Microorganisms

22 pages, 3800 KB

Open AccessEditor’s ChoiceArticle

Comparative Genomic Analysis of Virulent Vibrio (Listonella) anguillarum Serotypes Revealed Genetic Diversity and Genomic Signatures in the O-Antigen Biosynthesis Gene Cluster

by Vimbai Irene Machimbirike, Ignacio Vasquez, Trung Cao, Joy Chukwu-Osazuwa, Oluwatoyin Onireti, Cristopher Segovia, Pongsak Khunrae, Triwit Rattanarojpong, Marije Booman, Simon Jones, Manuel Soto-Davila, Brian Dixon and Javier Santander

Microorganisms 2023, 11(3), 792; https://doi.org/10.3390/microorganisms11030792 - 20 Mar 2023

Cited by 17 | Viewed by 4997

Abstract

Vibrio anguillarum is the most frequent pathogen affecting fish worldwide. The only known virulent strains of V. anguillarum are serotypes O1, O2, and O3. Genetic differences between the serotypes that could shed insight on the evolution and serotype differences of this marine pathogen [...] Read more.

Vibrio anguillarum is the most frequent pathogen affecting fish worldwide. The only known virulent strains of V. anguillarum are serotypes O1, O2, and O3. Genetic differences between the serotypes that could shed insight on the evolution and serotype differences of this marine pathogen are unknown. Here, we fully sequenced and characterized a strain of V. anguillarum O1 (J382) isolated from winter steelhead trout (Oncorhynchus mykiss irideus) in British Columbia, Canada. Koch’s postulates using the O1 strain were replicated in naïve lumpfish (Cyclopterus lumpus) and compared to O2. Phenotypic and genotypic comparisons were conducted for serotypes O1, O2, and O3, using biochemical tests and bioinformatic tools, respectively. The genome of V. anguillarum O1 (J382) contains two chromosomes (3.13 Mb and 1.03 Mb) and two typical pJM1-like plasmids (65,573 and 76,959 bp). Furthermore, V. anguillarum O1 (J382) displayed resistance to colistin sulphate, which differs from serotype O2 and could be attributed to the presence of the ugd gene. Comparative genomic analysis, among the serotypes, showed that intra-species evolution is driven by insertion sequences, bacteriophages, and a different repertoire of putative ncRNAs. Genetic heterogeneity in the O-antigen biosynthesis gene cluster is characterized by the absence or the presence of unique genes, which could result in differences in the immune evasion mechanisms employed by the respective serotypes. This study contributes to understanding the genetic differences among V. anguillarum serovars and their evolution. Full article

(This article belongs to the Special Issue Microorganisms and Diseases Associated with Aquatic Animals)

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15 pages, 5622 KB

Open AccessEditor’s ChoiceArticle

Isolation and Characterisation of Electrogenic Bacteria from Mud Samples

by György Schneider, Dorina Pásztor, Péter Szabó, László Kőrösi, Nandyala Siva Kishan, Penmetsa Appala Rama Krishna Raju and Rajnish Kaur Calay

Microorganisms 2023, 11(3), 781; https://doi.org/10.3390/microorganisms11030781 - 17 Mar 2023

Cited by 7 | Viewed by 6474

Abstract

To develop efficient microbial fuel cell systems for green energy production using different waste products, establishing characterised bacterial consortia is necessary. In this study, bacteria with electrogenic potentials were isolated from mud samples and examined to determine biofilm-formation capacities and macromolecule degradation. Matrix-assisted [...] Read more.

To develop efficient microbial fuel cell systems for green energy production using different waste products, establishing characterised bacterial consortia is necessary. In this study, bacteria with electrogenic potentials were isolated from mud samples and examined to determine biofilm-formation capacities and macromolecule degradation. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry identifications have revealed that isolates represented 18 known and 4 unknown genuses. They all had the capacities to reduce the Reactive Black 5 stain in the agar medium, and 48 of them were positive in the wolfram nanorod reduction assay. The isolates formed biofilm to different extents on the surfaces of both adhesive and non-adhesive 96-well polystyrene plates and glass. Scanning electron microscopy images revealed the different adhesion potentials of isolates to the surface of carbon tissue fibres. Eight of them (15%) were able to form massive amounts of biofilm in three days at 23 °C. A total of 70% of the isolates produced proteases, while lipase and amylase production was lower, at 38% and 27% respectively. All of the macromolecule-degrading enzymes were produced by 11 isolates, and two isolates of them had the capacity to form a strong biofilm on the carbon tissue one of the most used anodic materials in MFC systems. This study discusses the potential of the isolates for future MFC development applications. Full article

(This article belongs to the Special Issue New Electrogenic Microbes)

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15 pages, 841 KB

Open AccessEditor’s ChoiceArticle

High-Resolution Taxonomic Characterization Reveals Novel Human Microbial Strains with Potential as Risk Factors and Probiotics for Prediabetes and Type 2 Diabetes

by Sarah A. Hendricks, Chantal A. Vella, Daniel D. New, Afiya Aunjum, Maximilian Antush, Rayme Geidl, Kimberly R. Andrews and Onesmo B. Balemba

Microorganisms 2023, 11(3), 758; https://doi.org/10.3390/microorganisms11030758 - 15 Mar 2023

Cited by 14 | Viewed by 4993

Abstract

Alterations in the composition of the gut microbiota is thought to play a key role in causing type 2 diabetes, yet is not fully understood, especially at the strain level. Here, we used long-read DNA sequencing technology of 16S-ITS-23S rRNA genes for high-resolution [...] Read more.

Alterations in the composition of the gut microbiota is thought to play a key role in causing type 2 diabetes, yet is not fully understood, especially at the strain level. Here, we used long-read DNA sequencing technology of 16S-ITS-23S rRNA genes for high-resolution characterization of gut microbiota in the development of type 2 diabetes. Gut microbiota composition was characterized from fecal DNA from 47 participants divided into 4 cohorts based on glycemic control: normal glycemic control (healthy; n = 21), reversed prediabetes (prediabetes/healthy; n = 8), prediabetes (n = 8), or type 2 diabetes (n = 10). A total of 46 taxa were found to be possibly related to progression from healthy state to type 2 diabetes. Bacteroides coprophilus DSM 18228, Bifidobacterium pseudocatenulatum DSM 20438, and Bifidobacterium adolescentis ATCC 15703 could confer resistance to glucose intolerance. On the other hand, Odoribacter laneus YIT 12061 may be pathogenic as it was found to be more abundant in type 2 diabetes participants than other cohorts. This research increases our understanding of the structural modulation of gut microbiota in the pathogenesis of type 2 diabetes and highlights gut microbiota strains, with the potential for targeted opportunistic pathogen control or consideration for probiotic prophylaxis and treatment. Full article

(This article belongs to the Special Issue Gut Microbiota in Disease)

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16 pages, 2308 KB

Open AccessEditor’s ChoiceArticle

New Insights into the Physiology of the Propionate Producers Anaerotignum propionicum and Anaerotignum neopropionicum (Formerly Clostridium propionicum and Clostridium neopropionicum)

by Tina Baur and Peter Dürre

Microorganisms 2023, 11(3), 685; https://doi.org/10.3390/microorganisms11030685 - 7 Mar 2023

Cited by 15 | Viewed by 5146

Abstract

Propionate is an important platform chemical that is available through petrochemical synthesis. Bacterial propionate formation is considered an alternative, as bacteria can convert waste substrates into valuable products. In this regard, research primarily focused on propionibacteria due to high propionate titers achieved from [...] Read more.

