Microorganisms

14 pages, 1107 KiB

Open AccessArticle

Next-Generation Sequencing-Based Study of Helicobacter pylori Isolates from Myanmar and Their Susceptibility to Antibiotics

by Phawinee Subsomwong, Dalla Doohan, Kartika Afrida Fauzia, Junko Akada, Takashi Matsumoto, Than Than Yee, Kyaw Htet, Langgeng Agung Waskito, Vo Phuoc Tuan, Tomohisa Uchida, Takeshi Matsuhisa and Yoshio Yamaoka

Microorganisms 2022, 10(1), 196; https://doi.org/10.3390/microorganisms10010196 - 17 Jan 2022

Cited by 12 | Viewed by 4577

Abstract

Evaluation of Helicobacter pylori resistance to antibiotics is crucial for treatment strategy in Myanmar. Moreover, the genetic mechanisms involved remain unknown. We aimed to investigate the prevalence of H. pylori infection, antibiotic resistance, and genetic mechanisms in Myanmar. One hundred fifty patients from [...] Read more.

Evaluation of Helicobacter pylori resistance to antibiotics is crucial for treatment strategy in Myanmar. Moreover, the genetic mechanisms involved remain unknown. We aimed to investigate the prevalence of H. pylori infection, antibiotic resistance, and genetic mechanisms in Myanmar. One hundred fifty patients from two cities, Mawlamyine (n = 99) and Yangon (n = 51), were recruited. The prevalence of H. pylori infection was 43.3% (65/150). The successfully cultured H. pylori isolates (n = 65) were tested for antibiotic susceptibility to metronidazole, levofloxacin, clarithromycin, amoxicillin, and tetracycline by Etest, and the resistance rates were 80%, 33.8%, 7.7%, 4.6%, and 0%, respectively. In the multidrug resistance pattern, the metronidazole–levofloxacin resistance was highest for double-drug resistance (16/19; 84.2%), and all triple-drug resistance (3/3) was clarithromycin–metronidazole–levofloxacin resistance. Twenty-three strains were subjected to next-generation sequencing to study their genetic mechanisms. Interestingly, none of the strains resistant to clarithromycin had well-known mutations in 23S rRNA (e.g., A2142G, A2142C, and A2143G). New type mutation genotypes such as pbp1-A (e.g., V45I, S/R414R), 23S rRNA (e.g., T248C), gyrA (e.g., D210N, K230Q), gyrB (e.g., A584V, N679H), rdxA (e.g., V175I, S91P), and frxA (e.g., L33M) were also detected. In conclusion, the prevalence of H. pylori infection and its antibiotic resistance to metronidazole was high in Myanmar. The H. pylori eradication regimen with classical triple therapy, including amoxicillin and clarithromycin, can be used as the first-line therapy in Myanmar. In addition, next-generation sequencing is a powerful high-throughput method for identifying mutations within antibiotic resistance genes and monitoring the spread of H. pylori antibiotic-resistant strains. Full article

(This article belongs to the Special Issue Antibiotic Resistance of Helicobacter pylori)

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25 pages, 6195 KiB

Open AccessArticle

Selective Isolation of Eggerthella lenta from Human Faeces and Characterisation of the Species Prophage Diversity

by Colin Buttimer, Francesca Bottacini, Andrey N. Shkoporov, Lorraine A. Draper, Paul Ross and Colin Hill

Microorganisms 2022, 10(1), 195; https://doi.org/10.3390/microorganisms10010195 - 17 Jan 2022

Cited by 7 | Viewed by 5105

Abstract

Eggerthella lenta is an anaerobic, high GC, Gram-positive bacillus commonly found in the human digestive tract that belongs to the class Coriobacteriia of the phylum Actinobacteria. This species has been of increasing interest as an important player in the metabolism of xenobiotics and [...] Read more.

Eggerthella lenta is an anaerobic, high GC, Gram-positive bacillus commonly found in the human digestive tract that belongs to the class Coriobacteriia of the phylum Actinobacteria. This species has been of increasing interest as an important player in the metabolism of xenobiotics and dietary compounds. However, little is known regarding its susceptibility to bacteriophage predation and how this may influence its fitness. Here, we report the isolation of seven novel E. lenta strains using cefotaxime and ceftriaxone as selective agents. We conducted comparative and pangenome analyses of these strains and those publicly available to investigate the diversity of prophages associated with this species. Prophage gene products represent a minimum of 5.8% of the E. lenta pangenome, comprising at least ten distantly related prophage clades that display limited homology to currently known bacteriophages. All clades possess genes implicated in virion structure, lysis, lysogeny and, to a limited extent, DNA replication. Some prophages utilise tyrosine recombinases and diversity generating retroelements to generate phase variation among targeted genes. The prophages have differing levels of sensitivity to the CRISPR/cas systems of their hosts, with spacers from 44 E. lenta isolates found to target only five out of the ten identified prophage clades. Furthermore, using a PCR-based approach targeting the prophage attP site, we were able to determine that several of these elements can excise from the host chromosome, thus supporting the notion that these are active prophages. The findings of this study provide further insights into the diversity of prophages infecting species of the phylum Actinobacteria. Full article

(This article belongs to the Special Issue Comparative Genomics of the Human Gut Microbiome)

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18 pages, 3598 KiB

Open AccessArticle

Inoculation with Plant Growth-Promoting Bacteria to Reduce Phosphate Fertilization Requirement and Enhance Technological Quality and Yield of Sugarcane

by Poliana Aparecida Leonel Rosa, Fernando Shintate Galindo, Carlos Eduardo da Silva Oliveira, Arshad Jalal, Emariane Satin Mortinho, Guilherme Carlos Fernandes, Evelyn Maria Rocha Marega, Salatiér Buzetti and Marcelo Carvalho Minhoto Teixeira Filho

Microorganisms 2022, 10(1), 192; https://doi.org/10.3390/microorganisms10010192 - 17 Jan 2022

Cited by 33 | Viewed by 4445

Abstract

Phosphorus (P) is a critical nutrient for high sugarcane yields throughout its cultivation cycles, however, a higher amount of P becomes rapidly unavailable to plants due to its adsorption to soil colloids. Some plant growth-promoting bacteria (PGPBs) may be able to enhance P [...] Read more.

Phosphorus (P) is a critical nutrient for high sugarcane yields throughout its cultivation cycles, however, a higher amount of P becomes rapidly unavailable to plants due to its adsorption to soil colloids. Some plant growth-promoting bacteria (PGPBs) may be able to enhance P availability to plants and produce phytohormones that contribute to crop development, quality, and yield. Thus, this study aimed to evaluate leaf concentrations of nitrogen (N) and P, yield, and technological quality of sugarcane as a function of different levels of phosphate fertilization associated with inoculation of PGPBs. The experiment was carried out at Ilha Solteira, São Paulo—Brazil. The experimental design was randomized blocks with three replications, consisting of five phosphorus rates (0, 25, 50, 75, and 100% of the recommended P₂O₅ rate) and eight inoculations, involving three species of PGPBs (Azospirillum brasilense, Bacillus subtilis, and Pseudomonas fluorescens) which were applied combined or in a single application into the planting furrow of RB92579 sugarcane variety. The inoculation of B. subtilis and P. fluorescens provided a higher concentration of leaf P in sugarcane. The P₂O₅ rates combined with inoculation of bacteria alter technological variables and stalk yield of sugarcane. The excess and lack of phosphate fertilizer is harmful to sugarcane cultivation, regardless of the use of growth-promoting bacteria. We recommend the inoculation with A. brasilense + B. subtilis associated with 45 kg ha⁻¹ of P₂O₅ aiming at greater stalk yield. This treatment also increases sugar yield, resulting in a savings of 75% of the recommended P₂O₅ rate, thus being a more efficient and sustainable alternative for reducing sugarcane crop production costs. Full article

(This article belongs to the Special Issue Probiotic Microorganism in Plants, Rhizosphere and Soil 2021)

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17 pages, 2804 KiB

Open AccessArticle

Regulation of Tomato Specialised Metabolism after Establishment of Symbiosis with the Endophytic Fungus Serendipita indica

by Fani Ntana, Sean R. Johnson, Björn Hamberger, Birgit Jensen, Hans J. L. Jørgensen and David B. Collinge

Microorganisms 2022, 10(1), 194; https://doi.org/10.3390/microorganisms10010194 - 16 Jan 2022

Cited by 9 | Viewed by 4064

Abstract

Specialised metabolites produced during plant-fungal associations often define how symbiosis between the plant and the fungus proceeds. They also play a role in the establishment of additional interactions between the symbionts and other organisms present in the niche. However, specialised metabolism and its [...] Read more.

