine and challenging the quest for biomarkers in ancient sedimentary rocks. In addressing this challenge, a comprehensive analysis utilizing Gas Chromatography Mass Spectrometry (GC-MS) and Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) was conducted on a 520-Ma-old Cambrian rock. This investigation revealed a diverse molecular assemblage with comprising alkanols, sterols, fatty acids, glycerolipids, wax esters, and nitrogen-bearing compounds. Notably, elevated levels of bacterial C16, C18 and C14 fatty acids, iso and anteiso methyl-branched fatty acids, as well as fungal sterols, long-chained fatty acids, and alcohols, consistently align with a consortium of bacteria and fungi accessing complex organic matter within a soil-type ecosystem. The prominence of bacterial and fungal lipids alongside maturity indicators denotes derivation from heterotrophic activity rather than ancient preservation or marine sources. Moreover, the identification of long-chain (>C22) n-alkanols, even-carbon-numbered long chain (>C20) fatty acids, and campesterol, as well as stigmastanol, provides confirmation of plant residue inputs. Furthermore, findings highlight the ability of contemporary soil microbiota to inhabit rocky substrates actively, requiring strict contamination controls when evaluating ancient molecular biosignatures or extraterrestrial materials collected.
]]>Microorganisms doi: 10.3390/microorganisms12030512
Authors: Anna Grizon Sébastien Theil Sandra Helinck Pauline Gerber Pascal Bonnarme Christophe Chassard
Investigating the diversity of a given species could give clues for the development of autochthonous starter cultures. However, few studies have focused on the intraspecies diversity of Lactobacillus delbrueckii strains, a technologically important lactic acid bacterium for the dairy industry. For this reason, Lactobacillus delbrueckii strains from the Saint-Nectaire Protected Designation of Origin (PDO) area were isolated and characterized. Genetic diversity was determined based on core genome phylogenetic reconstruction and pangenome analysis, while phenotypic assessments encompassed proteolysis and volatile compound production potential. A total of 15 L. delbrueckii ssp. lactis unique new strains were obtained. The genetic analysis and further proteolytic activities measurement revealed low variability among these Saint-Nectaire strains, while substantial genetic variability was observed within the L. delbrueckii ssp. lactis subspecies as a whole. The volatile compound profiles slightly differed among strains, and some strains produced volatile compounds that could be of particular interest for cheese flavor development. While the genetic diversity among Saint-Nectaire strains was relatively modest compared to overall subspecies diversity, their distinct characteristics and pronounced differentiation from publicly available genomes position them as promising candidates for developing autochthonous starter cultures for cheese production.
]]>Microorganisms doi: 10.3390/microorganisms12030510
Authors: Kedibone Masenya Madira Coutlyne Manganyi Tshegofatso Bridget Dikobe
Food security is an urgent global challenge, with cereals playing a crucial role in meeting the nutritional requirements of populations worldwide. In recent years, the field of metagenomics has emerged as a powerful tool for studying the microbial communities associated with cereal crops and their impact on plant health and growth. This chapter aims to provide a comprehensive overview of cereal metagenomics and its role in enhancing food security through the exploration of beneficial and pathogenic microbial interactions. Furthermore, we will examine how the integration of metagenomics with other tools can effectively address the adverse effects on food security. For this purpose, we discuss the integration of metagenomic data and machine learning in providing novel insights into the dynamic interactions shaping plant-microbe relationships. We also shed light on the potential applications of leveraging microbial diversity and epigenetic modifications in improving crop resilience and yield sustainability. Ultimately, cereal metagenomics has revolutionized the field of food security by harnessing the potential of beneficial interactions between cereals and their microbiota, paving the way for sustainable agricultural practices.
]]>Microorganisms doi: 10.3390/microorganisms12030511
Authors: Jörg Böllmann Marion Martienssen
This study describes the seasonal course of denitrifying and nitrate-reducing bacteria in a dimictic mesotrophic lake (Lake Scharmützelsee, Brandenburg, Germany) within a three-year period from 2011 to 2013. The bacterial cell numbers were quantified by the fluorescence microscopy, most probable number (MPN) and PCR-dependent quantification of the chromosomal 16S rDNA and of the nirS and nirK gene copy number. The highest seasonal differences (up to three orders of magnitudes) have been measured using MPN in the epilimnion. This variation was not reflected by PCR-dependent approaches or direct microscopical enumeration. At adverse conditions (low temperature and/or low nitrate concentrations), the differences between MPN and gene copy numbers increased by up to five orders of magnitudes and decreased to one magnitude at favourable environmental conditions. These results can be explained best by an increasing ratio of viable but not cultivable (VBNC) cells or dead cells at impairing conditions. In the hypolimnion, the courses of MPN and nir gene copy numbers were similar. This can be explained by a higher feeding pressure and therefore smaller amounts of dormant cells. In the pelagial in general, the total cell numbers enumerated by either microscopical or molecular approaches were similar. In the sediment, more than 99% of the DNA was obviously not related to viable bacteria but was rather DNA in dead cells or adsorbed to particle surfaces.