Propionate is an important platform chemical that is available through petrochemical synthesis. Bacterial propionate formation is considered an alternative, as bacteria can convert waste substrates into valuable products. In this regard, research primarily focused on propionibacteria due to high propionate titers achieved from different substrates. Whether other bacteria could also be attractive producers is unclear, mostly because little is known about these strains. Therefore, two thus far less researched strains, Anaerotignum propionicum and Anaerotignum neopropionicum, were investigated with regard to their morphologic and metabolic features. Microscopic analyses revealed a negative Gram reaction despite a Gram-positive cell wall as well as surface layers for both strains. Furthermore, growth, product profiles, and the potential for propionate formation from sustainable substrates, i.e., ethanol or lignocellulosic sugars, were assessed. Results showed that both strains can oxidize ethanol to different extents. While A. propionicum only partially used ethanol, A. neopropionicum converted 28.3 mM ethanol to 16.4 mM propionate. Additionally, the ability of A. neopropionicum to produce propionate from lignocellulose-derived substrates was analyzed, leading to propionate concentrations of up to 14.5 mM. Overall, this work provides new insights into the physiology of the Anaerotignum strains, which can be used to develop effective propionate producer strains. Full article

(This article belongs to the Special Issue Physiology, Genetic and Industrial Applications of Clostridia)

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12 pages, 4470 KB

Open AccessEditor’s ChoiceArticle

Nanoparticle Coatings on Glass Surfaces to Prevent Pseudomonas fluorescens AR 11 Biofilm Formation

by Daniele Marra, Irene Perna, Giulio Pota, Giuseppe Vitiello, Alessandro Pezzella, Giuseppe Toscano, Giuseppina Luciani and Sergio Caserta

Microorganisms 2023, 11(3), 621; https://doi.org/10.3390/microorganisms11030621 - 28 Feb 2023

Cited by 9 | Viewed by 3825

Abstract

Microbial colonization of surfaces is a sanitary and industrial issue for many applications, leading to product contamination and human infections. When microorganisms closely interact with a surface, they start to produce an exo-polysaccaridic matrix to adhere to and protect themselves from adverse environmental [...] Read more.

Microbial colonization of surfaces is a sanitary and industrial issue for many applications, leading to product contamination and human infections. When microorganisms closely interact with a surface, they start to produce an exo-polysaccaridic matrix to adhere to and protect themselves from adverse environmental conditions. This type of structure is called a biofilm. The aim of our work is to investigate novel technologies able to prevent biofilm formation by surface coatings. We coated glass surfaces with melanin-ZnO₂, melanin-TiO₂, and TiO₂ hybrid nanoparticles. The functionalization was performed using cold plasma to activate glass-substrate-coated surfaces, that were characterized by performing water and soybean oil wetting tests. A quantitative characterization of the antibiofilm properties was done using Pseudomonas fluorescens AR 11 as a model organism. Biofilm morphologies were observed using confocal laser scanning microscopy and image analysis techniques were used to obtain quantitative morphological parameters. The results highlight the efficacy of the proposed surface coating to prevent biofilm formation. Melanin-TiO₂ proved to be the most efficient among the particles investigated. Our results can be a valuable support for future implementation of the technique proposed here in an extended range of applications that may include further testing on other strains and other support materials. Full article

(This article belongs to the Special Issue Feature Papers in Microbial Biofilm Formation)

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10 pages, 960 KB

Open AccessEditor’s ChoiceArticle

An Evaluation of Avian Influenza Virus Whole-Genome Sequencing Approaches Using Nanopore Technology

by Hon S. Ip, Sarah Uhm, Mary Lea Killian and Mia K. Torchetti

Microorganisms 2023, 11(2), 529; https://doi.org/10.3390/microorganisms11020529 - 19 Feb 2023

Cited by 19 | Viewed by 7991

Abstract

As exemplified by the global response to the SARS-CoV-2 pandemic, whole-genome sequencing played an important role in monitoring the evolution of novel viral variants and provided guidance on potential antiviral treatments. The recent rapid and extensive introduction and spread of highly pathogenic avian [...] Read more.

As exemplified by the global response to the SARS-CoV-2 pandemic, whole-genome sequencing played an important role in monitoring the evolution of novel viral variants and provided guidance on potential antiviral treatments. The recent rapid and extensive introduction and spread of highly pathogenic avian influenza virus in Europe, North America, and elsewhere raises the need for similarly rapid sequencing to aid in appropriate response and mitigation activities. To facilitate this objective, we investigate a next-generation sequencing platform that uses a portable nanopore sequencing device to generate and present data in real time. This platform offers the potential to extend in-house sequencing capacities to laboratories that may otherwise lack resources to adopt sequencing technologies requiring large benchtop instruments. We evaluate this platform for routine use in a diagnostic laboratory. In this study, we evaluate different primer sets for the whole genome amplification of influenza A virus and evaluate five different library preparation approaches for sequencing on the nanopore platform using the MinION flow cell. A limited amplification procedure and a rapid procedure are found to be best among the approaches taken. Full article

(This article belongs to the Special Issue Viral Metagenomic Analysis in Animals)

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14 pages, 1750 KB

Open AccessEditor’s ChoiceArticle

Systematic Survey of Vibrio spp. and Salmonella spp. in Bivalve Shellfish in Apulia Region (Italy): Prevalence and Antimicrobial Resistance

by Maria Emanuela Mancini, Alessandra Alessiani, Adelia Donatiello, Antonella Didonna, Luigi D’Attoli, Simona Faleo, Gilda Occhiochiuso, Francesco Carella, Pietro Di Taranto, Lorenzo Pace, Valeria Rondinone, Annita Maria Damato, Rosa Coppola, Carmine Pedarra and Elisa Goffredo

Microorganisms 2023, 11(2), 450; https://doi.org/10.3390/microorganisms11020450 - 10 Feb 2023

Cited by 27 | Viewed by 6772

Abstract

The emergence of antimicrobial resistance (AMR) is increasingly common across the globe and aquatic ecosystems could be considered a reservoir of antibiotic-resistant bacteria. This study aimed to determine prevalence and antibiotic susceptibility of the potential pathogenic bacteria Salmonella spp. and Vibrio spp. in [...] Read more.