Specialised metabolites produced during plant-fungal associations often define how symbiosis between the plant and the fungus proceeds. They also play a role in the establishment of additional interactions between the symbionts and other organisms present in the niche. However, specialised metabolism and its products are sometimes overlooked when studying plant-microbe interactions. This limits our understanding of the specific symbiotic associations and potentially future perspectives of their application in agriculture. In this study, we used the interaction between the root endophyte Serendipita indica and tomato (Solanum lycopersicum) plants to explore how specialised metabolism of the host plant is regulated upon a mutualistic symbiotic association. To do so, tomato seedlings were inoculated with S. indica chlamydospores and subjected to RNAseq analysis. Gene expression of the main tomato specialised metabolism pathways was compared between roots and leaves of endophyte-colonised plants and tissues of endophyte-free plants. S. indica colonisation resulted in a strong transcriptional response in the leaves of colonised plants. Furthermore, the presence of the fungus in plant roots appears to induce expression of genes involved in the biosynthesis of lignin-derived compounds, polyacetylenes, and specific terpenes in both roots and leaves, whereas pathways producing glycoalkaloids and flavonoids were expressed in lower or basal levels. Full article

(This article belongs to the Special Issue Microbial Endophytes: Functional Biology and Applications)

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12 pages, 3232 KiB

Open AccessArticle

Biochemical Properties of Two Plasmodium malariae Cysteine Proteases, Malapain-2 and Malapain-4

by Hương Giang Lê, Jung-Mi Kang, Tuấn Cường Võ, Won Gi Yoo, Kon Ho Lee and Byoung-Kuk Na

Microorganisms 2022, 10(1), 193; https://doi.org/10.3390/microorganisms10010193 - 16 Jan 2022

Cited by 1 | Viewed by 1994

Abstract

Cysteine proteases belonging to the falcipain (FP) family play a pivotal role in the biology of malaria parasites and have been extensively investigated as potential antimalarial drug targets. Three paralogous FP-family cysteine proteases of Plasmodium malariae, termed malapains 2–4 (MP2–4), were identified [...] Read more.

Cysteine proteases belonging to the falcipain (FP) family play a pivotal role in the biology of malaria parasites and have been extensively investigated as potential antimalarial drug targets. Three paralogous FP-family cysteine proteases of Plasmodium malariae, termed malapains 2–4 (MP2–4), were identified in PlasmoDB. The three MPs share similar structural properties with the FP-2/FP-3 subfamily enzymes and exhibit a close phylogenetic lineage with vivapains (VXs) and knowpains (KPs), FP orthologues of P. vivax and P. knowlesi. Recombinant MP-2 and MP-4 were produced in a bacterial expression system, and their biochemical properties were characterized. Both recombinant MP-2 and MP-4 showed enzyme activity across a broad range of pH values with an optimum activity at pH 5.0 and relative stability at neutral pHs. Similar to the FP-2/FP-3 subfamily enzymes in other Plasmodium species, recombinant MP-2 and MP-4 effectively hydrolyzed hemoglobin at acidic pHs. They also degraded erythrocyte cytoskeletal proteins, such as spectrin and band 3, at a neutral pH. These results imply that MP-2 and MP-4 are redundant hemoglobinases of P. malariae and may also participate in merozoite egression by degrading erythrocyte cytoskeletal proteins. However, compared with other FP-2/FP-3 enzymes, MP-2 showed a strong preference for arginine at the P2 position. Meanwhile, MP-4 showed a primary preference for leucine at the P2 position but a partial preference for phenylalanine. These different substrate preferences of MPs underscore careful consideration in the design of optimized inhibitors targeting the FP-family cysteine proteases of human malaria parasites. Full article

(This article belongs to the Section Parasitology)

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23 pages, 2970 KiB

Open AccessArticle

Circulating Phylotypes of White Spot Syndrome Virus in Bangladesh and Their Virulence

by Mehedi Mahmudul Hasan, M. Nazmul Hoque, Firoz Ahmed, Md. Inja-Mamun Haque, Munawar Sultana and M. Anwar Hossain

Microorganisms 2022, 10(1), 191; https://doi.org/10.3390/microorganisms10010191 - 16 Jan 2022

Cited by 7 | Viewed by 3392

Abstract

White Spot Syndrome Virus (WSSV) has emerged as one of the most prevalent and lethal viruses globally and infects both shrimps and crabs in the aquatic environment. This study aimed to investigate the occurrence of WSSV in different ghers of Bangladesh and the [...] Read more.

White Spot Syndrome Virus (WSSV) has emerged as one of the most prevalent and lethal viruses globally and infects both shrimps and crabs in the aquatic environment. This study aimed to investigate the occurrence of WSSV in different ghers of Bangladesh and the virulence of the circulating phylotypes. We collected 360 shrimp (Penaeus monodon) and 120 crab (Scylla sp.) samples from the south-east (Cox’s Bazar) and south-west (Satkhira) coastal regions of Bangladesh. The VP28 gene-specific PCR assays and sequencing revealed statistically significant (p < 0.05, Kruskal–Wallis test) differences in the prevalence of WSSV in shrimps and crabs between the study areas (Cox’s Bazar and Satkhira) and over the study periods (2017–2019). The mean Log load of WSSV varied from 8.40 (Cox’s Bazar) to 10.48 (Satkhira) per gram of tissue. The mean values for salinity, dissolved oxygen, temperature and pH were 14.71 ± 0.76 ppt, 3.7 ± 0.1 ppm, 34.11 ± 0.38 °C and 8.23 ± 0.38, respectively, in the WSSV-positive ghers. The VP28 gene-based phylogenetic analysis showed an amino-acid substitution (E→G) at the 167th position in the isolates from Cox’s Bazar (referred to as phylotype BD2) compared to the globally circulating one (BD1). Shrimp PL artificially challenged with BD1 and BD2 phylotypes with filtrates of tissue containing 0.423 × 10⁹ copies of WSSV per mL resulted in a median LT50 value of 73 h and 75 h, respectively. The in vivo trial showed higher mean Log WSSV copies (6.47 ± 2.07 per mg tissue) in BD1-challenged shrimp PL compared to BD2 (4.75 ± 0.35 per mg tissue). Crabs infected with BD1 and BD2 showed 100% mortality within 48 h and 62 h of challenge, respectively, with mean Log WSSV copies of 12.06 ± 0.48 and 9.95 ± 0.37 per gram tissue, respectively. Moreover, shrimp antimicrobial peptides (AMPs), penaeidin and lysozyme expression were lower in the BD1-challenged group compared to BD2 challenged shrimps. These results collectively demonstrated that relative virulence properties of WSSV based on mortality rate, viral load and expression of host immune genes in artificially infected shrimp PL could be affected by single aa substitution in VP28. Full article

(This article belongs to the Section Virology)

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16 pages, 2639 KiB

Open AccessArticle

Effects of Ionizing Radiation and Long-Term Storage on Hydrated vs. Dried Cell Samples of Extremophilic Microorganisms

by Ida Romano, Carlo Camerlingo, Lisa Vaccari, Giovanni Birarda, Annarita Poli, Akira Fujimori, Maria Lepore, Ralf Moeller and Paola Di Donato

Microorganisms 2022, 10(1), 190; https://doi.org/10.3390/microorganisms10010190 - 16 Jan 2022

Cited by 6 | Viewed by 2589

Abstract

A main factor hampering life in space is represented by high atomic number nuclei and energy (HZE) ions that constitute about 1% of the galactic cosmic rays. In the frame of the “STARLIFE” project, we accessed the Heavy Ion Medical Accelerator (HIMAC) facility [...] Read more.

