Microorganisms

27 pages, 1105 KiB

Open AccessReview

Aflatoxins Contamination in Feed Commodities: From Occurrence and Toxicity to Recent Advances in Analytical Methods and Detoxification

by Slim Smaoui, Teresa D’Amore, Maria Tarapoulouzi, Sofia Agriopoulou and Theodoros Varzakas

Microorganisms 2023, 11(10), 2614; https://doi.org/10.3390/microorganisms11102614 - 23 Oct 2023

Cited by 10 | Viewed by 3021

Abstract

Synthesized by the secondary metabolic pathway in Aspergilli, aflatoxins (AFs) cause economic and health issues and are culpable for serious harmful health and economic matters affecting consumers and global farmers. Consequently, the detection and quantification of AFs in foods/feeds are paramount from [...] Read more.

Synthesized by the secondary metabolic pathway in Aspergilli, aflatoxins (AFs) cause economic and health issues and are culpable for serious harmful health and economic matters affecting consumers and global farmers. Consequently, the detection and quantification of AFs in foods/feeds are paramount from food safety and security angles. Nowadays, incessant attempts to develop sensitive and rapid approaches for AFs identification and quantification have been investigated, worldwide regulations have been established, and the safety of degrading enzymes and reaction products formed in the AF degradation process has been explored. Here, occurrences in feed commodities, innovative methods advanced for AFs detection, regulations, preventive strategies, biological detoxification, removal, and degradation methods were deeply reviewed and presented. This paper showed a state-of-the-art and comprehensive review of the recent progress on AF contamination in feed matrices with the intention of inspiring interests in both academia and industry. Full article

(This article belongs to the Special Issue Mycotoxins in Food Safety, Food Security and Sustainability)

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13 pages, 1479 KiB

Open AccessArticle

Effect of Lactiplantibacillus plantarum on the Conversion of Linoleic Acid of Vegetable Oil to Conjugated Linoleic Acid, Lipolysis, and Sensory Properties of Cheddar Cheese

by Awais Khan, Muhammad Nadeem, Fahad Al-Asmari, Muhammad Imran, Saadia Ambreen, Muhammad Abdul Rahim, Sadaf Oranab, Tuba Esatbeyoglu, Elena Bartkiene and João Miguel Rocha

Microorganisms 2023, 11(10), 2613; https://doi.org/10.3390/microorganisms11102613 - 23 Oct 2023

Cited by 4 | Viewed by 1623

Abstract

Conjugated linoleic acid (CLA) is perceived to protect the body from metabolic diseases. This study was conducted to determine the effect of Lactiplantibacillus plantarum (Lp. plantarum) on CLA production and sensory characteristics of cheddar cheese. Lp. plantarum can convert linoleic acid [...] Read more.

Conjugated linoleic acid (CLA) is perceived to protect the body from metabolic diseases. This study was conducted to determine the effect of Lactiplantibacillus plantarum (Lp. plantarum) on CLA production and sensory characteristics of cheddar cheese. Lp. plantarum can convert linoleic acid (LA) to CLA. To increase CLA in cheddar cheese and monitor the conversion of LA to CLA by Lp. plantarum, the LA content of cheese milk (3.4% fat) was increased by partially replacing fat with safflower oil (85% LA of oil) at 0, 3, 6, and 9% concentrations (T₁, T₂, T₃, and T₄). Furthermore, Lp. plantarum 10⁸ colony-forming units (CFU)/mL (8 log CFU mL⁻¹) was added in all treatments along with traditional cheddar cheese culture (Lactococcus lactis ssp. lactis and L. lactis ssp. cremoris). After 30 days of ripening, Lp. plantarum in T₁, T₂, T₃, and T₄ was 6.75, 6.72, 6.65, and 6.55 log CFU g⁻¹. After 60 days of ripening, Lp. plantarum in T₁, T₂, T₃, and T₄ was 6.35, 6.27, 6.19, and 6.32 log CFU g⁻¹. After 60 days of ripening, Lp. plantarum in T₁, T₂, T₃, and T₄ was 6.41, 6.25, 6.69, and 6.65 log CFU g⁻¹. GC-MS analysis showed that concentrations of CLA in the 90 days’ control, T₁, T₂, T₃, and T₄ were 1.18, 2.73, 4.44, 6.24, and 9.57 mg/100 g, respectively. HPLC analysis revealed that treatments containing Lp. plantarum and LA presented higher concentrations of organic acids than the control sample. The addition of safflower oil at all concentrations did not affect cheese composition, free fatty acids (FFA), and the peroxide value (POV) of cheddar cheese. Color flavor and texture scores of experimental cheeses were not different from the control cheese. It was concluded that Lp. plantarum and safflower oil can be used to increase CLA production in cheddar cheese. Full article

(This article belongs to the Special Issue Screening and Characterization of the Diversity of Food Microorganisms and Their Metabolites 2022)

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19 pages, 2121 KiB

Open AccessArticle

Taxonomic Re-Classification and Expansion of the Phylum Chloroflexota Based on over 5000 Genomes and Metagenome-Assembled Genomes

by Sandra Wiegand, Morgan Sobol, Luca Kristina Schnepp-Pesch, Geng Yan, Sajid Iqbal, John Vollmers, Jochen A. Müller and Anne-Kristin Kaster

Microorganisms 2023, 11(10), 2612; https://doi.org/10.3390/microorganisms11102612 - 23 Oct 2023

Cited by 4 | Viewed by 2353

Abstract

The phylum Chloroflexota (formerly Chloroflexi) encompasses metabolically diverse bacteria that often have high prevalence in terrestrial and aquatic habitats, some even with biotechnological application. However, there is substantial disagreement in public databases which lineage should be considered a member of the phylum and [...] Read more.

The phylum Chloroflexota (formerly Chloroflexi) encompasses metabolically diverse bacteria that often have high prevalence in terrestrial and aquatic habitats, some even with biotechnological application. However, there is substantial disagreement in public databases which lineage should be considered a member of the phylum and at what taxonomic level. Here, we addressed these issues through extensive phylogenomic analyses. The analyses were based on a collection of >5000 Chloroflexota genomes and metagenome-assembled genomes (MAGs) from public databases, novel environmental sites, as well as newly generated MAGs from publicly available sequence reads via an improved binning approach incorporating covariance information. Based on calculated relative evolutionary divergence, we propose that Candidatus Dormibacterota should be listed as a class (i.e., Ca. Dormibacteria) within Chloroflexota together with the classes Anaerolineae, Chloroflexia, Dehalococcoidia, Ktedonobacteria, Ca. Limnocylindria, Thermomicrobia, and two other classes containing only uncultured members. All other Chloroflexota lineages previously listed at the class rank appear to be rather orders or families in the Anaerolineae and Dehalococcoidia, which contain the vast majority of genomes and exhibited the strongest phylogenetic radiation within the phylum. Furthermore, the study suggests that a common ecophysiological capability of members of the phylum is to successfully cope with low energy fluxes. Full article

(This article belongs to the Section Environmental Microbiology)

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12 pages, 1446 KiB

Open AccessArticle

Antimycobacterial Activities of Hydroxamic Acids and Their Iron(II/III), Nickel(II), Copper(II) and Zinc(II) Complexes

by Dong Yang, Yanfang Zhang, Ibrahima Sory Sow, Hongping Liang, Naïma El Manssouri, Michel Gelbcke, Lina Dong, Guangxin Chen, François Dufrasne, Véronique Fontaine and Rongshan Li

Microorganisms 2023, 11(10), 2611; https://doi.org/10.3390/microorganisms11102611 - 23 Oct 2023

Cited by 2 | Viewed by 1498

Abstract

Hydroxamic acid (HA) derivatives display antibacterial and antifungal activities. HA with various numbers of carbon atoms (C₂, C₆, C₈, C₁₀, C₁₂ and C₁₇), complexed with different metal ions, including Fe(II/III), Ni(II), Cu(II) [...] Read more.