The emergence of antimicrobial resistance (AMR) is increasingly common across the globe and aquatic ecosystems could be considered a reservoir of antibiotic-resistant bacteria. This study aimed to determine prevalence and antibiotic susceptibility of the potential pathogenic bacteria Salmonella spp. and Vibrio spp. in bivalve molluscs intended for human consumption, collected over a period of 19 months along the northern coast of Apulia region. The AMR profile was also determined in non-pathogenic Vibrio species, common natural inhabitants of seawater and a useful indicator for the surveillance of AMR in the environment. The current study presents data on the AMR of 5 Salmonella and 126 Vibrio isolates by broth microdilution MIC. Multidrug resistance (MDR) was observed in one S. Typhimurium strain towards sulfamethoxazole, trimethoprim, tetracycline, gentamicin, and ampicillin and in 41.3% of the Vibrio strains, mostly towards sulphonamides, penicillin, and cephems. All Vibrio isolates were sensitive to azithromycin, chloramphenicol, tetracycline, amoxicillin/clavulanic acid, gentamicin, streptomycin, amikacin, and levofloxacin. The AMR phenomenon in the investigated area is not highly worrying but not entirely negligible; therefore, in-depth continuous monitoring is suggested. Results concerning the antibiotic agents without available specific clinical breakpoints could be useful to upgrade the MIC distribution for Vibrio spp. but, also, the establishment of interpretative criteria for environmental species is necessary to obtain a more complete view of this issue. Full article

(This article belongs to the Special Issue Seafood-Borne Pathogens)

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20 pages, 3387 KB

Open AccessEditor’s ChoiceArticle

Metagenomic Analysis of Anaerobic Microbial Communities Degrading Short-Chain Fatty Acids as Sole Carbon Sources

by Daniela Becker, Denny Popp, Fabian Bonk, Sabine Kleinsteuber, Hauke Harms and Florian Centler

Microorganisms 2023, 11(2), 420; https://doi.org/10.3390/microorganisms11020420 - 7 Feb 2023

Cited by 9 | Viewed by 5105

Abstract

Analyzing microbial communities using metagenomes is a powerful approach to understand compositional structures and functional connections in anaerobic digestion (AD) microbiomes. Whereas short-read sequencing approaches based on the Illumina platform result in highly fragmented metagenomes, long-read sequencing leads to more contiguous assemblies. To [...] Read more.

Analyzing microbial communities using metagenomes is a powerful approach to understand compositional structures and functional connections in anaerobic digestion (AD) microbiomes. Whereas short-read sequencing approaches based on the Illumina platform result in highly fragmented metagenomes, long-read sequencing leads to more contiguous assemblies. To evaluate the performance of a hybrid approach of these two sequencing approaches we compared the metagenome-assembled genomes (MAGs) resulting from five AD microbiome samples. The samples were taken from reactors fed with short-chain fatty acids at different feeding regimes (continuous and discontinuous) and organic loading rates (OLR). Methanothrix showed a high relative abundance at all feeding regimes but was strongly reduced in abundance at higher OLR, when Methanosarcina took over. The bacterial community composition differed strongly between reactors of different feeding regimes and OLRs. However, the functional potential was similar regardless of feeding regime and OLR. The hybrid sequencing approach using Nanopore long-reads and Illumina MiSeq reads improved assembly statistics, including an increase of the N50 value (on average from 32 to 1740 kbp) and an increased length of the longest contig (on average from 94 to 1898 kbp). The hybrid approach also led to a higher share of high-quality MAGs and generated five potentially circular genomes while none were generated using MiSeq-based contigs only. Finally, 27 hybrid MAGs were reconstructed of which 18 represent potentially new species—15 of them bacterial species. During pathway analysis, selected MAGs revealed similar gene patterns of butyrate degradation and might represent new butyrate-degrading bacteria. The demonstrated advantages of adding long reads to metagenomic analyses make the hybrid approach the preferable option when dealing with complex microbiomes. Full article

(This article belongs to the Special Issue Microbial Communities in Anaerobic Digesters)

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15 pages, 1955 KB

Open AccessEditor’s ChoiceArticle

Differential Effects of Viruses on the Growth Efficiency of Freshwater Bacterioplankton in Eutrophic Relative to Non-Eutrophic Lakes

by Angia Sriram Pradeep Ram and Télesphore Sime-Ngando

Microorganisms 2023, 11(2), 384; https://doi.org/10.3390/microorganisms11020384 - 2 Feb 2023

Cited by 7 | Viewed by 2755

Abstract

In aquatic environments, the consensus of viral impact on bacterial carbon metabolism with the nutrient environment as an important axis is limited. Henceforth, we explored the viral regulation of carbon-based bacterial growth efficiency (BGE) in a set of freshwater systems from French Massif [...] Read more.

In aquatic environments, the consensus of viral impact on bacterial carbon metabolism with the nutrient environment as an important axis is limited. Henceforth, we explored the viral regulation of carbon-based bacterial growth efficiency (BGE) in a set of freshwater systems from French Massif Central, which were broadly classified based on two trophic statuses: eutrophic and non-eutrophic lakes. Comparative analysis showed that microbial abundances (viruses and bacteria) were 3-fold higher in eutrophic compared with non-eutrophic lakes, and so were bacterial production and viral lytic infection. The observed variability in BGE (10–60%) was explained by the uncoupling between bacterial respiration and production. Viruses through selective lysis of susceptible host communities had an antagonistic impact on BGE in the eutrophic lakes, whereas the release of substrates via viral shunt exerted a synergistic influence on the carbon metabolism of non-targeted host populations in non-eutrophic lakes. The decisive effect of the two individual processes (i.e., lysis and substrate release) on BGE was supported by regressions of bacterial abundance as a function of bacterial production, which is considered as a proxy of top-down processes. The role of viruses through their negative impact via mortality and positive impact via substrate supply can eventually have implications on carbon transfer through bacterioplankton in freshwaters. Full article

(This article belongs to the Special Issue Microbiomes of Aquatic Organisms)

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17 pages, 1541 KB

Open AccessEditor’s ChoiceArticle

C-di-AMP Is a Second Messenger in Corynebacterium glutamicum That Regulates Expression of a Cell Wall-Related Peptidase via a Riboswitch

by Sebastian J. Reich, Oliver Goldbeck, Tsenguunmaa Lkhaasuren, Dominik Weixler, Tamara Weiß and Bernhard J. Eikmanns

Microorganisms 2023, 11(2), 296; https://doi.org/10.3390/microorganisms11020296 - 23 Jan 2023

Cited by 6 | Viewed by 4624

Abstract

Cyclic di-adenosine monophosphate (c-di-AMP) is a bacterial second messenger discovered in Bacillus subtilis and involved in potassium homeostasis, cell wall maintenance and/or DNA stress response. As the role of c-di-AMP has been mostly studied in Firmicutes, we sought to increase the understanding of [...] Read more.