A main factor hampering life in space is represented by high atomic number nuclei and energy (HZE) ions that constitute about 1% of the galactic cosmic rays. In the frame of the “STARLIFE” project, we accessed the Heavy Ion Medical Accelerator (HIMAC) facility of the National Institute of Radiological Sciences (NIRS) in Chiba, Japan. By means of this facility, the extremophilic species Haloterrigena hispanica and Parageobacillus thermantarcticus were irradiated with high LET ions (i.e., Fe, Ar, and He ions) at doses corresponding to long permanence in the space environment. The survivability of HZE-treated cells depended upon either the storage time and the hydration state during irradiation; indeed, dry samples were shown to be more resistant than hydrated ones. With particular regard to spores of the species P. thermantarcticus, they were the most resistant to irradiation in a water medium: an analysis of the changes in their biochemical fingerprinting during irradiation showed that, below the survivability threshold, the spores undergo to a germination-like process, while for higher doses, inactivation takes place as a consequence of the concomitant release of the core’s content and a loss of integrity of the main cellular components. Overall, the results reported here suggest that the selected extremophilic microorganisms could serve as biological model for space simulation and/or real space condition exposure, since they showed good resistance to ionizing radiation exposure and were able to resume cellular growth after long-term storage. Full article

(This article belongs to the Special Issue Astrobiology and Microorganisms: Life to the Extreme, on Earth and Beyond)

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29 pages, 4855 KiB

Open AccessArticle

Comparative Genomics of Typical and Atypical Aeromonas salmonicida Complete Genomes Revealed New Insights into Pathogenesis Evolution

by Ignacio Vasquez, Ahmed Hossain, Hajarooba Gnanagobal, Katherinne Valderrama, Briony Campbell, Michael Ness, Steve J. Charette, Anthony K. Gamperl, Rocco Cipriano, Cristopher Segovia and Javier Santander

Microorganisms 2022, 10(1), 189; https://doi.org/10.3390/microorganisms10010189 - 15 Jan 2022

Cited by 20 | Viewed by 4193

Abstract

Aeromonas salmonicida is a global distributed Gram-negative teleost pathogen, affecting mainly salmonids in fresh and marine environments. A. salmonicida strains are classified as typical or atypical depending on their origin of isolation and phenotype. Five subspecies have been described, where A. salmonicida [...] Read more.

Aeromonas salmonicida is a global distributed Gram-negative teleost pathogen, affecting mainly salmonids in fresh and marine environments. A. salmonicida strains are classified as typical or atypical depending on their origin of isolation and phenotype. Five subspecies have been described, where A. salmonicida subsp. salmonicida is the only typical subspecies, and the subsp. achromogenes, masoucida, smithia, and pectinolytica are considered atypical. Genomic differences between A. salmonicida subsp. salmonicida isolates and their relationship with the current classification have not been explored. Here, we sequenced and compared the complete closed genomes of four virulent strains to elucidate their molecular diversity and pathogenic evolution using the more accurate genomic information so far. Phenotypes, biochemical, and enzymatic profiles were determined. PacBio and MiSeq sequencing platforms were utilized for genome sequencing. Comparative genomics showed that atypical strains belong to the subsp. salmonicida, with 99.55% ± 0.25% identity with each other, and are closely related to typical strains. The typical strain A. salmonicida J223 is closely related to typical strains, with 99.17% identity with the A. salmonicida A449. Genomic differences between atypical and typical strains are strictly related to insertion sequences (ISs) activity. The absence and presence of genes encoding for virulence factors, transcriptional regulators, and non-coding RNAs are the most significant differences between typical and atypical strains that affect their phenotypes. Plasmidome plays an important role in A. salmonicida virulence and genome plasticity. Here, we determined that typical strains harbor a larger number of plasmids and virulence-related genes that contribute to its acute virulence. In contrast, atypical strains harbor a single, large plasmid and a smaller number of virulence genes, reflected by their less acute virulence and chronic infection. The relationship between phenotype and A. salmonicida subspecies’ taxonomy is not evident. Comparative genomic analysis based on completed genomes revealed that the subspecies classification is more of a reflection of the ecological niche occupied by bacteria than their divergences at the genomic level except for their accessory genome. Full article

(This article belongs to the Special Issue Aeromonas salmonicida: Genomics, Taxonomy, Diversity, Pathogenesis, Treatments and Beyond)

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14 pages, 2994 KiB

Open AccessArticle

Antiviral Property of the Fungal Metabolite 3-O-Methylfunicone in Bovine Herpesvirus 1 Infection

by Filomena Fiorito, Claudia Cerracchio, Maria Michela Salvatore, Francesco Serra, Alessia Pucciarelli, Maria Grazia Amoroso, Rosario Nicoletti and Anna Andolfi

Microorganisms 2022, 10(1), 188; https://doi.org/10.3390/microorganisms10010188 - 15 Jan 2022

Cited by 10 | Viewed by 2187

Abstract

Bovine herpesvirus type-1 (BoHV-1) is a widespread pathogen that provokes infectious rhinotracheitis and polymicrobial infections in cattle, resulting in serious economic losses to the farm animal industry and trade restrictions. To date, non-toxic active drugs against BoHV-1 are not available. The exploitation of [...] Read more.

Bovine herpesvirus type-1 (BoHV-1) is a widespread pathogen that provokes infectious rhinotracheitis and polymicrobial infections in cattle, resulting in serious economic losses to the farm animal industry and trade restrictions. To date, non-toxic active drugs against BoHV-1 are not available. The exploitation of bioactive properties of microbial products is of great pharmaceutical interest. In fact, fungi are a promising source of novel drugs with a broad spectrum of activities and functions, including antiviral properties. Hence, the potential antiviral properties of 3-O-methylfunicone (OMF), a secondary metabolite produced by Talaromyces pinophilus, were evaluated on BoHV-1. In this study, during BoHV-1 infection in bovine cells (MDBK), the non-toxic concentration of 5 µM OMF considerably reduced signs of cell death and increased cell proliferation. Furthermore, OMF significantly decreased the virus titer as well as the cytopathic effect and strongly inhibited the expression of bICP0, the major regulatory protein in the BoHV-1 lytic cycle. These findings were accompanied by a considerable up-regulation in the expression of the aryl hydrocarbon receptor (AhR), a multifunctional transcription factor also linked to the host’s response to a herpesvirus infection. Overall, our results suggest that by involving AhR, OMF shows potential against a BoHV-1 infection. Full article

(This article belongs to the Special Issue Mediation of Bacterial and Fungal Secondary Metabolites in Agro-Environmental Interactions)

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14 pages, 1270 KiB

Open AccessPerspective

Bridging the Gap: Type III Secretion Systems in Plant-Beneficial Bacteria

by Antoine Zboralski, Adrien Biessy and Martin Filion

Microorganisms 2022, 10(1), 187; https://doi.org/10.3390/microorganisms10010187 - 15 Jan 2022

Cited by 17 | Viewed by 3971

Abstract

Type III secretion systems (T3SSs) are bacterial membrane-embedded nanomachines translocating effector proteins into the cytoplasm of eukaryotic cells. They have been intensively studied for their important roles in animal and plant bacterial diseases. Over the past two decades, genome sequencing has unveiled their [...] Read more.