Hydroxamic acid (HA) derivatives display antibacterial and antifungal activities. HA with various numbers of carbon atoms (C₂, C₆, C₈, C₁₀, C₁₂ and C₁₇), complexed with different metal ions, including Fe(II/III), Ni(II), Cu(II) and Zn(II), were evaluated for their antimycobacterial activities and their anti-biofilm activities. Some derivatives showed antimycobacterial activities, especially in biofilm growth conditions. For example, 20–100 µM of HA10Fe2, HA10FeCl, HA10Fe3, HA10Ni2 or HA10Cu2 inhibited Mycobacterium tuberculosis, Mycobacterium bovis BCG and Mycobacterium marinum biofilm development. HA10Fe2, HA12Fe2 and HA12FeCl could even attack pre-formed Pseudomonas aeruginosa biofilms at higher concentrations (around 300 µM). The phthiocerol dimycocerosate (PDIM)-deficient Mycobacterium tuberculosis H37Ra was more sensitive to the ion complexes of HA compared to other mycobacterial strains. Furthermore, HA10FeCl could increase the susceptibility of Mycobacterium bovis BCG to vancomycin. Proteomic profiles showed that the potential targets of HA10FeCl were mainly related to mycobacterial stress adaptation, involving cell wall lipid biosynthesis, drug resistance and tolerance and siderophore metabolism. This study provides new insights regarding the antimycobacterial activities of HA and their complexes, especially about their potential anti-biofilm activities. Full article

(This article belongs to the Special Issue Mechanisms of Mycobacteria Drug Escape – an Opportunity for Innovative Antimycobacterial Drug Development)

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12 pages, 313 KiB

Open AccessArticle

Multidrug-Resistant and Extensively Drug-Resistant Escherichia coli in Sewage in Kuwait: Their Implications

by Mahdi A. Redha, Noura Al Sweih and M. John Albert

Microorganisms 2023, 11(10), 2610; https://doi.org/10.3390/microorganisms11102610 - 23 Oct 2023

Cited by 1 | Viewed by 1634

Abstract

In Kuwait, some sewage is discharged into the sea untreated, causing a health risk. Previously, we investigated the presence of pathogenic E. coli among the 140 isolates of E. coli cultured from the raw sewage from three sites in Kuwait. The aim of [...] Read more.

In Kuwait, some sewage is discharged into the sea untreated, causing a health risk. Previously, we investigated the presence of pathogenic E. coli among the 140 isolates of E. coli cultured from the raw sewage from three sites in Kuwait. The aim of the current study was to characterize the antimicrobial resistance of these isolates and the implications of resistance. Susceptibility to 15 antibiotic classes was tested. Selected genes mediating resistance to cephalosporins and carbapenems were sought. ESBL and carbapenemase production were also determined. Two virulent global clones, ST131 and ST648, were sought. A total of 136 (97.1%), 14 (10.0%), 128 (91.4%), and 2 (1.4%) isolates were cephalosporin-resistant, carbapenem-resistant, multidrug-resistant (MDR), and extensively drug-resistant (XDR), respectively. Among the cephalosporin-resistant isolates, ampC, bla_TEM, bla_CTX-M, bla_OXA-1, and bla_CMY-2 were found. Eighteen (12.9%) samples were ESBL producers. All carbapenem-resistant isolates were negative for carbapenemase genes (bla_OXA-48, bla_IMP, bla_GES, bla_VIM, bla_NDM, and bla_KPC), and for carbapenemase production. Resistance rates in carbapenem-resistant isolates to many other antibiotics were significantly higher than in susceptible isolates. A total of four ST131 and ST648 isolates were detected. The presence of MDR and XDR E. coli and global clones in sewage poses a threat in treating E. coli infections. Full article

(This article belongs to the Special Issue Antimicrobial Resistance and Multidrug-Resistant Bacteria in Infectious Patients)

14 pages, 2768 KiB

Open AccessArticle

Heterogeneous Habitats in Taiga Forests with Different Important Values of Constructive Species Changes Bacterial Beta Diversity

by Tian Zhou, Song Wu, Hong Pan, Xinming Lu, Jun Du and Libin Yang

Microorganisms 2023, 11(10), 2609; https://doi.org/10.3390/microorganisms11102609 - 23 Oct 2023

Cited by 2 | Viewed by 1883

Abstract

As a crucial link between the aboveground and belowground components of forest ecosystems, soil bacterial communities are extremely sensitive to changes in plant communities and soil conditions. To investigate the impact of the difference of constructive species on soil bacterial communities in taiga [...] Read more.

As a crucial link between the aboveground and belowground components of forest ecosystems, soil bacterial communities are extremely sensitive to changes in plant communities and soil conditions. To investigate the impact of the difference of constructive species on soil bacterial communities in taiga forests, we conducted a vegetation survey at the international monitoring plot of the Larix gmelinii forests in the Great Khingan Mountains and calculated the important value of Larix gmelinii to determine experimental groups based on this survey. Subsequently, we collected soil samples for high-throughput sequencing to analyze how the soil bacterial community composition and diversity changed, and which factors affected them. The results showed that taiga forests with different important values of Larix gmelinii had heterogeneous habitats, in which the soil AP content significantly increased, and the SOC, MBC, pH, and C/N content decreased significantly (p < 0.05). A total of 32 phyla, 91 classes, 200 orders, 308 families, 496 genera, and 975 species of soil bacteria were obtained by sequencing. Among them, Proteobacteria, Actinobacteriota, and Acidobacteriota were the dominant phyla, and Mycobacterium was the dominant genus, and the relative abundance of each bacterial group was varied. The beta diversity of soil bacteria showed extremely significant differences (p = 0.001), with SOC, C/N, MBC, AP, TN, pH, AN, and WC being the main influencing factors. Functional prediction analysis showed that chemoheterotrophy and aerobic chemoheterotrophy were the main bacterial functional groups, and the relative abundance of each functional group was significantly different (p < 0.05). Overall, taiga forests with differences in constructive species had heterogeneous habitats, which changed the community composition, beta diversity, and potential functions of soil bacteria. Full article

(This article belongs to the Special Issue Soil Microbial Communities under Environmental Change)

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14 pages, 4850 KiB

Open AccessArticle

Human Cutaneous Leishmaniasis in North Africa and Its Threats to Public Health: A Statistical Study Focused on Djelfa (Algeria)

by Fatma Messaoudene, Slimane Boukraa, Said Chaouki Boubidi, Ahlem Guerzou and Abdeldjalil Ouahabi

Microorganisms 2023, 11(10), 2608; https://doi.org/10.3390/microorganisms11102608 - 22 Oct 2023

Cited by 1 | Viewed by 2135

Abstract

Cutaneous leishmaniasis, the most common form of leishmaniasis, causes long-term skin lesions on exposed areas of the skin. It is caused by a protozoan parasite belonging to the genus Leishmania and is transmitted via infected phlebotomine sand flies. In North Africa, particularly Algeria, [...] Read more.

Cutaneous leishmaniasis, the most common form of leishmaniasis, causes long-term skin lesions on exposed areas of the skin. It is caused by a protozoan parasite belonging to the genus Leishmania and is transmitted via infected phlebotomine sand flies. In North Africa, particularly Algeria, the disease represents a major public health problem. This retrospective study, which focuses on the agropastoral region of Djelfa (central Algeria) during a period of 16 years, from 2006 to 2021, is part of the surveillance of cutaneous leishmaniasis to identify the key factors favouring its probable spread. The analyzed data reveal that this disease is more prevalent in male patients (53.60%) and is highly widespread in this vast area of 66,415 km² with a total of 3864 CL cases, reaching a peak of 1407 cases in 2006. Statistically, the Pearson correlation validated by the p-value shows, in an original and sometimes unexpected way, that certain factors, such as temperature linked to climate change, are playing a significant role in the probable spread of the disease in Djelfa and its surrounding regions. The concentration of the population in some specific rural areas with limited or nonexistent access to public health services is another potential factor in disease transmission. The results were highlighted by a significant correlation coefficient (

r = 0.66

) with a p-value less than 0.01. While there is currently no vaccine or prophylactic drug available, our research represents a preliminary approach that addresses various epidemiological aspects of the disease. This paves the way for a proactive preventive strategy involving the control of vector-borne diseases. Full article

(This article belongs to the Special Issue Research on Leishmania and Leishmaniasis)

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12 pages, 596 KiB

Open AccessArticle

Does Nirmatrelvir/Ritonavir Influence the Immune Response against SARS-CoV-2, Independently from Rebound?

by Francesca Panza, Fabio Fiorino, Gabiria Pastore, Lia Fiaschi, Mario Tumbarello, Donata Medaglini, Annalisa Ciabattini, Francesca Montagnani and Massimiliano Fabbiani

Microorganisms 2023, 11(10), 2607; https://doi.org/10.3390/microorganisms11102607 - 22 Oct 2023

Cited by 2 | Viewed by 1739

Abstract

Recurrence of coronavirus disease 19 (COVID-19) symptoms and SARS-CoV-2 viral load relapse have been reported in people treated with nirmatrelvir/ritonavir (NM/r). However, little is understood about the etiology of this phenomenon. Our aim was to investigate the relation between the host’s immune response [...] Read more.