Cyclic di-adenosine monophosphate (c-di-AMP) is a bacterial second messenger discovered in Bacillus subtilis and involved in potassium homeostasis, cell wall maintenance and/or DNA stress response. As the role of c-di-AMP has been mostly studied in Firmicutes, we sought to increase the understanding of its role in Actinobacteria, namely in Corynebacterium glutamicum. This organism is a well-known industrial production host and a model organism for pathogens, such as C. diphtheriae or Mycobacterium tuberculosis. Here, we identify and analyze the minimal set of two C. glutamicum enzymes, the diadenylate cyclase DisA and the phosphodiesterase PdeA, responsible for c-di-AMP metabolism. DisA synthesizes c-di-AMP from two molecules of ATP, whereas PdeA degrades c-di-AMP, as well as the linear degradation intermediate phosphoadenylyl-(3′→5′)-adenosine (pApA) to two molecules of AMP. Here, we show that a ydaO/kimA-type c-di-AMP-dependent riboswitch controls the expression of the strictly regulated cell wall peptidase gene nlpC in C. glutamicum. In contrast to previously described members of the ydaO/kimA-type riboswitches, our results suggest that the C. glutamicum nlpC riboswitch likely affects the translation instead of the transcription of its downstream gene. Although strongly regulated by different mechanisms, we show that the absence of nlpC, the first known regulatory target of c-di-AMP in C. glutamicum, is not detrimental for this organism under the tested conditions. Full article

(This article belongs to the Special Issue Complex Signal Transduction Systems in Bacteria)

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22 pages, 4130 KB

Open AccessEditor’s ChoiceArticle

Immunomodulatory and Antioxidant Properties of a Novel Potential Probiotic Bacillus clausii CSI08

by Ekaterina Khokhlova, Joan Colom, Annie Simon, Shahneela Mazhar, Guillermo García-Lainez, Silvia Llopis, Nuria Gonzalez, María Enrique-López, Beatriz Álvarez, Patricia Martorell, Marta Tortajada, John Deaton and Kieran Rea

Microorganisms 2023, 11(2), 240; https://doi.org/10.3390/microorganisms11020240 - 18 Jan 2023

Cited by 28 | Viewed by 12376

Abstract

Spore-forming bacteria of the Bacillus genus have demonstrated potential as probiotics for human use. Bacillus clausii have been recognized as efficacious and safe agents for preventing and treating diarrhea in children and adults, with pronounced immunomodulatory properties during several in vitro and clinical [...] Read more.

Spore-forming bacteria of the Bacillus genus have demonstrated potential as probiotics for human use. Bacillus clausii have been recognized as efficacious and safe agents for preventing and treating diarrhea in children and adults, with pronounced immunomodulatory properties during several in vitro and clinical studies. Herein, we characterize the novel strain of B. clausii CSI08 (Munispore^®) for probiotic attributes including resistance to gastric acid and bile salts, the ability to suppress the growth of human pathogens, the capacity to assimilate wide range of carbohydrates and to produce potentially beneficial enzymes. Both spores and vegetative cells of this strain were able to adhere to a mucous-producing intestinal cell line and to attenuate the LPS- and Poly I:C-triggered pro-inflammatory cytokine gene expression in HT-29 intestinal cell line. Vegetative cells of B. clausii CSI08 were also able to elicit a robust immune response in U937-derived macrophages. Furthermore, B. clausii CSI08 demonstrated cytoprotective effects in in vitro cell culture and in vivo C. elegans models of oxidative stress. Taken together, these beneficial properties provide strong evidence for B. clausii CSI08 as a promising potential probiotic. Full article

(This article belongs to the Special Issue Probiotics and the Immune System: The Potential for Postimmunobiotics)

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26 pages, 5673 KB

Open AccessEditor’s ChoiceArticle

The Development of the Bacterial Community of Brown Trout (Salmo trutta) during Ontogeny

by Katharina Keiz, Sebastian Ulrich, Jasmin Wenderlein, Patrick Keferloher, Anna Wiesinger, Klaus Neuhaus, Ilias Lagkouvardos, Helmut Wedekind and Reinhard K. Straubinger

Microorganisms 2023, 11(1), 211; https://doi.org/10.3390/microorganisms11010211 - 14 Jan 2023

Cited by 10 | Viewed by 4719

Abstract

Brown trout (Salmo trutta) is an important aquaculture species in Germany, but its production faces challenges due to global warming and a high embryo mortality. Climate factors might influence the fish’s bacterial community (BC) and thus increase embryo mortality. Yet, knowledge [...] Read more.

Brown trout (Salmo trutta) is an important aquaculture species in Germany, but its production faces challenges due to global warming and a high embryo mortality. Climate factors might influence the fish’s bacterial community (BC) and thus increase embryo mortality. Yet, knowledge of the physiological BC during ontogeny in general is scarce. In this project, the BC of brown trout has been investigated in a period from unfertilized egg to 95 days post fertilization (dpf) using 16S rRNA gene amplicon sequencing. Developmental changes differed between early and late ontogeny and major differences in BC occurred especially during early developmental stages. Thus, analysis was conducted separately for 0 to 67 dpf and from 67 to 95 dpf. All analyzed stages were sampled in toto to avoid bias due to different sampling methods in different developmental stages. The most abundant phylum in the BC of all developmental stages was Pseudomonadota, while only two families (Comamonadaceae and Moraxellaceae) occurred in all developmental stages. The early developmental stages until 67 dpf displayed greater shifts in their BC regarding bacterial richness, microbial diversity, and taxonomic composition. Thereafter, in the fry stages, the BC seemed to stabilize and changes were moderate. In future studies, a reduction in the sampling time frames during early development, an increase in sampling numbers, and an attempt for biological reproduction in order to characterize the causes of these variations is recommended. Full article

(This article belongs to the Special Issue Dietary Components and Gut Microbes in Fish)

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14 pages, 2140 KB

Open AccessEditor’s ChoiceArticle

A 63-kDa Periplasmic Protein of the Endonuclear Symbiotic Bacterium Holospora obtusa Secreted to the Outside of the Bacterium during the Early Infection Process Binds Weakly to the Macronuclear DNA of the Host Paramecium caudatum

by Masahiro Fujishima, Hideaki Kawano and Isamu Miyakawa

Microorganisms 2023, 11(1), 155; https://doi.org/10.3390/microorganisms11010155 - 7 Jan 2023

Cited by 5 | Viewed by 5558

Abstract

The Gram-negative bacterium Holospora obtusa is a macronucleus-specific symbiont of the ciliate Paramecium caudatum. It is known that an infection of this bacterium induces high level expressions of the host hsp60 and hsp70 genes, and the host cell acquires both heat-shock and [...] Read more.