Type III secretion systems (T3SSs) are bacterial membrane-embedded nanomachines translocating effector proteins into the cytoplasm of eukaryotic cells. They have been intensively studied for their important roles in animal and plant bacterial diseases. Over the past two decades, genome sequencing has unveiled their ubiquitous distribution in many taxa of Gram-negative bacteria, including plant-beneficial ones. Here, we discuss the distribution and functions of the T3SS in two agronomically important bacterial groups: the symbiotic nodule-forming nitrogen-fixing rhizobia and the free-living plant-beneficial Pseudomonas spp. In legume-rhizobia symbiosis, T3SSs and their cognate effectors play important roles, including the modulation of the plant immune response and the initiation of the nodulation process in some cases. In plant-beneficial Pseudomonas spp., the roles of T3SSs are not fully understood, but pertain to plant immunity suppression, biocontrol against eukaryotic plant pathogens, mycorrhization facilitation, and possibly resistance against protist predation. The diversity of T3SSs in plant-beneficial bacteria points to their important roles in multifarious interkingdom interactions in the rhizosphere. We argue that the gap in research on T3SSs in plant-beneficial bacteria must be bridged to better understand bacteria/eukaryotes rhizosphere interactions and to support the development of efficient plant-growth promoting microbial inoculants. Full article

(This article belongs to the Section Plant Microbe Interactions)

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14 pages, 2758 KiB

Open AccessArticle

Spatiotemporal Changes in Plasmodium vivax msp1₄₂ Haplotypes in Southern Mexico: From the Control to the Pre-Elimination Phase

by Alejandro Flores-Alanis, Lilia González-Cerón, Frida Santillán-Valenzuela, Cecilia Ximenez, Marco A. Sandoval-Bautista and Rene Cerritos

Microorganisms 2022, 10(1), 186; https://doi.org/10.3390/microorganisms10010186 - 15 Jan 2022

Cited by 6 | Viewed by 2517

Abstract

For 20 years, Plasmodium vivax has been the only prevalent malaria species in Mexico, and cases have declined significantly and continuously. Spatiotemporal genetic studies can be helpful for understanding parasite dynamics and developing strategies to weaken malaria transmission, thus facilitating the elimination of [...] Read more.

For 20 years, Plasmodium vivax has been the only prevalent malaria species in Mexico, and cases have declined significantly and continuously. Spatiotemporal genetic studies can be helpful for understanding parasite dynamics and developing strategies to weaken malaria transmission, thus facilitating the elimination of the parasite. The aim of the current contribution was to analyze P. vivax-infected blood samples from patients in southern Mexico during the control (1993–2007) and pre-elimination phases (2008–2011). Nucleotide and haplotype changes in the pvmsp1₄₂ fragment were evaluated over time. The majority of multiple genotype infections occurred in the 1990s, when the 198 single nucleotide sequences exhibited 57 segregating sites, 64 mutations, and 17 haplotypes. Nucleotide and genetic diversity parameters showed subtle fluctuations from across time, in contrast to the reduced haplotype diversity and the increase in the R² index and Tajima’s D value from 2008 to 2011. The haplotype network consisted of four haplogroups, the geographical distribution of which varied slightly over time. Haplogroup-specific B-cell epitopes were predicted. Since only high-frequency and divergent haplotypes persisted, there was a contraction of the parasite population. Given that 84% of haplotypes were exclusive to Mesoamerica, P. vivax flow is likely circumscribed to this region, representing important information for parasite surveillance. Full article

(This article belongs to the Section Parasitology)

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16 pages, 915 KiB

Open AccessPerspective

Targeting of Regulators as a Promising Approach in the Search for Novel Antimicrobial Agents

by Davide Roncarati, Vincenzo Scarlato and Andrea Vannini

Microorganisms 2022, 10(1), 185; https://doi.org/10.3390/microorganisms10010185 - 15 Jan 2022

Cited by 15 | Viewed by 3279

Abstract

Since the discovery of penicillin in the first half of the last century, antibiotics have become the pillars of modern medicine for fighting bacterial infections. However, pathogens resistant to antibiotic treatment have increased in recent decades, and efforts to discover new antibiotics have [...] Read more.

Since the discovery of penicillin in the first half of the last century, antibiotics have become the pillars of modern medicine for fighting bacterial infections. However, pathogens resistant to antibiotic treatment have increased in recent decades, and efforts to discover new antibiotics have decreased. As a result, it is becoming increasingly difficult to treat bacterial infections successfully, and we look forward to more significant efforts from both governments and the scientific community to research new antibacterial drugs. This perspective article highlights the high potential of bacterial transcriptional and posttranscriptional regulators as targets for developing new drugs. We highlight some recent advances in the search for new compounds that inhibit their biological activity and, as such, appear very promising for treating bacterial infections. Full article

(This article belongs to the Special Issue Regulation of Gene Expression in Response to Environmental Changes in Bacterial Pathogens)

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14 pages, 1497 KiB

Open AccessArticle

Biosynthesis of Polyhydroxyalkanoate Terpolymer from Methanol via the Reverse β-Oxidation Pathway in the Presence of Lanthanide

by Izumi Orita, Gento Unno, Risa Kato and Toshiaki Fukui

Microorganisms 2022, 10(1), 184; https://doi.org/10.3390/microorganisms10010184 - 15 Jan 2022

Cited by 9 | Viewed by 3316 | Correction

Abstract

Methylorubrum extorquens AM1 is the attractive platform for the production of value-added products from methanol. We previously demonstrated that M. extorquens equipped with PHA synthase with broad substrate specificity synthesized polyhydroxyalkanoates (PHAs) composed of (R)-3-hydroxybutyrate and small fraction of (R [...] Read more.

Methylorubrum extorquens AM1 is the attractive platform for the production of value-added products from methanol. We previously demonstrated that M. extorquens equipped with PHA synthase with broad substrate specificity synthesized polyhydroxyalkanoates (PHAs) composed of (R)-3-hydroxybutyrate and small fraction of (R)-3-hydroxyvalerate (3HV) and (R)-3-hydroxyhexanoate (3HHx) units on methanol. This study further engineered M. extorquens for biosynthesis of PHAs with higher 3HV and 3HHx composition focusing on the EMC pathway involved in C₁ assimilation. The introduction of ethylmalonyl-CoA decarboxylase, catalyzing a backward reaction in the EMC pathway, aiming to increase intracellular propionyl/butyryl-CoA precursors did not affect PHA composition. Reverse β-oxidation pathway and subsequent (R)-specific hydration of 2-enoyl-CoA were then enhanced by heterologous expression of four genes derived from Ralstonia eutropha for the conversion of propionyl/butyryl-CoAs to the corresponding (R)-3-hydroxyacyl-CoA monomers. The resulting strains produced PHAs with higher 3HV and 3HHx compositions, while the methylotrophic growth was severely impaired. This growth impairment was interestingly restored by the addition of La³⁺ without a negative impact on PHA biosynthesis, suggesting the activation of the EMC pathway by La³⁺. The engineered M. extorquens synthesized PHA terpolymer composed of 5.4 mol% 3HV and 0.9% of 3HHx with 41% content from methanol as a sole carbon source in the presence of La³⁺. Full article

(This article belongs to the Special Issue Lanthanide-Dependent Methylotrophy and Methylotrophs)

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24 pages, 6404 KiB

Open AccessReview

Citrus Stubborn Disease: Current Insights on an Enigmatic Problem Prevailing in Citrus Orchards

by Tourya Sagouti, Zineb Belabess, Naima Rhallabi, Essaid Ait Barka, Abdessalem Tahiri and Rachid Lahlali

Microorganisms 2022, 10(1), 183; https://doi.org/10.3390/microorganisms10010183 - 14 Jan 2022

Cited by 7 | Viewed by 4170

Abstract

Citrus stubborn was initially observed in California in 1915 and was later proven as a graft-transmissible disease in 1942. In the field, diseased citrus trees have compressed and stunted appearances, and yield poor-quality fruits with little market value. The disease is caused by [...] Read more.