Recurrence of coronavirus disease 19 (COVID-19) symptoms and SARS-CoV-2 viral load relapse have been reported in people treated with nirmatrelvir/ritonavir (NM/r). However, little is understood about the etiology of this phenomenon. Our aim was to investigate the relation between the host’s immune response and viral rebound. We described three cases of COVID-19 rebound that occurred after treatment with nirmatrelvir/ritonavir (group A). In addition, we compared spike-specific antibody response and plasma cytokine/chemokine patterns of the rebound cases with those of (i) control patients treated with nirmatrelvir/ritonavir who did not show rebound (group B), and (ii) subjects not treated with any anti-SARS-CoV-2 drug (group C). The anti-spike antibodies and plasma cytokines/chemokines were similar in groups A and B. However, we observed a higher anti-BA.2 spike IgG response in patients without antiviral treatment (group C) [geometric mean titer 210,807, 5.1- and 8.2-fold higher compared to group A (p = 0.039) and group B (p = 0.032)]. Moreover, the patients receiving antiviral treatment (groups A-B) showed higher circulating levels of platelet-derived growth factor subunit B (PDGF-BB) and vascular endothelial growth Factors (VEGF) and lower levels of interleukin-9 (IL-9), interleukine-1 receptor antagonist (IL-1 RA), and regulated upon activation normal T cell expressed and presumably secreted chemokine (RANTES) when compared to group C. In conclusion, we observed lower anti-spike IgG levels and different cytokine patterns in nirmatrelvir/ritonavir-treated patients compared to those not treated with anti-SARS-CoV-2 drugs. This suggests that early antiviral treatment, by reducing viral load and antigen presentation, could mitigate the immune response against SARS-CoV-2. The clinical relevance of such observation should be further investigated in larger populations. Full article

(This article belongs to the Special Issue Immune Modulation to SARS-CoV-2 Vaccination and Infection)

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13 pages, 794 KiB

Open AccessArticle

Detection and Quantification of the Epstein-Barr Virus in Lymphoma Patients from Ethiopia: Molecular and Serological Approaches

by Seifegebriel Teshome, Kidist Zealiyas, Abdulaziz Abubeker, Fisihatsion Tadesse, Jayalakshmi Balakrishna, Christoph Weigel, Tamrat Abebe, Elshafa Hassan Ahmed and Robert A. Baiocchi

Microorganisms 2023, 11(10), 2606; https://doi.org/10.3390/microorganisms11102606 - 22 Oct 2023

Viewed by 1642

Abstract

The Epstein-Barr virus (EBV) is a known oncogenic virus associated with various lymphoma subtypes throughout the world. However, there is a lack of information regarding EBV prevalence in lymphoma patients, specifically in Ethiopia. This study aimed to investigate the presence of the EBV [...] Read more.

The Epstein-Barr virus (EBV) is a known oncogenic virus associated with various lymphoma subtypes throughout the world. However, there is a lack of information regarding EBV prevalence in lymphoma patients, specifically in Ethiopia. This study aimed to investigate the presence of the EBV and determine its viral load in lymphoma patients from Ethiopia using molecular and serological approaches. Lymphoma patient samples were collected from the Ethiopian population. DNA and serum samples were extracted and subjected to molecular detection methods, including quantitative polymerase chain reaction (qPCR) analysis targeting the EBNA1 gene. Serological analyses were performed using an enzyme-linked immunosorbent assay (ELISA) to detect EBV viral capsid antigen IgG antibodies. EBV DNA was detected in 99% of lymphoma patients using qPCR, and serological analyses showed EBV presence in 96% of cases. A high EBV viral load (>10,000 EBV copies/mL) was observed in 56.3% of patients. The presence of high EBV viral loads was observed in 59.3% of HL patients and 54.8% of NHL patients. This study provides important insights into the prevalence and viral load of the EBV among lymphoma patients in Ethiopia. The findings contribute to the limited knowledge in this area and can serve as a foundation for future research. Full article

(This article belongs to the Special Issue Epstein–Barr Virus Infection and Associated Diseases 2.0)

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17 pages, 4064 KiB

Open AccessArticle

Effects of Two Different Proportions of Microbial Formulations on Microbial Communities in Kitchen Waste Composting

by Hairong Jiang, Yuling Zhang, Ruoqi Cui, Lianhai Ren, Minglu Zhang and Yongjing Wang

Microorganisms 2023, 11(10), 2605; https://doi.org/10.3390/microorganisms11102605 - 21 Oct 2023

Cited by 1 | Viewed by 2188

Abstract

The objective of this research was to investigate the effect of bulking agents on the maturity and gaseous emissions of composting kitchen waste. The composing experiments were carried out by selected core bacterial agents and universal bacterial agents for 20 days. The results [...] Read more.

The objective of this research was to investigate the effect of bulking agents on the maturity and gaseous emissions of composting kitchen waste. The composing experiments were carried out by selected core bacterial agents and universal bacterial agents for 20 days. The results demonstrated that the addition of core microbial agents effectively controlled the emission of typical odor-producing compounds. The addition of core and universal bacterial agents drastically reduced NH₃ emissions by 94% and 74%, and decreased H₂S emissions by 78% and 27%. The application of core microbial agents during composting elevated the peak temperature to 65 °C and in terms of efficient temperature evolution (>55 °C for 8 consecutive days). The organic matter degradation decreased by 65% from the initial values for core microbial agents were added, while for the other treatments the reduction was slight. Adding core microbial agents to kitchen waste produced mature compost with a higher germination index (GI) 112%, while other treatments did not fully mature and had a GI of <70%. Microbial analysis demonstrated that the core microbial agents in composting increased the relative abundances of Weissella, Ignatzschineria, and Bacteroides. Network and redundancy analysis (RDA) revealed that the core microbial agents enhanced the relationship between bacteria and the eight indicators (p < 0.01), thereby improving the bio transformation of compounds during composting. Overall, these results suggest that the careful selection of appropriate inoculation microorganisms is crucial for improved biological transformation and nutrient content composting efficacy of kitchen waste. Full article

(This article belongs to the Section Environmental Microbiology)

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24 pages, 4523 KiB

Open AccessReview

Bridging Molecular and Clinical Sciences to Achieve the Best Treatment of Enterococcus faecalis Endocarditis

by Francesco Nappi, Sanjeet Singh Avtaar Singh, Vikram Jitendra and Antonio Fiore

Microorganisms 2023, 11(10), 2604; https://doi.org/10.3390/microorganisms11102604 - 21 Oct 2023

Cited by 4 | Viewed by 2040

Abstract

Enterococcus faecalis (E. faecalis) is a commensal bacterium that causes various infections in surgical sites, the urinary tract, and blood. The bacterium is becoming a significant concern because it tends to affect the elderly population, which has a high prevalence of [...] Read more.