The Gram-negative bacterium Holospora obtusa is a macronucleus-specific symbiont of the ciliate Paramecium caudatum. It is known that an infection of this bacterium induces high level expressions of the host hsp60 and hsp70 genes, and the host cell acquires both heat-shock and high salt resistances. In addition, an infectious form of H. obtusa-specific 63-kDa periplasmic protein with a DNA-binding domain in its amino acid sequence is secreted into the host macronucleus after invasion into the macronucleus and remain within the nucleus. These facts suggest that binding of the 63-kDa protein to the host macronuclear DNA causes changes in the host gene expressions and enhances an environmental adaptability of the host cells. This 63-kDa protein was renamed as periplasmic region protein 1 (PRP1) to distinguish it from other proteins with similar molecular weights. To confirm whether PRP1 indeed binds to the host DNA, SDS-DNA PAGE and DNA affinity chromatography with calf thymus DNA and P. caudatum DNA were conducted and confirmed that PRP1 binds weakly to the P. caudatum DNA with a monoclonal antibody raised for the 63-kDa protein. Full article

(This article belongs to the Special Issue Paramecium as Modern Model System)

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9 pages, 269 KB

Open AccessEditor’s ChoiceArticle

Intestinal Shedding of SARS-CoV-2 in Children: No Evidence for Infectious Potential

by Filomena Nogueira, Klara Obrova, Meryl Haas, Evelyn Tucek, Karin Kosulin, Michaela Fortschegger, Paola Fürhacker, Christina Walter, Lisa Größlinger, Susanne Peter, Julia Othman Hassan, Martin Probst, Hans Salzer and Thomas Lion

Microorganisms 2023, 11(1), 33; https://doi.org/10.3390/microorganisms11010033 - 22 Dec 2022

Cited by 5 | Viewed by 4624

Abstract

The clinical courses of COVID-19 in children are often mild and may remain undiagnosed, but prolonged intestinal virus shedding has been documented, thus potentially enabling fecal–oral transmission. However, the infectious potential of SARS-CoV-2 viruses excreted with feces has remained unclear. Here, we investigated [...] Read more.

The clinical courses of COVID-19 in children are often mild and may remain undiagnosed, but prolonged intestinal virus shedding has been documented, thus potentially enabling fecal–oral transmission. However, the infectious potential of SARS-CoV-2 viruses excreted with feces has remained unclear. Here, we investigated 247 stool specimens from 213 pediatric patients to assess the prevalence of intestinal SARS-CoV-2 shedding in hospitalized children without or with COVID-19 and determined the infectious capacity of stool-borne viruses. Upon RT-qPCR screening, the infectivity of virus-positive samples was tested in cell culture using the Vero-E6 permissive cell line. SARS-CoV-2 RNA was detected by RT-qPCR in 32 (13%) stool specimens, but the analysis of virus-positive samples in cell culture revealed no cytopathic effects attributable to SARS-CoV-2-related cell damage. Our findings do not support the notion of potential fecal–oral SARS-CoV-2 spreading, thus questioning the role of hygienic measures designed to prevent this mode of viral transmission. Full article

(This article belongs to the Section Virology)

26 pages, 3341 KB

Open AccessEditor’s ChoiceArticle

Cross-Feeding and Enzymatic Catabolism for Mannan-Oligosaccharide Utilization by the Butyrate-Producing Gut Bacterium Roseburia hominis A2-183

by Abhishek Bhattacharya, Lovisa Majtorp, Simon Birgersson, Mathias Wiemann, Krishnan Sreenivas, Phebe Verbrugghe, Olivier Van Aken, Ed W. J. Van Niel and Henrik Stålbrand

Microorganisms 2022, 10(12), 2496; https://doi.org/10.3390/microorganisms10122496 - 16 Dec 2022

Cited by 22 | Viewed by 5045

Abstract

β-Mannan is abundant in the human diet and in hemicellulose derived from softwood. Linear or galactose-substituted β-mannan-oligosaccharides (MOS/GMOSs) derived from β-mannan are considered emerging prebiotics that could stimulate health-associated gut microbiota. However, the underlying mechanisms are not yet resolved. Therefore, this study investigated [...] Read more.

β-Mannan is abundant in the human diet and in hemicellulose derived from softwood. Linear or galactose-substituted β-mannan-oligosaccharides (MOS/GMOSs) derived from β-mannan are considered emerging prebiotics that could stimulate health-associated gut microbiota. However, the underlying mechanisms are not yet resolved. Therefore, this study investigated the cross-feeding and metabolic interactions between Bifidobacterium adolescentis ATCC 15703, an acetate producer, and Roseburia hominis A2-183 DSMZ 16839, a butyrate producer, during utilization of MOS/GMOSs. Cocultivation studies suggest that both strains coexist due to differential MOS/GMOS utilization, along with the cross-feeding of acetate from B. adolescentis E194a to R. hominis A2-183. The data suggest that R. hominis A2-183 efficiently utilizes MOS/GMOS in mono- and cocultivation. Notably, we observed the transcriptional upregulation of certain genes within a dedicated MOS/GMOS utilization locus (RhMosUL), and an exo-oligomannosidase (RhMan113A) gene located distally in the R. hominis A2-183 genome. Significantly, biochemical analysis of β-1,4 mannan-oligosaccharide phosphorylase (RhMOP130A), α-galactosidase (RhGal36A), and exo-oligomannosidase (RhMan113A) suggested their potential synergistic role in the initial utilization of MOS/GMOSs. Thus, our results enhance the understanding of MOS/GMOS utilization by potential health-promoting human gut microbiota and highlight the role of cross-feeding and metabolic interactions between two secondary mannan degraders inhabiting the same ecological niche in the gut. Full article

(This article belongs to the Special Issue Regulation and Workings of the Gastrointestinal Microbiota)

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20 pages, 3836 KB

Open AccessEditor’s ChoiceArticle

Potential Probiotic Properties of Exopolysaccharide-Producing Lacticaseibacillus paracasei EPS DA-BACS and Prebiotic Activity of Its Exopolysaccharide

by Min-Gyu Lee, Huijin Joeng, Jaein Shin, Suin Kim, Chaeeun Lee, Youngbo Song, Byung-Hoo Lee, Hyoung-Geun Park, Tae-Ho Lee, Hai-Hua Jiang, Young-Sun Han, Bong-Gyeong Lee, Ho-Jin Lee, Min-Ju Park, Yun-Ju Jun and Young-Seo Park

Microorganisms 2022, 10(12), 2431; https://doi.org/10.3390/microorganisms10122431 - 8 Dec 2022

Cited by 56 | Viewed by 8437

Abstract

Exopolysaccharide (EPS)-producing Lacticaseibacillus paracasei EPS DA-BACS was isolated from healthy human feces and its probiotic properties, as well as the structure and prebiotic activity of the EPS from this strain were examined. EPS from L. paracasei EPS DA-BACS had a ropy phenotype, which [...] Read more.