Citrus stubborn was initially observed in California in 1915 and was later proven as a graft-transmissible disease in 1942. In the field, diseased citrus trees have compressed and stunted appearances, and yield poor-quality fruits with little market value. The disease is caused by Spiroplasma citri, a phloem-restricted pathogenic mollicute, which belongs to the Spiroplasmataceae family (Mollicutes). S. citri has the largest genome of any Mollicutes investigated, with a genome size of roughly 1780 Kbp. It is a helical, motile mollicute that lacks a cell wall and peptidoglycan. Several quick and sensitive molecular-based and immuno-enzymatic pathogen detection technologies are available. Infected weeds are the primary source of transmission to citrus, with only a minor percentage of transmission from infected citrus to citrus. Several phloem-feeding leafhopper species (Cicadellidae, Hemiptera) support the natural spread of S. citri in a persistent, propagative manner. S. citri-free buds are used in new orchard plantings and bud certification, and indexing initiatives have been launched. Further, a quarantine system for newly introduced types has been implemented to limit citrus stubborn disease (CSD). The present state of knowledge about CSD around the world is summarized in this overview, where recent advances in S. citri detection, characterization, control and eradication were highlighted to prevent or limit disease spread through the adoption of best practices. Full article

(This article belongs to the Special Issue The Hidden World within Plants)

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14 pages, 2005 KiB

Open AccessArticle

Morpho-Functional Traits Reveal Differences in Size Fractionated Phytoplankton Communities but Do Not Significantly Affect Zooplankton Grazing

by Jessica Titocci, Melanie Bon and Patrick Fink

Microorganisms 2022, 10(1), 182; https://doi.org/10.3390/microorganisms10010182 - 14 Jan 2022

Cited by 5 | Viewed by 2700

Abstract

The recent emergence of approaches based on functional traits allows a more comprehensive evaluation of the role of functions and interactions within communities. As phytoplankton size and shape are the major determinants of its edibility to herbivores, alteration or loss of some morpho-functional [...] Read more.

The recent emergence of approaches based on functional traits allows a more comprehensive evaluation of the role of functions and interactions within communities. As phytoplankton size and shape are the major determinants of its edibility to herbivores, alteration or loss of some morpho-functional phytoplankton traits should affect zooplankton grazing, fitness and population dynamics. Here, we investigated the response of altered phytoplankton morpho-functional trait distribution to grazing by zooplankton with contrasting food size preferences and feeding behaviors. To test this, we performed feeding trials in laboratory microcosms with size-fractionated freshwater phytoplankton (3 size classes, >30 µm; 5–30 µm and <5 µm) and two different consumer types: the cladoceran Daphnia longispina, (generalist unselective filter feeder) and the calanoid copepod Eudiaptomus sp. (selective feeder). We observed no significant changes in traits and composition between the controls and grazed phytoplankton communities. However, community composition and structure varied widely between the small and large size fractions, demonstrating the key role of size in structuring natural phytoplankton communities. Our findings also highlight the necessity to combine taxonomy and trait-based morpho-functional approaches when studying ecological dynamics in phytoplankton-zooplankton interactions. Full article

(This article belongs to the Special Issue New Insights on Phytoplankton Morpho-Functional Traits)

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14 pages, 2244 KiB

Open AccessArticle

Modelling the Potential Risk of Infection Associated with Listeria monocytogenes in Irrigation Water and Agricultural Soil in Two District Municipalities in South Africa

by Chidozie Declan Iwu, Chinwe Juliana Iwu-Jaja, Rami Elhadi, Lucy Semerjian and Anthony Ifeanyin Okoh

Microorganisms 2022, 10(1), 181; https://doi.org/10.3390/microorganisms10010181 - 14 Jan 2022

Cited by 5 | Viewed by 2809

Abstract

Listeria monocytogenes (L. monocytogenes) is the etiologic agent of listeriosis which significantly affects immunocompromised individuals. The potential risk of infection attributed to L. monocytogenes in irrigation water and agricultural soil, which are key transmission pathways of microbial hazards to the human [...] Read more.

Listeria monocytogenes (L. monocytogenes) is the etiologic agent of listeriosis which significantly affects immunocompromised individuals. The potential risk of infection attributed to L. monocytogenes in irrigation water and agricultural soil, which are key transmission pathways of microbial hazards to the human population, was evaluated using the quantitative microbial risk assessment modelling. A Monte Carlo simulation with 10,000 iterations was used to characterize the risks. High counts of L. monocytogenes in irrigation water (mean: 11.96 × 10² CFU/100 mL; range: 0.00 to 56.67 × 10² CFU/100 mL) and agricultural soil samples (mean: 19.64 × 10² CFU/g; range: 1.33 × 10² to 62.33 × 10² CFU/g) were documented. Consequently, a high annual infection risk of 5.50 × 10⁻² (0.00 to 48.30 × 10⁻²), 54.50 × 10⁻² (9.10 × 10⁻³ to 1.00) and 70.50 × 10⁻² (3.60 × 10⁻² to 1.00) was observed for adults exposed to contaminated irrigation water, adults exposed to contaminated agricultural soil and children exposed to agricultural soil, respectively. This study, therefore, documents a huge public health threat attributed to the high probability of infection in humans exposed to L. monocytogenes in irrigation water and agricultural soil in Amathole and Chris Hani District Municipalities in the Eastern Cape province of South Africa. Full article

(This article belongs to the Special Issue An Update on Listeria monocytogenes)

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14 pages, 1882 KiB

Open AccessArticle

Moso Bamboo Invasion Reshapes Community Structure of Denitrifying Bacteria in Rhizosphere of Alsophila spinulosa

by Youwei Zuo, Huanhuan Qu, Changying Xia, Huan Zhang, Jiahui Zhang and Hongping Deng

Microorganisms 2022, 10(1), 180; https://doi.org/10.3390/microorganisms10010180 - 14 Jan 2022

Cited by 8 | Viewed by 2355

Abstract

The uncontrolled invasion of moso bamboo (Phyllostachys pubescens) dramatically alters soil nitrogen cycling and destroys the natural habitat of Alsophila spinulosa. Nevertheless, no clear evidence points out the role of denitrifying bacteria in the invasion of bamboo into the habitat [...] Read more.

The uncontrolled invasion of moso bamboo (Phyllostachys pubescens) dramatically alters soil nitrogen cycling and destroys the natural habitat of Alsophila spinulosa. Nevertheless, no clear evidence points out the role of denitrifying bacteria in the invasion of bamboo into the habitat of A. spinulosa. In the present study, we found that low (importance value 0.0008), moderate (0.6551), and high (0.9326) bamboo invasions dramatically altered the underground root biomass of both P. pubescens and A. spinulosa. The root biomass of A. spinulosa was maximal at moderate invasion, indicating that intermediate disturbance might contribute to the growth and survival of the colonized plant. Successful bamboo invasion significantly increased rhizospheric soil available nitrogen content of A. spinulosa, coupled with elevated denitrifying bacterial abundance and diversity. Shewanella, Chitinophaga, and Achromobacter were the primary genera in the three invasions, whereas high bamboo invasion harbored more denitrifying bacteria and higher abundance than moderate and low invasions. Further correlation analysis found that most soil denitrifying bacteria were positively correlated with soil organic matter and available nitrogen but negatively correlated with pH and water content. In addition, our findings illustrated that two denitrifying bacteria, Chitinophaga and Sorangium, might be essential indicators for evaluating the effects of bamboo invasion on the growth of A. spinulosa. Collectively, this study found that moso bamboo invasion could change the nitrogen cycling of colonized habitats through alterations of denitrifying bacteria and provided valuable perspectives for profound recognizing the invasive impacts and mechanisms of bamboo expansion. Full article

(This article belongs to the Section Environmental Microbiology)

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15 pages, 9234 KiB

Open AccessArticle

Acute Pneumonia Caused by Clinically Isolated Legionella pneumophila Sg 1, ST 62: Host Responses and Pathologies in Mice

by Jiří Trousil, Lucia Frgelecová, Pavla Kubíčková, Kristína Řeháková, Vladimír Drašar, Jana Matějková, Petr Štěpánek and Oto Pavliš

Microorganisms 2022, 10(1), 179; https://doi.org/10.3390/microorganisms10010179 - 14 Jan 2022

Cited by 1 | Viewed by 2822

Abstract

Legionnaires’ disease is a severe form of lung infection caused by bacteria belonging to the genus Legionella. The disease severity depends on both host immunity and L. pneumophila virulence. The objective of this study was to describe the pathological spectrum of acute [...] Read more.