Enterococcus faecalis (E. faecalis) is a commensal bacterium that causes various infections in surgical sites, the urinary tract, and blood. The bacterium is becoming a significant concern because it tends to affect the elderly population, which has a high prevalence of undiagnosed degenerative valvular disease and is often subjected to invasive procedures and implanted medical devices. The bacterium’s actions are influenced by specific characteristics like pili activity and biofilm formation. This resistance significantly impedes the effectiveness of numerous antibiotic therapies, particularly in cases of endocarditis. While current guidelines recommend antimicrobial therapy, the emergence of resistant strains has introduced complexity in managing these patients, especially with the increasing use of transcatheter therapies for those who are not suitable for surgery. Presentations of the condition are often varied and associated with generalised symptoms, which may pose a diagnostic challenge. We share our encounter with a case study that concerns an octogenarian who had a TAVI valve and developed endocarditis. We also conducted a literature review to identify the essential treatment algorithms for such cases. Full article

(This article belongs to the Section Molecular Microbiology and Immunology)

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20 pages, 7226 KiB

Open AccessArticle

The Imperative Use of Bacillus Consortium and Quercetin Contributes to Suppress Fusarium Wilt Disease by Direct Antagonism and Induced Resistance

by Ali Hassan, Waheed Akram, Humaira Rizwana, Zill-e-Huma Aftab, Sana Hanif, Tehmina Anjum and Mona S. Alwahibi

Microorganisms 2023, 11(10), 2603; https://doi.org/10.3390/microorganisms11102603 - 21 Oct 2023

Cited by 5 | Viewed by 1716

Abstract

Fusarium wilt diseases severely influence the growth and productivity of numerous crop plants. The consortium of antagonistic rhizospheric Bacillus strains and quercetin were evaluated imperatively as a possible remedy to effectively manage the Fusarium wilt disease of tomato plants. The selection of Bacillus [...] Read more.

Fusarium wilt diseases severely influence the growth and productivity of numerous crop plants. The consortium of antagonistic rhizospheric Bacillus strains and quercetin were evaluated imperatively as a possible remedy to effectively manage the Fusarium wilt disease of tomato plants. The selection of Bacillus strains was made based on in-vitro antagonistic bioassays against Fusarium oxysporum f.sp. lycoprsici (FOL). Quercetin was selected after screening a library of phytochemicals during in-silico molecular docking analysis using tomato LysM receptor kinases “SILKY12” based on its dual role in symbiosis and plant defense responses. After the selection of test materials, pot trials were conducted where tomato plants were provided consortium of Bacillus strains as soil drenching and quercetin as a foliar spray in different concentrations. The combined application of consortium (Bacillus velezensis strain BS6, Bacillus thuringiensis strain BS7, Bacillus fortis strain BS9) and quercetin (1.0 mM) reduced the Fusarium wilt disease index up to 69%, also resulting in increased plant growth attributes. Likewise, the imperative application of the Bacillus consortium and quercetin (1.0 mM) significantly increased total phenolic contents and activities of the enzymes of the phenylpropanoid pathway. Non-targeted metabolomics analysis was performed to investigate the perturbation in metabolites. FOL pathogen negatively affected a range of metabolites including carbohydrates, amino acids, phenylpropanoids, and organic acids. Thereinto, combined treatment of Bacillus consortium and quercetin (1.0 mM) ameliorated the production of different metabolites in tomato plants. These findings prove the imperative use of Bacillus consortium and quercetin as an effective and sustainable remedy to manage Fusarium wilt disease of tomato plants and to promote the growth of tomato plants under pathogen stress conditions. Full article

(This article belongs to the Special Issue Antifungal Activity of Bacillus Species against Plant Pathogens)

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13 pages, 4209 KiB

Open AccessArticle

UHPLC/MS-Based Untargeted Metabolomics Reveals Metabolic Characteristics of Clinical Strain of Mycoplasma bovis

by Fei Yang, Mengmeng Yang, Duoduo Si, Jialin Sun, Fan Liu, Yanrong Qi, Shenghu He and Yanan Guo

Microorganisms 2023, 11(10), 2602; https://doi.org/10.3390/microorganisms11102602 - 21 Oct 2023

Cited by 2 | Viewed by 1479

Abstract

Mycoplasma bovis is a global concern for the cattle industry owing to its high rates of infection and resulting morbidity, but its pathogenesis remains poorly understood. Metabolic pathways and characteristics of M. bovis clinical strain were elucidated by comparing the differential expression of [...] Read more.

Mycoplasma bovis is a global concern for the cattle industry owing to its high rates of infection and resulting morbidity, but its pathogenesis remains poorly understood. Metabolic pathways and characteristics of M. bovis clinical strain were elucidated by comparing the differential expression of metabolites between M. bovis clinical strain NX114 and M. bovis international reference strain PG45. Metabolites of M. bovis in the logarithmic stage were analyzed based on the non-targeted metabolomic technology of ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS). We found 596 metabolites with variable expression, of which, 190 had substantial differences. Differential metabolite analysis of M. bovis NX114 showed organic acids and their derivatives, nucleosides, and nucleotide analogs as important components. We found O-Phospho-L-serine (SEP) as a potential signature metabolite and indicator of pathogenicity. The difference in nucleic acid metabolites reflects the difference in growth phenotypes between both strains of M. bovis. According to KEGG enrichment analysis, the ABC transporter synthesis route had the most differential metabolites of the first 15 differential enrichment pathways. This study reflects the species-specific differences between two strains of M. bovis and further enriches our understanding of its metabolism, paving the way for further research into its pathogenesis. Full article

(This article belongs to the Section Veterinary Microbiology)

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22 pages, 4966 KiB

Open AccessArticle

Study of the Interface between Wild Bird Populations and Poultry and Their Potential Role in the Spread of Avian Influenza

by Luca Martelli, Diletta Fornasiero, Francesco Scarton, Arianna Spada, Francesca Scolamacchia, Grazia Manca and Paolo Mulatti

Microorganisms 2023, 11(10), 2601; https://doi.org/10.3390/microorganisms11102601 - 21 Oct 2023

Cited by 5 | Viewed by 2658

Abstract

Water birds play a crucial role in disseminating and amplifying avian influenza viruses (AIVs) in the environment. However, they may have limited interactions with domestic facilities, raising the hypothesis that other wild birds may play the bridging role in introducing AIVs into poultry. [...] Read more.

Water birds play a crucial role in disseminating and amplifying avian influenza viruses (AIVs) in the environment. However, they may have limited interactions with domestic facilities, raising the hypothesis that other wild birds may play the bridging role in introducing AIVs into poultry. An ornithocoenosis study, based on census-transect and camera-trapping methods, was conducted in 2019 in ten poultry premises in northeast Italy to characterize the bird communities and envisage the species that might act as bridge hosts for AIVs. The data collected were explored through a series of multivariate analyses (correspondence analysis and non-metric multidimensional scaling), and biodiversity indices (observed and estimated richness, Shannon entropy and Pielou’s evenness). The analyses revealed a high level of complexity in the ornithic population, with 147 censused species, and significant qualitative and quantitative differences in wild bird species composition, both in space and in time. Among these, only a few were observed in close proximity to the farm premises (i.e., Magpies, Blackbirds, Cattle Egrets, Pheasants, Eurasian Collared Doves, and Wood Pigeons), thus suggesting their potential role in spilling over AIVs to poultry; contrarily, waterfowls appeared to be scarcely inclined to close visits, especially during autumn and winter seasons. These findings stress the importance of ongoing research on the wild–domestic bird interface, advocating for a wider range of species to be considered in AIVs surveillance and prevention programs. Full article

(This article belongs to the Special Issue Ecology of Influenza A Viruses: 2nd Edition)

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11 pages, 616 KiB

Open AccessReview

Thermophilic Fungi as the Microbial Agents of Choice for the Industrial Co-Fermentation of Wood Wastes and Nitrogen-Rich Organic Wastes to Bio-Methane

by John G. Ingersoll

Microorganisms 2023, 11(10), 2600; https://doi.org/10.3390/microorganisms11102600 - 21 Oct 2023

Cited by 1 | Viewed by 1553

Abstract

The novel industrial approach of co-fermenting wood wastes with agricultural wastes that are rich in nitrogen such as animal manures to produce bio-methane (renewable natural gas) fuel via thermophilic anaerobic digestion mimics an analogous process occurring in lower termites, but it relies instead [...] Read more.