Exopolysaccharide (EPS)-producing Lacticaseibacillus paracasei EPS DA-BACS was isolated from healthy human feces and its probiotic properties, as well as the structure and prebiotic activity of the EPS from this strain were examined. EPS from L. paracasei EPS DA-BACS had a ropy phenotype, which is known to have potential health benefits and is identified as loosely cell-bounded glucomannan-type EPS with a molecular size of 3.7 × 10⁶ Da. EPS promoted the acid tolerance of L. paracasei EPS DA-BACS and provided cells with tolerance to gastrointestinal stress. The purified EPS showed growth inhibitory activity against Clostridium difficile. L. paracasei EPS DA-BACS cells completely inhibited the growth of Bacillus subtilis, Pseudomonas aeruginosa, and Aspergillus brasiliensis, as well as showed high growth inhibitory activity against Staphylococcus aureus and Escherichia coli. Treatment of lipopolysaccharide-stimulated RAW 264.7 cells with heat-killed L. paracasei EPS DA-BACS cells led to a decrease in the production of nitric oxide, indicating the anti-inflammatory activity of L. paracasei EPS DA-BACS. Purified EPS promoted the growth of Lactobacillus gasseri, Bifidobacterium bifidum, B. animalis, and B. faecale which showed high prebiotic activity. L. paracasei EPS DA-BACS harbors no antibiotic resistance genes or virulence factors. Therefore, L. paracasei EPS DA-BACS exhibits anti-inflammatory and antimicrobial activities with high gut adhesion ability and gastrointestinal tolerance and can be used as a potential probiotic. Full article

(This article belongs to the Special Issue Environment Microorganisms and Their Enzymes with Biotechnological Application)

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12 pages, 22517 KB

Open AccessEditor’s ChoiceArticle

Molecular Characterization of Octopamine/Tyramine Receptor Gene of Amitraz-Resistant Rhipicephalus (Boophilus) decoloratus Ticks from Uganda

by Patrick Vudriko, Rika Umemiya-Shirafuji, Dickson Stuart Tayebwa, Joseph Byaruhanga, Benedicto Byamukama, Maria Tumwebaze, Xuenan Xuan and Hiroshi Suzuki

Microorganisms 2022, 10(12), 2384; https://doi.org/10.3390/microorganisms10122384 - 30 Nov 2022

Cited by 4 | Viewed by 4227

Abstract

We previously reported the emergence of amitraz-resistant Rhipicephalus (Boophilus) decoloratus ticks in the western region of Uganda. This study characterized the octopamine/tyramine receptor gene (OCT/Tyr) of amitraz-resistant and -susceptible R. (B.) decoloratus ticks from four regions of Uganda. The [...] Read more.

We previously reported the emergence of amitraz-resistant Rhipicephalus (Boophilus) decoloratus ticks in the western region of Uganda. This study characterized the octopamine/tyramine receptor gene (OCT/Tyr) of amitraz-resistant and -susceptible R. (B.) decoloratus ticks from four regions of Uganda. The OCT/Tyr gene was amplified from genomic DNA of 17 R. (B.) decoloratus larval populations of known susceptibility to amitraz. The amplicons were purified, cloned and sequenced to determine mutations in the partial coding region of the OCT/Tyr gene. The amplified R. (B.) decoloratus OCT/Tyr gene was 91–100% identical to the R. (B.) microplus OCT/Tyr gene. Up to 24 single nucleotide polymorphisms (SNPs) were found in the OCT/Tyr gene from ticks obtained from high acaricide pressure areas, compared to 8 from the low acaricide pressure areas. A total of eight amino acid mutations were recorded in the partial OCT/Tyr gene from ticks from the western region, and four of them were associated with amitraz-resistant tick populations. The amino acid mutations M1G, L16F, D41G and V72A were associated with phenotypic resistance to amitraz with no specific pattern. Phylogenetic analysis revealed that the OCT/Tyr gene sequence from this study clustered into two distinct groups that separated the genotype from high acaricide pressure areas from the susceptible populations. In conclusion, this study is the first to characterize the R. (B.) decoloratus OCT/Tyr receptor gene and reports four novel amino acid mutations associated with phenotypic amitraz resistance in Uganda. However, lack of mutations in the ORF of the OCT/Tyr gene fragment for some of the amitraz-resistant R. (B.) decoloratus ticks could suggest that other mechanisms of resistance may be responsible for amitraz resistance, hence the need for further investigation. Full article

(This article belongs to the Special Issue Advanced Research on Ticks and Tick-Borne Diseases)

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15 pages, 6666 KB

Open AccessEditor’s ChoiceArticle

Bacilli in the International Space Station

by Andrea Quagliariello, Angela Cirigliano and Teresa Rinaldi

Microorganisms 2022, 10(12), 2309; https://doi.org/10.3390/microorganisms10122309 - 22 Nov 2022

Cited by 8 | Viewed by 5885

Abstract

Astronauts remote from Earth, not least those who will inhabit the Moon or Mars, are vulnerable to disease due to their reduced immunity, isolation from clinical support, and the disconnect from any buffering capacity provided by the Earth. Here, we explore potential risks [...] Read more.

Astronauts remote from Earth, not least those who will inhabit the Moon or Mars, are vulnerable to disease due to their reduced immunity, isolation from clinical support, and the disconnect from any buffering capacity provided by the Earth. Here, we explore potential risks for astronaut health, focusing on key aspects of the biology of Bacillus anthracis and other anthrax-like bacilli. We examine aspects of Bacillus cereus group genetics in relation to their evolutionary biology and pathogenicity; a new clade of the Bacillus cereus group, close related to B. anthracis, has colonized the International Space Station (ISS), is still present, and could in theory at least acquire pathogenic plasmids from the other B. cereus group strains. The main finding is that the genomic sequence alignments of the B. cereus group ISS strains revealed a high sequence identity, indicating they originated from the same strain and that a close look to the genetic variations among the strains suggesting they lived, or they are living, in a vegetative form in the ISS enough time to accumulate genetic variations unique for each single strains. Full article

(This article belongs to the Special Issue Microorganisms from Extreme Environments: Versatile Tools from Biotechnology to Space Colonization)

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19 pages, 3110 KB

Open AccessEditor’s ChoiceArticle

Modulation of Virulence-Associated Traits in Aspergillus fumigatus by BET Inhibitor JQ1

by Anastasia Orekhova, Marta De Angelis, Andrea Cacciotti, Massimo Reverberi, Dante Rotili, Alessandra Giorgi, Virginia Protto, Graziana Bonincontro, Francesco Fiorentino, Victor Zgoda, Antonello Mai, Anna Teresa Palamara and Giovanna Simonetti

Microorganisms 2022, 10(11), 2292; https://doi.org/10.3390/microorganisms10112292 - 18 Nov 2022

Cited by 6 | Viewed by 3213

Abstract

Aspergillus fumigatus is a disease-causing, opportunistic fungus that can establish infection due to its capacity to respond to a wide range of environmental conditions. Secreted proteins and metabolites, which play a critical role in fungal–host interactions and pathogenesis, are modulated by epigenetic players, [...] Read more.