Legionnaires’ disease is a severe form of lung infection caused by bacteria belonging to the genus Legionella. The disease severity depends on both host immunity and L. pneumophila virulence. The objective of this study was to describe the pathological spectrum of acute pneumonia caused by a virulent clinical isolate of L. pneumophila serogroup 1, sequence type 62. In A/JOlaHsd mice, we compared two infectious doses, namely, 10⁴ and 10⁶ CFU, and their impact on the mouse status, bacterial clearance, lung pathology, and blood count parameters was studied. Acute pneumonia resembling Legionnaires’ disease has been described in detail. Full article

(This article belongs to the Special Issue Legionella pneumophila)

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7 pages, 669 KiB

Open AccessBrief Report

The Impact of the COVID-19 Pandemic Lockdown on Pediatric Infections—A Single-Center Retrospective Study

by Magdalena Grochowska, Dominika Ambrożej, Aneta Wachnik, Urszula Demkow, Edyta Podsiadły and Wojciech Feleszko

Microorganisms 2022, 10(1), 178; https://doi.org/10.3390/microorganisms10010178 - 14 Jan 2022

Cited by 24 | Viewed by 2886

Abstract

Since the SARS-CoV-2 outbreak, many countries have introduced measures to limit the transmission. The data based on ICD-10 codes of lower respiratory tract infections and microbiological analysis of respiratory and gastrointestinal infections were collected. The retrospective five-year analysis of the medical records revealed [...] Read more.

Since the SARS-CoV-2 outbreak, many countries have introduced measures to limit the transmission. The data based on ICD-10 codes of lower respiratory tract infections and microbiological analysis of respiratory and gastrointestinal infections were collected. The retrospective five-year analysis of the medical records revealed a substantial decrease in respiratory tract infections during the pandemic year (from April 2020 to March 2021). We noted an 81% decline in the LRTI-associated hospital admissions based on the ICD-10 analysis (from a mean of 1170 admissions per year in the previous four years to 225 admissions between April 2020 through March 2021). According to microbiological analysis, there were 100%, 99%, 87%, and 47% drops in influenza virus, respiratory syncytial virus, rotavirus, and norovirus cases reported respectively during the pandemic season until April 2021 in comparison to pre-pandemic years. However, the prevalence of gastrointestinal bacterial infections was stable. Moreover, in August 2021, an unexpected rise in RSV-positive cases was observed. The measures applied during the COVID-19 pandemic turned out to be effective but also had a substantial contribution to the so-far stable epidemiological situation of seasonal infections. Full article

(This article belongs to the Special Issue Respiratory Tract Infection in Children)

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17 pages, 13805 KiB

Open AccessEditor’s ChoiceArticle

Toxocara canis- and Toxocara cati-Induced Neurotoxocarosis Is Associated with Comprehensive Brain Transcriptomic Alterations

by Patrick Waindok, Elisabeth Janecek-Erfurth, Dimitri L. Lindenwald, Esther Wilk, Klaus Schughart, Robert Geffers and Christina Strube

Microorganisms 2022, 10(1), 177; https://doi.org/10.3390/microorganisms10010177 - 14 Jan 2022

Cited by 6 | Viewed by 4631

Abstract

Toxocara canis and Toxocara cati are globally occurring zoonotic roundworms of dogs and cats. Migration and persistence of Toxocara larvae in the central nervous system of paratenic hosts including humans may cause clinical signs of neurotoxocarosis (NT). As pathomechanisms of NT and host [...] Read more.

Toxocara canis and Toxocara cati are globally occurring zoonotic roundworms of dogs and cats. Migration and persistence of Toxocara larvae in the central nervous system of paratenic hosts including humans may cause clinical signs of neurotoxocarosis (NT). As pathomechanisms of NT and host responses against Toxocara larvae are mostly unknown, whole-genome microarray transcription analysis was performed in cerebra and cerebella of experimentally infected C57Bl/6J mice as paratenic host model at days 14, 28, 70, 98, and 120 post-infection. Neuroinvasion of T. cati evoked 220 cerebral and 215 cerebellar differentially transcribed genes (DTGs), but no particular PANTHER (Protein ANalysis THrough Evolutionary Relationships) pathway was affected. In T. canis-infected mice, 1039 cerebral and 2073 cerebellar DTGs were identified. Statistically significant dysregulations occurred in various pathways, including cholesterol biosynthesis, apoptosis signaling, and the Slit/Robo mediated axon guidance as well as different pathways associated with the immune and defense response. Observed dysregulations of the cholesterol biosynthesis, as well as the Alzheimer disease-amyloid secretase pathway in conjunction with previous histopathological neurodegenerative findings, may promote the discussion of T. canis as a causative agent for dementia and/or Alzheimer’s disease. Furthermore, results contribute to a deeper understanding of the largely unknown pathogenesis and host-parasite interactions during NT, and may provide the basis for prospective investigations evaluating pathogenic mechanisms or designing novel diagnostic and therapeutic approaches. Full article

(This article belongs to the Special Issue Zoonotic Parasites: Toxoplasma gondii, Trichinella spp., and Toxocara spp.)

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17 pages, 253 KiB

Open AccessArticle

The Effect of HSV-1 Seropositivity on the Course of Pregnancy, Childbirth and the Condition of Newborns

by Irina Anatolyevna Andrievskaya, Irina Valentinovna Zhukovets, Inna Victorovna Dovzhikova, Nataliya Alexandrovna Ishutina and Ksenia Konstantinovna Petrova

Microorganisms 2022, 10(1), 176; https://doi.org/10.3390/microorganisms10010176 - 14 Jan 2022

Cited by 5 | Viewed by 3958

Abstract

The goal of this research was to evaluate seropositivity to HSV-1 among pregnant women and its effect on the course of pregnancy, childbirth and the condition of newborns. Methods: The serological status, socio-demographic characteristics, parity of pregnancy and childbirth and condition of newborns [...] Read more.

The goal of this research was to evaluate seropositivity to HSV-1 among pregnant women and its effect on the course of pregnancy, childbirth and the condition of newborns. Methods: The serological status, socio-demographic characteristics, parity of pregnancy and childbirth and condition of newborns in women seronegative and seropositive to HSV-1 with recurrent infection and its latent course during pregnancy were analyzed. Newborns from these mothers made up the corresponding groups. Results: Low titers of IgG antibodies to HSV-1 in women in the first trimester of pregnancy are associated with threatened miscarriage, anemia in pregnancy and chronic placental insufficiency. High titers of IgG antibodies to HSV-1 in women in the second trimester of pregnancy are associated with late miscarriages and premature births, anemia in pregnancy, chronic placental insufficiency, labor anomalies, early neonatal complications (cerebral ischemia, respiratory distress syndrome) and localized skin rashes. Low titers of IgG antibodies to HSV-1 in women in the third trimester of pregnancy are associated with premature birth, anemia in pregnancy, chronic placental insufficiency, endometritis, complications of the early neonatal period and localized skin rashes. Conclusions: Our research showed that low or high titers of IgG antibodies to HSV-1, determined by the timing of recurrence of infection during pregnancy, are associated with a high incidence of somatic pathology and complications in pregnancy, childbirth and the neonatal period. Full article

(This article belongs to the Section Medical Microbiology)

18 pages, 2260 KiB

Open AccessArticle

Adult Alphitobius diaperinus Microbial Community during Broiler Production and in Spent Litter after Stockpiling

by Tawni L. Crippen, Baneshwar Singh, Robin C. Anderson and Cynthia L. Sheffield

Microorganisms 2022, 10(1), 175; https://doi.org/10.3390/microorganisms10010175 - 14 Jan 2022

Cited by 1 | Viewed by 2438

Abstract

The facilities used to raise broiler chickens are often infested with litter beetles (lesser mealworm, Alphitobius diaperinus). These beetles have been studied for their carriage of pathogenic microbes; however, a more comprehensive microbiome study on these arthropods is lacking. This study investigated [...] Read more.