The novel industrial approach of co-fermenting wood wastes with agricultural wastes that are rich in nitrogen such as animal manures to produce bio-methane (renewable natural gas) fuel via thermophilic anaerobic digestion mimics an analogous process occurring in lower termites, but it relies instead on thermophilic fungi along with other thermophilic microorganisms comprising suitable bacteria and archaea. Wood microbial hydrolysis under thermophilic temperatures (range of 55 °C to 70 °C) and aerobic or micro-aerobic conditions constitutes the first step of the two-step (hydrolysis and fermentation) dry thermophilic anaerobic digestion industrial process, designated as “W2M3+2”, that relies on thermophilic fungi species, most of which grow naturally in wood piles. Eleven thermophilic fungi have been identified as likely agents of the industrial process, and their known growth habitats and conditions have been reviewed. Future research is proposed such that the optimal growth temperature of these thermophilic fungi could be increased to the higher thermophilic range approaching 70 °C, and a tolerance to partial anaerobic conditions can be obtained by modifying the fungal microbiome via a symbiotic existence with bacteria and/or viruses. Full article

(This article belongs to the Special Issue Microorganisms in Biomass Conversion and Biofuel Production)

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34 pages, 26676 KiB

Open AccessReview

Anti-Malassezia Drug Candidates Based on Virulence Factors of Malassezia-Associated Diseases

by Muriel Billamboz and Samir Jawhara

Microorganisms 2023, 11(10), 2599; https://doi.org/10.3390/microorganisms11102599 - 20 Oct 2023

Cited by 7 | Viewed by 3924

Abstract

Malassezia is a lipophilic unicellular fungus that is able, under specific conditions, to cause severe cutaneous and systemic diseases in predisposed subjects. This review is divided into two complementary parts. The first one discusses how virulence factors contribute to Malassezia pathogenesis that triggers [...] Read more.

Malassezia is a lipophilic unicellular fungus that is able, under specific conditions, to cause severe cutaneous and systemic diseases in predisposed subjects. This review is divided into two complementary parts. The first one discusses how virulence factors contribute to Malassezia pathogenesis that triggers skin diseases. These virulence factors include Malassezia cell wall resistance, lipases, phospholipases, acid sphingomyelinases, melanin, reactive oxygen species (ROS), indoles, hyphae formation, hydrophobicity, and biofilm formation. The second section describes active compounds directed specifically against identified virulence factors. Among the strategies for controlling Malassezia spread, this review discusses the development of aryl hydrocarbon receptor (AhR) antagonists, inhibition of secreted lipase, and fighting biofilms. Overall, this review offers an updated compilation of Malassezia species, including their virulence factors, potential therapeutic targets, and strategies for controlling their spread. It also provides an update on the most active compounds used to control Malassezia species. Full article

(This article belongs to the Special Issue Human Pathogenic Fungi: Host-Pathogen Interactions and Virulence)

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12 pages, 734 KiB

Open AccessReview

Interplay between the Human Microbiome and Biliary Tract Cancer: Implications for Pathogenesis and Therapy

by Cheng Ye, Chunlu Dong, Yanyan Lin, Huaqing Shi and Wence Zhou

Microorganisms 2023, 11(10), 2598; https://doi.org/10.3390/microorganisms11102598 - 20 Oct 2023

Cited by 1 | Viewed by 2223

Abstract

Biliary tract cancer, encompassing intrahepatic and extrahepatic cholangiocarcinoma as well as gallbladder carcinoma, stands as a prevalent malignancy characterized by escalating incidence rates and unfavorable prognoses. The onset of cholangiocarcinoma involves a multitude of risk factors and could potentially be influenced by microbial [...] Read more.

Biliary tract cancer, encompassing intrahepatic and extrahepatic cholangiocarcinoma as well as gallbladder carcinoma, stands as a prevalent malignancy characterized by escalating incidence rates and unfavorable prognoses. The onset of cholangiocarcinoma involves a multitude of risk factors and could potentially be influenced by microbial exposure. The human microbiome, encompassing the entirety of human microbial genetic information, assumes a pivotal role in regulating key aspects such as host digestion, absorption, immune responses, and metabolism. The widespread application of next-generation sequencing technology has notably propelled investigations into the intricate relationship between the microbiome and diseases. An accumulating body of evidence strongly suggests a profound interconnection between biliary tract cancer and the human microbiome. This article critically appraises the existing evidence pertaining to the microbiome milieu within patients afflicted by biliary tract cancer. Furthermore, it delves into potential mechanisms through which dysregulation of the human microbiome could contribute to the advancement of biliary tract cancer. Additionally, the article expounds on its role in the context of chemotherapy and immunotherapy for biliary tract cancer. Full article

(This article belongs to the Section Gut Microbiota)

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12 pages, 2136 KiB

Open AccessArticle

Assessment of the Virulence of the Burkholderia mallei Strain BAC 86/19 in BALB/c Mice

by Emanuelle Baldo Gaspar, Lenita Ramires dos Santos, Andréa Alves do Egito, Maria Goretti dos Santos, Cynthia Mantovani, Juliana da Silva Gomes Rieger, Guilherme Augusto de Sousa Abrantes, Paula Adas Pereira Suniga, Júlia de Mendonça Favacho, Ingrid Batista Pinto, Alessandra Figueiredo de Castro Nassar, Fernando Leandro dos Santos and Flábio Ribeiro de Araújo

Microorganisms 2023, 11(10), 2597; https://doi.org/10.3390/microorganisms11102597 - 20 Oct 2023

Viewed by 1270

Abstract

Burkholderia mallei is an aerobic, Gram-negative, non-motile bacillus. As an obligate mammalian pathogen, it primarily affects solipeds. Although rarely transmitted to humans, the disease it causes, glanders, is classified as a zoonosis. The bacterium was officially eradicated in Brazil in 1969; however, it [...] Read more.

Burkholderia mallei is an aerobic, Gram-negative, non-motile bacillus. As an obligate mammalian pathogen, it primarily affects solipeds. Although rarely transmitted to humans, the disease it causes, glanders, is classified as a zoonosis. The bacterium was officially eradicated in Brazil in 1969; however, it reemerged after three decades. This study aims to assess the virulence of a specific B. mallei strain, isolated in Brazil, in BALB/c mice through intranasal infection. The strain, B. mallei BAC 86/19, was obtained from the tracheal secretion of a young mare displaying positive serology but no clinical signs of glanders. Post-mortem examinations revealed macroscopic lesions consistent with the disease, however. In mice, the LD₅₀ was determined to be approximately 1.59 × 10⁵ colony-forming units (CFU)/animal. Mice exposed to either 0.1 × LD₅₀ or 1 × LD₅₀ displayed transient weight loss, which resolved after three or five days, respectively. B. mallei persisted within the liver and lung for five days post-infection and in the spleen for seven days. These findings underscore the detectable virulence of the Brazilian B. mallei BAC 86/19 strain in mice, which are relatively resilient hosts. This research points to the importance of the continued investigation of the virulence mechanisms and potential countermeasures associated with B. mallei infections, including their Brazilian isolates. Full article

(This article belongs to the Special Issue Ecology, Evolution and Epidemiology of Zoonotic and Vector-Borne Infectious Diseases 2.0)

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17 pages, 2805 KiB

Open AccessArticle

Alteration in Community Dynamics of Chaetoceros curvisetus and Bacterioplankton Communities in Response to Surfactin Exposure

by Qianwen Shao, Zhujun Zhu and Chengxu Zhou

Microorganisms 2023, 11(10), 2596; https://doi.org/10.3390/microorganisms11102596 - 20 Oct 2023

Viewed by 1059

Abstract

The use of surfactin is a promising method to mitigate algal blooms. However, little is known about surfactin toxicity to algae and bacterioplankton. Here, we treated Chaetoceros curvisetus, the dominant species of algal blooms in the East China Sea, with 0, 0.5, [...] Read more.