Aspergillus fumigatus is a disease-causing, opportunistic fungus that can establish infection due to its capacity to respond to a wide range of environmental conditions. Secreted proteins and metabolites, which play a critical role in fungal–host interactions and pathogenesis, are modulated by epigenetic players, such as bromodomain and extraterminal domain (BET) proteins. In this study, we evaluated the in vitro and in vivo capability of the BET inhibitor JQ1 to modulate the extracellular proteins and virulence of A. fumigatus. The abundance of 25 of the 76 extracellular proteins identified through LC-MS/MS proteomic analysis changed following JQ1 treatment. Among them, a ribonuclease, a chitinase, and a superoxide dismutase were dramatically downregulated. Moreover, the proteomic analysis of A. fumigatus intracellular proteins indicated that Abr2, an intracellular laccase involved in the last step of melanin synthesis, was absent in the JQ1-treated group. To investigate at which level this downregulation occurred and considering the ability of JQ1 to modulate gene expression we checked the level of ABR2, Chitinase, and Superoxide dismutase mRNA expression by qRT-PCR. Finally, the capacity of JQ1 to reduce the virulence of A. fumigatus has been proved using Galleria mellonella larvae, which are an in vivo model to evaluate fungal virulence. Overall, the promising activity exhibited by JQ1 suggests that A. fumigatus is sensitive to BET inhibition and BET proteins may be a viable target for developing antifungal agents. Full article

(This article belongs to the Special Issue Virulence Regulation and Drug-Resistance Mechanism of Fungal Infection)

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14 pages, 3835 KB

Open AccessEditor’s ChoiceArticle

Lipoproteins Are Potent Activators of Nuclear Factor Kappa B in Mammary Epithelial Cells and Virulence Factors in Mycoplasma bovis Mastitis

by Peleg Schneider, Re’ella Brill, Iftach Schouten, Einat Nissim-Eliraz, Inna Lysnyansky and Nahum Yehuda Shpigel

Microorganisms 2022, 10(11), 2209; https://doi.org/10.3390/microorganisms10112209 - 8 Nov 2022

Cited by 10 | Viewed by 3453

Abstract

Mastitis due to Mycoplasma bovis is a worldwide problem, which leads to significant economic losses and affects animal welfare. However, the mechanisms by which M. bovis establishes and maintains intra-mammary infections (IMI) in dairy cows are largely unknown. To study in further detail [...] Read more.

Mastitis due to Mycoplasma bovis is a worldwide problem, which leads to significant economic losses and affects animal welfare. However, the mechanisms by which M. bovis establishes and maintains intra-mammary infections (IMI) in dairy cows are largely unknown. To study in further detail the pathogenesis of M. bovis IMI, time- and cost-effective experimental models are needed. To this end, we established and characterized an in vitro murine mammary alveolar epithelial (EpH4) cell-based model and an in vivo murine mastitis model. Our results showed that live and UV-treated M. bovis field strain 161791 and its lipid-associated membrane proteins (LAMP) activated nuclear factor kappa B (NF-kB) in EpH4 cells in a dose-dependent manner. In the murine mastitis model, temporal and spatial dynamics of inflammation in the mammary tissues were evident. Live M. bovis elicited diffuse inflammation affecting the whole challenged gland peaking at 48 h post infection (pi) in contrast to LAMP challenge, which elicited only focal inflammation peaking at 24 h and resolving at 48 h pi. Inflammation was characterized by massive neutrophil recruitment into the milk spaces and by elevated expression of the inflammatory mediators TNF-α, KC, iNOS and NF-kB dependent genes: A20 and IkBα. Moreover, the presence of intraepithelial bacterial communities in glands challenged with live M. bovis bacteria was shown. The developed models can be used efficiently for future characterization of M. bovis virulence factors and host immune response to IMI. Full article

(This article belongs to the Special Issue Mycoplasma Pathogenicity, Persistence and Virulence)

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17 pages, 4114 KB

Open AccessEditor’s ChoiceArticle

The Emergence and Dynamics of Tick-Borne Encephalitis Virus in a New Endemic Region in Southern Germany

by Daniel Lang, Lidia Chitimia-Dobler, Malena Bestehorn-Willmann, Alexander Lindau, Marco Drehmann, Gabriele Stroppel, Helga Hengge, Ute Mackenstedt, Klaus Kaier, Gerhard Dobler and Johannes Borde

Microorganisms 2022, 10(11), 2125; https://doi.org/10.3390/microorganisms10112125 - 27 Oct 2022

Cited by 13 | Viewed by 3625

Abstract

Tick-borne encephalitis (TBE) is the most important viral tick-borne infection in Europe and Asia. It is emerging in new areas. The mechanisms of emergence are fairly unknown or speculative. In the Ravensburg district in southern Germany, TBE emerged, mainly over the last five [...] Read more.

Tick-borne encephalitis (TBE) is the most important viral tick-borne infection in Europe and Asia. It is emerging in new areas. The mechanisms of emergence are fairly unknown or speculative. In the Ravensburg district in southern Germany, TBE emerged, mainly over the last five years. Here, we analyzed the underlying epidemiology in humans. The resulting identified natural foci of the causal TBE virus (TBEV) were genetically characterized. We sampled 13 potential infection sites at these foci and detected TBEV in ticks (Ixodes ricinus) at eight sites. Phylogenetic analysis spurred the introduction of at least four distinct TBEV lineages of the European subtype into the Ravensburg district over the last few years. In two instances, a continuous spread of these virus strains over up to 10 km was observed. Full article

(This article belongs to the Special Issue Trends in Viral Zoonotic and Zooanthroponotic Diseases)

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13 pages, 2383 KB

Open AccessEditor’s ChoiceArticle

Bile Acids: Major Regulator of the Gut Microbiome

by Chihyeok An, Hyeyeon Chon, Wanrim Ku, Sunho Eom, Mingyu Seok, Sangha Kim, Jaesun Lee, Daesung Kim, Sanghyuk Lee, Hoonsup Koo, Hyunjung Cho, Seungyun Han, Juik Moon, Miil Kang and Kihyun Ryu

Microorganisms 2022, 10(9), 1792; https://doi.org/10.3390/microorganisms10091792 - 6 Sep 2022

Cited by 52 | Viewed by 8307

Abstract

Bile acids are synthesized from cholesterol and play an important role in regulating intestinal microflora. The different degrees of hydrophobicity and acidity of individual bile acids may affect their antimicrobial properties. We examined the antimicrobial effects of different bile acids on various microorganisms [...] Read more.