The facilities used to raise broiler chickens are often infested with litter beetles (lesser mealworm, Alphitobius diaperinus). These beetles have been studied for their carriage of pathogenic microbes; however, a more comprehensive microbiome study on these arthropods is lacking. This study investigated their microbial community in a longitudinal study throughout 2.5 years of poultry production and after the spent litter, containing the mealworms, was piled in pastureland for use as fertilizer. The mean most abundant phyla harbored by the beetles in house were the Proteobacteria (39.8%), then Firmicutes (30.8%), Actinobacteria (21.1%), Tenericutes (5.1%), and Bacteroidetes (1.6%). The community showed a modest decrease in Firmicutes and increase in Proteobacteria over successive flock rotations. The beetles were relocated within the spent litter to pastureland, where they were found at least 19 weeks later. Over time in the pastureland, their microbial profile underwent a large decrease in the percent of Firmicutes (20.5%). The lesser mealworm showed an ability to survive long-term in the open environment within the spent litter, where their microbiome should be further assessed to both reduce the risk of transferring harmful bacteria, as well as to enhance their contribution when the litter is used as a fertilizer. Full article

(This article belongs to the Special Issue Microbial Reservoirs and Dispersal Mechanisms)

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3 pages, 176 KiB

Open AccessEditorial

State-of-the-Art Clinical Microbiology in South Korea: Current Trends and Future Prospects

by Garima Sharma and Jin-Chul Kim

Microorganisms 2022, 10(1), 174; https://doi.org/10.3390/microorganisms10010174 - 14 Jan 2022

Viewed by 1932

Abstract

Researchers and clinicians have repeatedly explored the clinical aspects of microorganisms because the human body is inhabited by several different microbial species and their strains [...] Full article

(This article belongs to the Special Issue State-of-the-Art Clinical Microbiology Technology in Korea)

14 pages, 2622 KiB

Open AccessArticle

New Insights into the Genome Organization of Yeast Double-Stranded RNA LBC Viruses

by Manuel Ramírez, Alberto Martínez and Felipe Molina

Microorganisms 2022, 10(1), 173; https://doi.org/10.3390/microorganisms10010173 - 14 Jan 2022

Cited by 3 | Viewed by 2218

Abstract

The yeasts Torulaspora delbrueckii (Td) and Saccharomyces cerevisiae (Sc) may show a killer phenotype that is encoded in dsRNA M viruses (V-M), which require the helper activity of another dsRNA virus (V-LA or V-LBC) for replication. Recently, two TdV-LBCbarr genomes, which share sequence [...] Read more.

The yeasts Torulaspora delbrueckii (Td) and Saccharomyces cerevisiae (Sc) may show a killer phenotype that is encoded in dsRNA M viruses (V-M), which require the helper activity of another dsRNA virus (V-LA or V-LBC) for replication. Recently, two TdV-LBCbarr genomes, which share sequence identity with ScV-LBC counterparts, were characterized by high-throughput sequencing (HTS). They also share some similar characteristics with Sc-LA viruses. This may explain why TdV-LBCbarr has helper capability to maintain M viruses, whereas ScV-LBC does not. We here analyze two stretches with low sequence identity (LIS I and LIS II) that were found in TdV-LBCbarr Gag-Pol proteins when comparing with the homologous regions of ScV-LBC. These stretches may result from successive nucleotide insertions or deletions (indels) that allow compensatory frameshift events required to maintain specific functions of the RNA-polymerase, while modifying other functions such as the ability to bind V-M (+)RNA for packaging. The presence of an additional frameshifting site in LIS I may ensure the synthesis of a certain amount of RNA-polymerase until the new compensatory indel appears. Additional 5′- and 3′-extra sequences were found beyond V-LBC canonical genomes. Most extra sequences showed high identity to some stretches of the canonical genomes and can form stem-loop structures. Further, the 3′-extra sequence of two ScV-LBC genomes contains rRNA stretches. The origin and possible functions of these extra sequences are here discussed. Full article

(This article belongs to the Special Issue Recent Advances in the Yeast Killer Systems Research)

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13 pages, 2674 KiB

Open AccessArticle

In Silico Prediction and Design of Uropathogenic Escherichia coli Alpha-Hemolysin Generate a Soluble and Hemolytic Recombinant Toxin

by Bruna De Lucca Caetano, Marta de Oliveira Domingos, Miriam Aparecida da Silva, Jessika Cristina Alves da Silva, Juliana Moutinho Polatto, Fabio Montoni, Leo Kei Iwai, Daniel Carvalho Pimenta, Hugo Vigerelli, Paulo Cesar Gomes Vieira, Rita de Cassia Ruiz, José Salvatore Patané and Roxane Maria Fontes Piazza

Microorganisms 2022, 10(1), 172; https://doi.org/10.3390/microorganisms10010172 - 14 Jan 2022

Cited by 1 | Viewed by 2675

Abstract

The secretion of α-hemolysin by uropathogenic Escherichia coli (UPEC) is commonly associated with the severity of urinary tract infections, which makes it a predictor of poor prognosis among patients. Accordingly, this toxin has become a target for diagnostic tests and therapeutic interventions. However, [...] Read more.

The secretion of α-hemolysin by uropathogenic Escherichia coli (UPEC) is commonly associated with the severity of urinary tract infections, which makes it a predictor of poor prognosis among patients. Accordingly, this toxin has become a target for diagnostic tests and therapeutic interventions. However, there are several obstacles associated with the process of α-hemolysin purification, therefore limiting its utilization in scientific investigations. In order to overcome the problems associated with α-hemolysin expression, after in silico prediction, a 20.48 kDa soluble α-hemolysin recombinant denoted rHlyA was constructed. This recombinant is composed by a 182 amino acid sequence localized in the aa542–723 region of the toxin molecule. The antigenic determinants of the rHlyA were estimated by bioinformatics analysis taking into consideration the tertiary form of the toxin, epitope analysis tools, and solubility inference. The results indicated that rHlyA has three antigenic domains localized in the aa555–565, aa600–610, and aa674–717 regions. Functional investigation of rHlyA demonstrated that it has hemolytic activity against sheep red cells, but no cytotoxic effect against epithelial bladder cells. In summary, the results obtained in this study indicate that rHlyA is a soluble recombinant protein that can be used as a tool in studies that aim to understand the mechanisms involved in the hemolytic and cytotoxic activities of α-hemolysin produced by UPEC. In addition, rHlyA can be applied to generate monoclonal and/or polyclonal antibodies that can be utilized in the development of diagnostic tests and therapeutic interventions. Full article

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

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12 pages, 2745 KiB

Open AccessArticle

Boswellia serrata Extract as an Antibiofilm Agent against Candida spp.

by Petr Jaroš, Maria Vrublevskaya, Kristýna Lokočová, Jana Michailidu, Irena Kolouchová and Kateřina Demnerová

Microorganisms 2022, 10(1), 171; https://doi.org/10.3390/microorganisms10010171 - 13 Jan 2022

Cited by 5 | Viewed by 2953

Abstract

The use of antibiotics or antifungals to control infections caused by pathogenic microorganisms is currently insufficiently effective because of their emerging resistance. Thanks to the ability of microorganisms to form a biofilm and thus increase their resistance to administered drugs even more, modern [...] Read more.