The use of surfactin is a promising method to mitigate algal blooms. However, little is known about surfactin toxicity to algae and bacterioplankton. Here, we treated Chaetoceros curvisetus, the dominant species of algal blooms in the East China Sea, with 0, 0.5, 1, 2, 3, and 4 mg/L of surfactin for 96 h to investigate temporal variability. Our results showed that low concentrations of surfactin (<2 mg/L) changed the cell morphology of C. curvisetus, and higher concentrations (>3 mg/L) had lethal effects. Meanwhile, we examined the community dynamics of the free-living (FL, 0.22–5 μm) and particle-attached (PA, >5 μm) bacterioplankton of C. curvisetus in response to different surfactin concentrations and cultivation periods. Both PA and FL bacterioplankton were mainly composed of Proteobacteria, Actinobacteria, and Bacteroidetes, while FL bacterioplankton were more diverse than PA bacterioplankton. The variations of FL and PA bacterioplankton were significantly constrained by the surfactin concentration. Surfactin changed the lifestyle of some bacterioplankton from FL to PA, which mainly belonged to abundant bacterioplankton. Furthermore, we identified some surfactin-sensitive species/taxa. Our study will help enhance the ability to predict marine microbial responses under the effect of surfactin, providing a research foundation for this new harmful algal bloom mitigation method. Full article

(This article belongs to the Section Environmental Microbiology)

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19 pages, 1499 KiB

Open AccessReview

Biofilms as Battlefield Armor for Bacteria against Antibiotics: Challenges and Combating Strategies

by Sara Bano, Noor Hassan, Muhammad Rafiq, Farwa Hassan, Maliha Rehman, Naveed Iqbal, Hazrat Ali, Fariha Hasan and Ying-Qian Kang

Microorganisms 2023, 11(10), 2595; https://doi.org/10.3390/microorganisms11102595 - 20 Oct 2023

Cited by 7 | Viewed by 3174

Abstract

Bacterial biofilms are formed by communities, which are encased in a matrix of extracellular polymeric substances (EPS). Notably, bacteria in biofilms display a set of ‘emergent properties’ that vary considerably from free-living bacterial cells. Biofilms help bacteria to survive under multiple stressful conditions [...] Read more.

Bacterial biofilms are formed by communities, which are encased in a matrix of extracellular polymeric substances (EPS). Notably, bacteria in biofilms display a set of ‘emergent properties’ that vary considerably from free-living bacterial cells. Biofilms help bacteria to survive under multiple stressful conditions such as providing immunity against antibiotics. Apart from the provision of multi-layered defense for enabling poor antibiotic absorption and adaptive persistor cells, biofilms utilize their extracellular components, e.g., extracellular DNA (eDNA), chemical-like catalase, various genes and their regulators to combat antibiotics. The response of biofilms depends on the type of antibiotic that comes into contact with biofilms. For example, excessive production of eDNA exerts resistance against cell wall and DNA targeting antibiotics and the release of antagonist chemicals neutralizes cell membrane inhibitors, whereas the induction of protein and folic acid antibiotics inside cells is lowered by mutating genes and their regulators. Here, we review the current state of knowledge of biofilm-based resistance to various antibiotic classes in bacteria and genes responsible for biofilm development, and the key role of quorum sensing in developing biofilms and antibiotic resistance is also discussed. In this review, we also highlight new and modified techniques such as CRISPR/Cas, nanotechnology and bacteriophage therapy. These technologies might be useful to eliminate pathogens residing in biofilms by combating biofilm-induced antibiotic resistance and making this world free of antibiotic resistance. Full article

(This article belongs to the Special Issue Latest Review Papers on Antimicrobial Agents and Resistance 2023)

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15 pages, 1382 KiB

Open AccessArticle

Phenotypic and Genotypic Characterization of Cutibacterium acnes Isolated from Shoulder Surgery Reveals Insights into Genetic Diversity

by Mariana Neri Lucas Kurihara, Ingrid Nayara Marcelino Santos, Ana Karolina Antunes Eisen, Giovana Santos Caleiro, Jansen de Araújo, Romário Oliveira de Sales, Antônio Carlos Pignatari and Mauro José Salles

Microorganisms 2023, 11(10), 2594; https://doi.org/10.3390/microorganisms11102594 - 20 Oct 2023

Cited by 1 | Viewed by 2071

Abstract

Specific virulence factors that likely influence C. acnes invasion into deep tissues remain to be elucidated. Herein, we describe the frequency of C. acnes identification in deep tissue specimens of patients undergoing clean shoulder surgery and assess its phenotypic and genetic traits associated [...] Read more.

Specific virulence factors that likely influence C. acnes invasion into deep tissues remain to be elucidated. Herein, we describe the frequency of C. acnes identification in deep tissue specimens of patients undergoing clean shoulder surgery and assess its phenotypic and genetic traits associated with virulence and antibiotic resistance patterns, compared with isolates from the skin of healthy volunteers. Multiple deep tissue specimens from the bone fragments, tendons, and bursa of 84 otherwise healthy patients undergoing primary clean-open and arthroscopic shoulder surgeries were aseptically collected. The overall yield of tissue sample cultures was 21.5% (55/255), with 11.8% (30/255) identified as C. acnes in 27.3% (23/84) of patients. Antibiotic resistance rates were low, with most strains expressing susceptibility to first-line antibiotics, while a few were resistant to penicillin and rifampicin. Phylotypes IB (73.3%) and II (23.3%) were predominant in deep tissue samples. Genomic analysis demonstrated differences in the pangenome of the isolates from the same clade. Even though strains displayed a range of pathogenic markers, such as biofilm formation, patients did not evolve to infection during the 1-year follow-up. This suggests that the presence of polyclonal C. acnes in multiple deep tissue samples does not necessarily indicate infection. Full article

(This article belongs to the Special Issue Prosthetic and Bone Infections: A Multidisciplinary Approach)

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18 pages, 4065 KiB

Open AccessArticle

Loss of Biliverdin Reductase Increases Oxidative Stress in the Cyanobacterium Synechococcus sp. PCC 7002

by Wendy M. Schluchter, Courtney H. Babin, Xindi Liu, Amori Bieller, Gaozhong Shen, Richard M. Alvey and Donald A. Bryant

Microorganisms 2023, 11(10), 2593; https://doi.org/10.3390/microorganisms11102593 - 20 Oct 2023

Viewed by 1871

Abstract

Oxygenic photosynthesis requires metal-rich cofactors and electron-transfer components that can produce reactive oxygen species (ROS) that are highly toxic to cyanobacterial cells. Biliverdin reductase (BvdR) reduces biliverdin IXα to bilirubin, which is a potent scavenger of radicals and ROS. The enzyme is widespread [...] Read more.

Oxygenic photosynthesis requires metal-rich cofactors and electron-transfer components that can produce reactive oxygen species (ROS) that are highly toxic to cyanobacterial cells. Biliverdin reductase (BvdR) reduces biliverdin IXα to bilirubin, which is a potent scavenger of radicals and ROS. The enzyme is widespread in mammals but is also found in many cyanobacteria. We show that a previously described bvdR mutant of Synechocystis sp. PCC 6803 contained a secondary deletion mutation in the cpcB gene. The bvdR gene from Synechococcus sp. PCC 7002 was expressed in Escherichia coli, and recombinant BvdR was purified and shown to reduce biliverdin to bilirubin. The bvdR gene was successfully inactivated in Synechococcus sp. PCC 7002, a strain that is naturally much more tolerant of high light and ROS than Synechocystis sp. PCC 6803. The bvdR mutant strain, BR2, had lower total phycobiliprotein and chlorophyll levels than wild-type cells. As determined using whole-cell fluorescence at 77 K, the photosystem I levels were also lower than those in wild-type cells. The BR2 mutant had significantly higher ROS levels compared to wild-type cells after exposure to high light for 30 min. Together, these results suggest that bilirubin plays an important role as a scavenger for ROS in Synechococcus sp. PCC 7002. The oxidation of bilirubin by ROS could convert bilirubin to biliverdin IXα, and thus BvdR might be important for regenerating bilirubin. These results further suggest that BvdR is a key component of a scavenging cycle by which cyanobacteria protect themselves from the toxic ROS byproducts generated during oxygenic photosynthesis. Full article

(This article belongs to the Special Issue Phototrophic Bacteria 2.0)

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14 pages, 1844 KiB

Open AccessArticle

Bivariate One Strain Many Compounds Designs Expand the Secondary Metabolite Production Space in Corallococcus coralloides

by Anton Lindig, Jenny Schwarz, Georg Hubmann, Katrin Rosenthal and Stephan Lütz

Microorganisms 2023, 11(10), 2592; https://doi.org/10.3390/microorganisms11102592 - 20 Oct 2023

Cited by 1 | Viewed by 1511

Abstract

The scarcely investigated myxobacterium Corallococcus coralloides holds a large genome containing many uncharacterized biosynthetic gene clusters (BGCs) that potentially encode the synthesis of entirely new natural products. Despite its promising genomic potential, suitable cultivation conditions have not yet been found to activate the [...] Read more.