]]>Microorganisms doi: 10.3390/microorganisms12030509
Authors: Keun Ju Kim Seo-Jin Park Seung Gyu Yun Sang Wook Kim Myung-Hyun Nam Eun Kyong Shin Eun-Ah Chang Dae Won Park Chang Kyu Lee Young Kyung Yoon Yunjung Cho
Background: Understanding the immune response to evolving viral strains is crucial for evidence-informed public health strategies. The main objective of this study is to assess the influence of vaccination on the neutralizing activity of SARS-CoV-2 delta and omicron infection against various SARS-CoV-2 variants. Methods: A total of 97 laboratory-confirmed COVID-19 cases were included. To assess the influence of vaccination on neutralizing activity, we measured the neutralizing activity of SARS-CoV-2 delta or omicron (BA.1 or BA.2) infection against wild-type (WT), delta, BA.1, and BA.2, with the results stratified based on vaccination status. Results: The neutralizing activity against the WT, delta, and omicron variants (BA.1 and BA.2) was significantly higher in the vaccinated patients than those in the unvaccinated patients. In the unvaccinated individuals infected with the delta variant, the decrease in binding to BA.1 and BA.2 was statistically significant (3.9- and 2.7-fold, respectively) compared to the binding to delta. In contrast, vaccination followed by delta breakthrough infection improved the cross-neutralizing activity against omicron variants, with only 1.3- and 1.2-fold decreases in BA.1 and BA.2, respectively. Vaccination followed by infection improved cross-neutralizing activity against WT, delta, and BA.2 variants in patients infected with the BA.1 variant, compared to that in unvaccinated patients. Conclusions: Vaccination followed by delta or BA.1 infection is associated with improved cross-neutralizing activity against different SARS-CoV-2 variants. The enhanced protection provided by breakthrough infections could have practical implications for optimizing vaccination strategies.
]]>Microorganisms doi: 10.3390/microorganisms12030508
Authors: Ikhyun Kim Manh Ha Nguyen Sanggon Lee Byoungkoo Choi Keumchul Shin
Pollutants can exist in the soil for a long time and alter the bacterial community. Using lubricants to prevent the wear of chainsaw blades is necessary for thinning activities and wood harvesting. We investigated the influences of soil contamination with chainsaw lubricants on soil bacterial communities. Bio-oil, mineral oil, and recycled oil were scattered on each treatment to investigate variations in soil bacterial structure during treated periods using the Illumina MiSeq sequencing platform. The results obtained were 5943 ASVs, 5112 ASVs, and 6136 ASVs after treatment at one month, six months, and twelve months, respectively. There was a significant difference in Shannon and Simpson indices between treatments and controls. A total of 46 bacterial genera with an average relative abundance of more than 1.0% were detected in all soil samples. Massilia was the most common genus detected in control at one month, with an average relative abundance of 14.99%, while Chthoniobacter was the most abundant genus detected in bio-oil, mineral oil, and recycled oil treatments at one month, with an average relative abundance of 13.39%, 14.32%, and 10.47%, respectively. Among the three chainsaw lubricants, bio-oil and mineral oil had fewer impacts than recycled oil. The abundances of several functional bacteria groups in the bio-oil treatment were higher than in other treatments and controls. Our results indicated that different chainsaw lubricants and their time of application affected the soil bacterial community composition.
]]>Microorganisms doi: 10.3390/microorganisms12030507
Authors: Johnes Pinto Sanches Sávio Souza Costa Diego Assis das Graças Artur Silva Guilherme Costa Baião Rennan G. Moreira Marcelo Murad Magalhães Roberto Lisboa Cunha Rafael Azevedo Baraúna
Palm oil derived from the fruits of Elaeis guineensis Jacq. has global economic importance and is largely produced in tropical regions. The palm oil production process leads to a highly polluting waste called palm oil mill effluent (POME). A strategy commonly used by producers to overcome environmental issues and to improve soil fertility is the reuse of POME as a fertilizer due to the chemical and biological characteristics of the effluent. In this research, three groups were analyzed: soil without POME application (control group) and soil samples after 4 and 9 days of POME application. An environmental DNA metabarcoding approach was used. eDNA was extracted, and the V4 region of the 16S rRNA gene was amplified and sequenced in the Illumina MiSeq platform. The abundance of Proteobacteria (48.1%) and Firmicutes (9.0%) was higher in fertilized soil, while Bacteroidetes (20.3%) and Verrucomicrobia (7.8%) were more abundant in control soil. Additionally, the effluent seemed to modify soil characteristics favoring taxa responsible for the mineralization of organic compounds and nitrogen fixation such as species of Gammaproteobacteria class. Our study highlights the influence of POME on soil biological components and contributes to the sustainable production of palm oil in the Amazon.
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