The use of antibiotics or antifungals to control infections caused by pathogenic microorganisms is currently insufficiently effective because of their emerging resistance. Thanks to the ability of microorganisms to form a biofilm and thus increase their resistance to administered drugs even more, modern medicine faces the task of finding novel substances to combat infections caused by them. In this regard, the effects of essential oils or plant extracts are often studied. Among the relatively neglected plants is Boswellia serrata, which has a high content of biologically active boswellic acids. In this study, we focused on one of the most common nosocomial infections, which are caused by Candida species. The most common representative is C. albicans, although the number of infections caused by non-albicans species has recently been increasing. We focused on the antifungal activity of Boswellia serrata extract Bioswellix against planktonic and adhering cells of Candida albicans, Candida parapsilosis and Candida krusei. The antifungal activity against adhering cells was further explored by determining the metabolic activity of cells (MTT) and determining the total amount of biofilm using crystal violet. Boswellic acid-containing plant extract was shown to suppress the growth of a suspension population of all tested Candida species. Boswellia serrata extract Bioswellix was most effective in inhibiting C. albicans biofilm formation. Full article

(This article belongs to the Special Issue Diagnosis, Resistance and Treatment of Infections by Candida Species)

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17 pages, 1801 KiB

Open AccessArticle

Highly Distinct Microbial Communities in Elevated Strings and Submerged Flarks in the Boreal Aapa-Type Mire

by Andrey L. Rakitin, Shahjahon Begmatov, Alexey V. Beletsky, Dmitriy A. Philippov, Vitaly V. Kadnikov, Andrey V. Mardanov, Svetlana N. Dedysh and Nikolai V. Ravin

Microorganisms 2022, 10(1), 170; https://doi.org/10.3390/microorganisms10010170 - 13 Jan 2022

Cited by 5 | Viewed by 2920

Abstract

Large areas in the northern hemisphere are covered by extensive wetlands, which represent a complex mosaic of raised bogs, eutrophic fens, and aapa mires all in proximity to each other. Aapa mires differ from other types of wetlands by their concave surface, heavily [...] Read more.

Large areas in the northern hemisphere are covered by extensive wetlands, which represent a complex mosaic of raised bogs, eutrophic fens, and aapa mires all in proximity to each other. Aapa mires differ from other types of wetlands by their concave surface, heavily watered by the central part, as well as by the presence of large-patterned string-flark complexes. In this paper, we characterized microbial diversity patterns in the surface peat layers of the neighboring string and flark structures located within the mire site in the Vologda region of European North Russia, using 16S rRNA gene sequencing. The microbial communities in raised strings were clearly distinct from those in submerged flarks. Strings were dominated by the Alpha- and Gammaproteobacteria. Other abundant groups were the Acidobacteriota, Bacteroidota, Verrucomicrobiota, Actinobacteriota, and Planctomycetota. Archaea accounted for only 0.4% of 16S rRNA gene sequences retrieved from strings. By contrast, they comprised about 22% of all sequences in submerged flarks and mostly belonged to methanogenic lineages. Methanotrophs were nearly absent. Other flark-specific microorganisms included the phyla Chloroflexi, Spirochaetota, Desulfobacterota, Beijerinckiaceae- and Rhodomicrobiaceae-affiliated Alphaproteobacteria, and uncultivated groups env.OPS_17 and vadinHA17 of the Bacteroidota. Such pattern probably reflects local anaerobic conditions in the submerged peat layers in flarks. Full article

(This article belongs to the Special Issue Soil Microbiome: Biotic and Abiotic Interactions)

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17 pages, 3769 KiB

Open AccessArticle

Dietary Beta-Hydroxy-Beta-Methyl Butyrate Supplementation Inhibits Hepatic Fat Deposition via Regulating Gut Microbiota in Broiler Chickens

by Shiyu Zhang, Zhiyi Tang, Changbing Zheng, Yinzhao Zhong, Jie Zheng, Geyan Duan, Yulong Yin, Yehui Duan and Zehe Song

Microorganisms 2022, 10(1), 169; https://doi.org/10.3390/microorganisms10010169 - 13 Jan 2022

Cited by 11 | Viewed by 2521

Abstract

The present study is aimed to explore the effects of different dietary beta-hydroxy-beta-methyl butyrate (HMB) levels (0, 0.05%, 0.10%, or 0.15%) on liver lipid metabolism on Wenshi broiler chickens. Results showed that HMB reduced the liver weight as well as liver concentrations of [...] Read more.

The present study is aimed to explore the effects of different dietary beta-hydroxy-beta-methyl butyrate (HMB) levels (0, 0.05%, 0.10%, or 0.15%) on liver lipid metabolism on Wenshi broiler chickens. Results showed that HMB reduced the liver weight as well as liver concentrations of triacylglycerol (TG) and total cholesterol (TC) (quadratically, p < 0.05), and the lowest values were observed in the 0.10% HMB group. Meanwhile, HMB supplementation significantly altered the expression levels of key genes related to lipid metabolism in the liver of broiler chickens (p < 0.05). Furthermore, 16S rRNA gene sequencing revealed that HMB supplementation could greatly change the richness, diversity, and composition of the broiler gut microbiota, and the Bacteroidetes relative abundance at the phylum level and the Alistipes relative abundance at the genus level were affected (p < 0.05). Correlation analysis further suggested a strong association between Bacteroidetes relative abundance and lipid metabolism-related parameters (p < 0.05). Together, these data suggest that 0.10% HMB supplementation could inhibit hepatic fat deposition via regulating gut microbiota in broilers. Full article

(This article belongs to the Section Veterinary Microbiology)

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13 pages, 885 KiB

Open AccessReview

The Potential of Esteya spp. for the Biocontrol of the Pinewood Nematode, Bursaphelenchus xylophilus

by David Pires, Cláudia S. L. Vicente, Maria L. Inácio and Manuel Mota

Microorganisms 2022, 10(1), 168; https://doi.org/10.3390/microorganisms10010168 - 13 Jan 2022

Cited by 17 | Viewed by 6372

Abstract

The pinewood nematode (PWN), Bursaphelenchus xylophilus, is the causal agent of pine wilt disease (PWD) and a quarantine organism in many countries. Managing PWD involves strict regulations and heavy contingency plans, and present climate change scenarios predict a spread of the disease. [...] Read more.

The pinewood nematode (PWN), Bursaphelenchus xylophilus, is the causal agent of pine wilt disease (PWD) and a quarantine organism in many countries. Managing PWD involves strict regulations and heavy contingency plans, and present climate change scenarios predict a spread of the disease. The urgent need for sustainable management strategies has led to an increasing interest in promising biocontrol agents capable of suppressing the PWN, like endoparasitic nematophagous fungi of the Esteya genus. Here, we review different aspects of the biology and ecology of these nematophagous fungi and provide future prospects. Full article

(This article belongs to the Section Microbial Biotechnology)

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29 pages, 1346 KiB

Open AccessReview

Food Additives, a Key Environmental Factor in the Development of IBD through Gut Dysbiosis

by Pauline Raoul, Marco Cintoni, Marta Palombaro, Luisa Basso, Emanuele Rinninella, Antonio Gasbarrini and Maria Cristina Mele

Microorganisms 2022, 10(1), 167; https://doi.org/10.3390/microorganisms10010167 - 13 Jan 2022

Cited by 46 | Viewed by 22025

Abstract

Diet is a key environmental factor in inflammatory bowel disease (IBD) and, at the same time, represents one of the most promising therapies for IBD. Our daily diet often contains food additives present in numerous processed foods and even in dietary supplements. Recently, [...] Read more.

Diet is a key environmental factor in inflammatory bowel disease (IBD) and, at the same time, represents one of the most promising therapies for IBD. Our daily diet often contains food additives present in numerous processed foods and even in dietary supplements. Recently, researchers and national authorities have been paying much attention to their toxicity and effects on gut microbiota and health. This review aims to gather the latest data focusing on the potential role of food additives in the pathogenesis of IBDs through gut microbiota modulation. Some artificial emulsifiers and sweeteners can induce the dysbiosis associated with an alteration of the intestinal barrier, an activation of chronic inflammation, and abnormal immune response accelerating the onset of IBD. Even if most of these results are retrieved from in vivo and in vitro studies, many artificial food additives can represent a potential hidden driver of gut chronic inflammation through gut microbiota alterations, especially in a population with IBD predisposition. In this context, pending the confirmation of these results by large human studies, it would be advisable that IBD patients avoid the consumption of processed food containing artificial food additives and follow a personalized nutritional therapy prescribed by a clinical nutritionist. Full article

(This article belongs to the Special Issue Gastrointestinal Microbiota and Gut Barrier Impact Human Health and Disease)

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Microorganisms, Volume 10, Issue 1 (January 2022) – 196 articles

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