The scarcely investigated myxobacterium Corallococcus coralloides holds a large genome containing many uncharacterized biosynthetic gene clusters (BGCs) that potentially encode the synthesis of entirely new natural products. Despite its promising genomic potential, suitable cultivation conditions have not yet been found to activate the synthesis of new secondary metabolites (SMs). Finding the right cultivation conditions to activate BGCs in the genome remains a major bottleneck, and its full biosynthetic potential has so far not been determined. We therefore applied a bivariate “one strain many compounds” (OSMAC) approach, using a combination of two elicitor changes at once, for the activation of BGCs and concomitant SM production by C. coralloides. The screening was carried out in Duetz-System 24-well plates, applying univariate and bivariate OSMAC conditions. We combined biotic additives and organic solvents with a complex growth medium for univariate conditions and with minimal medium for bivariate conditions. The success in the activation of BGCs was evaluated by determining the number of new mass features detected in the respective extracts. We found synergistic effects in the bivariate OSMAC designs, evidenced by the detection of completely new mass features in the bivariate OSMAC experiments, which were not detected in the univariate OSMAC designs with only one elicitor. Overall, the bivariate OSMAC screening led to 55 new mass features, which were not detected in the univariate OSMAC design. Molecular networks revealed that these new mass features embody potential novel natural compounds and chemical derivatives like the N-acyl fatty amine N-pentyloctadecanamide and possibly sulfur-containing natural products. Hence, the presence of multiple elicitors in the bivariate OSMAC designs successfully activated the biosynthetic potential in C. coralloides. We propose bivariate OSMAC designs with a complex combination of elicitors as a straightforward strategy to robustly expand the SM space of microorganisms with large genomes. Full article

(This article belongs to the Special Issue Advances in Microbial Cell Factories, 2nd Edition)

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2 pages, 188 KiB

Open AccessEditorial

Editorial for Special Issue “Interactions between Plant Beneficial Pseudomonas spp. and Their Host”

by Martin Filion

Microorganisms 2023, 11(10), 2591; https://doi.org/10.3390/microorganisms11102591 - 20 Oct 2023

Viewed by 966

Abstract

Plant-beneficial Pseudomonas spp [...] Full article

(This article belongs to the Special Issue Interactions between Plant Beneficial Pseudomonas spp. and Their Host)

16 pages, 2485 KiB

Open AccessArticle

Genome-Wide Analysis of the Cytochrome P450 Monooxygenases in the Lichenized Fungi of the Class Lecanoromycetes

by Gugulethu Mlambo, Tiara Padayachee, David R. Nelson and Khajamohiddin Syed

Microorganisms 2023, 11(10), 2590; https://doi.org/10.3390/microorganisms11102590 - 19 Oct 2023

Cited by 1 | Viewed by 1519

Abstract

Lichens are unique organisms that exhibit a permanent symbiosis between fungi and algae or fungi and photosynthetic bacteria. Lichens have been found to produce biotechnologically valuable secondary metabolites. A handful of studies showed that tailoring enzymes such as cytochrome P450 monooxygenases (CYPs/P450s) play [...] Read more.

Lichens are unique organisms that exhibit a permanent symbiosis between fungi and algae or fungi and photosynthetic bacteria. Lichens have been found to produce biotechnologically valuable secondary metabolites. A handful of studies showed that tailoring enzymes such as cytochrome P450 monooxygenases (CYPs/P450s) play a key role in synthesizing these metabolites. Despite the critical role of P450s in the biosynthesis of secondary metabolites, the systematic analysis of P450s in lichens has yet to be reported. This study is aimed to address this research gap. A genome-wide analysis of P450s in five lichens from the fungal class Lecanoromycetes revealed the presence of 434 P450s that are grouped into 178 P450 families and 345 P450 subfamilies. The study indicated that none of the P450 families bloomed, and 15 P450 families were conserved in all five Lecanoromycetes. Lecanoromycetes have more P450s and higher P450 family diversity compared to Pezizomycetes. A total of 73 P450s were found to be part of secondary metabolite gene clusters, indicating their potential involvement in the biosynthesis of secondary metabolites. Annotation of P450s revealed that CYP682BG1 and CYP682BG2 from Cladonia grayi and Pseudevernia furfuracea (physodic acid chemotype) are involved in the synthesis of grayanic acid and physodic acid, CYP65FQ2 from Stereocaulon alpinum is involved in the synthesis of atranorin, and CYP6309A2 from Cladonia uncialis is involved in the synthesis of usnic acid. This study serves as a reference for future annotation of P450s in lichens. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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11 pages, 2130 KiB

Open AccessArticle

Examining the Shift in the Decomposition Channel Structure of the Soil Decomposer Food Web: A Methods Comparison

by Wen Xing, Ning Hu, Zhongfang Li, Meng Yuan, Meiling Luo, Shuo Han, Evgenia Blagodatskaya, Shunbao Lu and Yilai Lou

Microorganisms 2023, 11(10), 2589; https://doi.org/10.3390/microorganisms11102589 - 19 Oct 2023

Cited by 1 | Viewed by 1206

Abstract

Selecting the appropriate indicators and measuring time point numbers is important for accurately examining the shift in soil gross decomposition channel structure. Through a selected case study on a natural forest vs. rainfed arable system over a two-month-long experiment, the utility of three [...] Read more.

Selecting the appropriate indicators and measuring time point numbers is important for accurately examining the shift in soil gross decomposition channel structure. Through a selected case study on a natural forest vs. rainfed arable system over a two-month-long experiment, the utility of three commonly employed indicators (fungi to bacteria ratio (F:B), fungivore to bacterivore ratio (FF:BF), and glucosamine to muramic acid ratio (GlcN:MurN)) were compared to reflect the shift in soil gross decomposition channel structure. The requirement of measuring the time point numbers for the three indicators was also assessed, and we suggest a potential methodology. Our results revealed that the GlcN:MurN ratio was more reliable for assessing the shifts in gross decomposition channel structure for long-term land use changes, while it was less sensitive to short-term drought compared with the other two indicators. The F:B ratio was more applicable than the FF:BF ratio for reflecting both long- and short-term changes. Furthermore, the reliability of the GlcN:MurN ratio was the least dependent on measuring time point numbers. We suggest the use of multiple indicators and the adoption of multiple measuring time points for the overall methodology. Full article

(This article belongs to the Special Issue BRICS Soil Microbiome)

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7 pages, 961 KiB

Open AccessCommunication

The Molecular Characterization of bla_NDM-1-Positive Acinetobacter baumannii Isolated in Central Greece

by Katerina Tsilipounidaki, Christos-George Gkountinoudis, Zoi Florou, George C. Fthenakis, Vivi Miriagou and Efthymia Petinaki

Microorganisms 2023, 11(10), 2588; https://doi.org/10.3390/microorganisms11102588 - 19 Oct 2023

Cited by 2 | Viewed by 1323

Abstract

The objective of the present study is to report the detection and the molecular characterization of nine bla_NDM-1-positive Acinetobacter baumannii isolates, which were isolated from patients in a tertiary care hospital in Central Greece from December 2022 to August 2023. The [...] Read more.

The objective of the present study is to report the detection and the molecular characterization of nine bla_NDM-1-positive Acinetobacter baumannii isolates, which were isolated from patients in a tertiary care hospital in Central Greece from December 2022 to August 2023. The isolates were characterized by whole genome sequencing to obtain Pasteur multilocus sequencing typing (MLST) and to identify the bla_NDM-1-environment, resistome, and virulence genes content. In silico MLST analysis showed that the isolates belonged to four different clones (STs 160, 2, 85, and 2493). All strains, apart from the bla_NDM-1-gene, possessed at least eight different genes, encoding resistance to various antimicrobial agents. Whole genome sequencing revealed two different structures of the bla_NDM-1 environment. The first, detected in ST160 strain, was identical with the Tn125, whereas the second, found in STs 2, 85, and 2493 was associated with Tn7382. To our knowledge, after a sole strain reported in 2016 and imported by a patient hospitalized in a Libyan hospital, this is the first report of the emergence of polyclonal bla_NDM-1-positive Acinetobacter baumannii in Greece. Our findings re-emphasize the need to apply diligent surveillance protocols in order to limit the horizontal transfer of the bla_NDM-1 gene to other A. baumannii clones or to other recipient strains. Full article

(This article belongs to the Special Issue ß-Lactamases 2.0)

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31 pages, 7818 KiB

Open AccessArticle

Haloalkalitolerant Fungi from Sediments of the Big Tambukan Saline Lake (Northern Caucasus): Diversity and Antimicrobial Potential

by Marina L. Georgieva, Elena N. Bilanenko, Valeria B. Ponizovskaya, Lyudmila Y. Kokaeva, Anton A. Georgiev, Tatiana A. Efimenko, Natalia N. Markelova, Anastasia E. Kuvarina and Vera S. Sadykova

Microorganisms 2023, 11(10), 2587; https://doi.org/10.3390/microorganisms11102587 - 19 Oct 2023

Cited by 1 | Viewed by 1574

Abstract

We have performed a characterization of cultivated haloalkalitolerant fungi from the sediments of Big Tambukan Lake in order to assess their biodiversity and antimicrobial activity. This saline, slightly alkaline lake is known as a source of therapeutic sulfide mud used in sanatoria of [...] Read more.

We have performed a characterization of cultivated haloalkalitolerant fungi from the sediments of Big Tambukan Lake in order to assess their biodiversity and antimicrobial activity. This saline, slightly alkaline lake is known as a source of therapeutic sulfide mud used in sanatoria of the Caucasian Mineral Waters, Russia. Though data on bacteria and algae observed in this lake are available in the literature, data on fungi adapted to the conditions of the lake are lacking. The diversity of haloalkalitolerant fungi was low and represented by ascomycetes of the genera Acremonium, Alternaria, Aspergillus, Chordomyces, Emericellopsis, Fusarium, Gibellulopsis, Myriodontium, Penicillium, and Pseudeurotium. Most of the fungi were characterized by moderate alkaline resistance, and they tolerated NaCl concentrations up to 10% w/v. The analysis of the antimicrobial activity of fungi showed that 87.5% of all strains were active against Bacillus subtilis, and 39.6% were also determined to be effective against Escherichia coli. The majority of the strains were also active against Aspergillus niger and Candida albicans, about 66.7% and 62.5%, respectively. These studies indicate, for the first time, the presence of polyextremotolerant fungi in the sediments of Big Tambukan Lake, which probably reflects their involvement in the formation of therapeutic muds. Full article

(This article belongs to the Special Issue New Insights into Diversity and Biotechnological Applications of Extremophiles)

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13 pages, 2236 KiB

Open AccessArticle

Exploring the Association between Gut Microbiota and Inflammatory Skin Diseases: A Two-Sample Mendelian Randomization Analysis

by Junhao Long, Jinglan Gu, Juexi Yang, Pu Chen, Yan Dai, Yun Lin, Ming Wu and Yan Wu

Microorganisms 2023, 11(10), 2586; https://doi.org/10.3390/microorganisms11102586 - 19 Oct 2023

Cited by 2 | Viewed by 3148

Abstract

Emerging research underscores the substantial link between gut flora and various inflammatory skin diseases. We hypothesize that there exists a complex gut–skin axis, possibly affecting the progression of conditions such as eczema, acne, psoriasis, and rosacea. However, the precise nature of the causal [...] Read more.

Emerging research underscores the substantial link between gut flora and various inflammatory skin diseases. We hypothesize that there exists a complex gut–skin axis, possibly affecting the progression of conditions such as eczema, acne, psoriasis, and rosacea. However, the precise nature of the causal connection between gut flora and skin diseases remains unestablished. In this study, we started by compiling summary data from genome-wide association studies (GWAS) featuring 211 unique gut microbiota and four types of skin conditions. We scrutinized these data across different taxonomic strata. Subsequently, we leveraged Mendelian randomization (MR) to ascertain if there is a causal link between gut microbiota and these skin conditions. We also performed a bidirectional MR analysis to identify the causality’s direction. By utilizing Mendelian randomization, we identified 26 causal connections between the gut microbiome and four recognized inflammatory skin conditions, including 9 positive and 17 negative causal directions. Additional sensitivity analyses of these results revealed no evidence of pleiotropy or heterogeneity. Our MR analysis suggests a causal connection between gut microbiota and skin diseases, potentially providing groundbreaking perspectives for future mechanistic and clinical studies on microbiota-affected skin conditions. Full article

(This article belongs to the Section Gut Microbiota)

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21 pages, 3177 KiB

Open AccessArticle

Streptococcal Arginine Deiminase Inhibits T Lymphocyte Differentiation In Vitro

by Eleonora A. Starikova, Jennet T. Mammedova, Arina Ozhiganova, Tatiana A. Leveshko, Aleksandra M. Lebedeva, Alexey V. Sokolov, Dmitry V. Isakov, Alena B. Karaseva, Larissa A. Burova and Igor V. Kudryavtsev

Microorganisms 2023, 11(10), 2585; https://doi.org/10.3390/microorganisms11102585 - 19 Oct 2023

Cited by 1 | Viewed by 1820

Abstract

Pathogenic microbes use arginine-metabolizing enzymes as an immune evasion strategy. In this study, the impact of streptococcal arginine deiminase (ADI) on the human peripheral blood T lymphocytes function in vitro was studied. The comparison of the effects of parental strain (Streptococcus pyogenes [...] Read more.

Pathogenic microbes use arginine-metabolizing enzymes as an immune evasion strategy. In this study, the impact of streptococcal arginine deiminase (ADI) on the human peripheral blood T lymphocytes function in vitro was studied. The comparison of the effects of parental strain (Streptococcus pyogenes M49-16) with wild type of ArcA gene and its isogenic mutant with inactivated ArcA gene (Streptococcus pyogenes M49-16delArcA) was carried out. It was found that ADI in parental strain SDSC composition resulted in a fivefold decrease in the arginine concentration in human peripheral blood mononuclear cell (PBMC) supernatants. Only parental strain SDSCs suppressed anti-CD2/CD3/CD28-bead-stimulated mitochondrial dehydrogenase activity and caused a twofold decrease in IL-2 production in PBMC. Flow cytometry analysis revealed that ADI decreased the percentage of CM (central memory) and increased the proportion of TEMRA (terminally differentiated effector memory) of CD4+ and CD8+ T cells subsets. Enzyme activity inhibited the proliferation of all CD8+ T cell subsets as well as CM, EM (effector memory), and TEMRA CD4+ T cells. One of the prominent ADI effects was the inhibition of autophagy processes in CD8+ CM and EM as well as CD4+ CM, EM, and TEMRA T cell subsets. The data obtained confirm arginine’s crucial role in controlling immune reactions and suggest that streptococcal ADI may downregulate adaptive immunity and immunological memory. Full article

(This article belongs to the Special Issue Group A Streptococcus: Infection, Immunity and Vaccine Development)

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