Bile acids are synthesized from cholesterol and play an important role in regulating intestinal microflora. The different degrees of hydrophobicity and acidity of individual bile acids may affect their antimicrobial properties. We examined the antimicrobial effects of different bile acids on various microorganisms in vitro and confirmed whether these remain consistent in vivo. Using human bile acids, including ursodeoxycholic acid, cholic acid, chenodeoxycholic acid, deoxycholic acid, and lithocholic acid, a disc diffusion test was performed, and a rodent model was created to determine the antimicrobial effects of each bile acid. The fecal bacterial population was analyzed using a real-time polymerase chain reaction. Each bile acid showed different microbial inhibitory properties. The inhibitory activity of bile acids against microbiota which normally resides in the gastrointestinal tract and biliary system, was low; however, normal flora of other organs was significantly inhibited. Changes in microbial counts after bile acid administration in a rodent model differed in the colon and cecum. The in vivo and in vitro results show that the antimicrobial effects of bile acids against intestinal microbiota were similar. In conclusion, bile acids could be a novel treatment strategy to regulate gut microbiota. Full article

(This article belongs to the Special Issue Regulation and Workings of the Gastrointestinal Microbiota)

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23 pages, 5724 KB

Open AccessEditor’s ChoiceArticle

Simultaneous Metabarcoding and Quantification of Neocallimastigomycetes from Environmental Samples: Insights into Community Composition and Novel Lineages

by Diana Young, Akshay Joshi, Liren Huang, Bernhard Munk, Christian Wurzbacher, Noha H. Youssef, Mostafa S. Elshahed, Christina D. Moon, Katrin Ochsenreither, Gareth W. Griffith, Tony M. Callaghan, Alexander Sczyrba, Michael Lebuhn and Veronika Flad

Microorganisms 2022, 10(9), 1749; https://doi.org/10.3390/microorganisms10091749 - 30 Aug 2022

Cited by 22 | Viewed by 6281

Abstract

Anaerobic fungi from the herbivore digestive tract (Neocallimastigomycetes) are primary lignocellulose modifiers and hold promise for biotechnological applications. Their molecular detection is currently difficult due to the non-specificity of published primer pairs, which impairs evolutionary and ecological research with environmental samples. [...] Read more.

Anaerobic fungi from the herbivore digestive tract (Neocallimastigomycetes) are primary lignocellulose modifiers and hold promise for biotechnological applications. Their molecular detection is currently difficult due to the non-specificity of published primer pairs, which impairs evolutionary and ecological research with environmental samples. We developed and validated a Neocallimastigomycetes-specific PCR primer pair targeting the D2 region of the ribosomal large subunit suitable for screening, quantifying, and sequencing. We evaluated this primer pair in silico on sequences from all known genera, in vitro with pure cultures covering 16 of the 20 known genera, and on environmental samples with highly diverse microbiomes. The amplified region allowed phylogenetic differentiation of all known genera and most species. The amplicon is about 350 bp long, suitable for short-read high-throughput sequencing as well as qPCR assays. Sequencing of herbivore fecal samples verified the specificity of the primer pair and recovered highly diverse and so far unknown anaerobic gut fungal taxa. As the chosen barcoding region can be easily aligned and is taxonomically informative, the sequences can be used for classification and phylogenetic inferences. Several new Neocallimastigomycetes clades were obtained, some of which represent putative novel lineages such as a clade from feces of the rodent Dolichotis patagonum (mara). Full article

(This article belongs to the Special Issue Unleashing the Hidden Potential of Anaerobic Fungi)

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10 pages, 258 KB

Open AccessEditor’s ChoiceArticle

Role of Intracellular Pulmonary Pathogens during SARS-CoV-2 Infection in the First Pandemic Wave of COVID-19: Clinical and Prognostic Significance in a Case Series of 1200 Patients

by Matteo Guarino, Benedetta Perna, Francesca Cuoghi, Michele Domenico Spampinato, Alice Eleonora Cesaro, Francesca Manza, Adriana Pretula, Anastasio Grilli, Martina Maritati, Giacomo Caio, Aldo Carnevale, Maria Elena Flacco, Roberto De Giorgio and Carlo Contini

Microorganisms 2022, 10(8), 1636; https://doi.org/10.3390/microorganisms10081636 - 12 Aug 2022

Cited by 11 | Viewed by 4090

Abstract

Background: Since 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic (COVID-19) has caused millions of deaths worldwide and is the second most serious pandemic after the Spanish flu. Despite SARS-CoV-2 infection having a dominant effect on morbidity and life-threatening outcomes, [...] Read more.

Background: Since 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic (COVID-19) has caused millions of deaths worldwide and is the second most serious pandemic after the Spanish flu. Despite SARS-CoV-2 infection having a dominant effect on morbidity and life-threatening outcomes, the role of bacterial co-infection in patients with COVID-19 is poorly understood. The present study aimed to verify the existence of bacterial co-infections and their possible role as cofactors worsening COVID-19-related clinical manifestations. Methods: All patients with suspected SARS-CoV-infection, hospitalised in COVID-19 wards at the Sant’Anna University Hospital of Ferrara, were retrospectively included in this single-centre study and their specific bacterial serologies were assessed. Univariate and logistic regression analyses were performed. Results: A total of 1204 individual records were retrieved. Among them, 959 were excluded because of a negative nasopharyngeal swab or missing data; of the eligible 245 patients, 51 were co-infected. Compared to patients with SARS-CoV-2 infection alone, those with Chlamydia pneumoniae or Mycoplasma pneumoniae co-infections had worse respiratory/radiological features and more intensive care unit admissions. However, the co-infection did not result in a higher mortality rate. Conclusions: The present study, comparing clinical, laboratory and radiological findings between patients with COVID-19 vs. those with co-infections (C. pneumoniae or M. pneumoniae) showed that, on admission, these features were worse in co-infected patients, although the mortality rate did not differ between the two groups. Full article

(This article belongs to the Special Issue Advances in SARS-CoV-2 Infection)

13 pages, 955 KB

Open AccessEditor’s ChoiceArticle

Controlling an Unprecedented Outbreak with Vancomycin-Resistant Enterococcus faecium in Germany, October 2015 to November 2019

by Jennifer K. Bender, Julia Hermes, Lutz T. Zabel, Sebastian Haller, Nadja Mürter, Hans-Peter Blank, Guido Werner, Ingo Hüttner and Tim Eckmanns

Microorganisms 2022, 10(8), 1603; https://doi.org/10.3390/microorganisms10081603 - 9 Aug 2022

Cited by 25 | Viewed by 5515

Abstract

Hospital outbreaks with vancomycin-resistant enterococci (VRE) pose a serious health threat and a challenge to infection prevention and control (IPC). We herein report on a VRE outbreak of unprecedented extent in Southern Germany (October 2015–November 2019). We used descriptive epidemiology and whole-genome sequencing [...] Read more.

Hospital outbreaks with vancomycin-resistant enterococci (VRE) pose a serious health threat and a challenge to infection prevention and control (IPC). We herein report on a VRE outbreak of unprecedented extent in Southern Germany (October 2015–November 2019). We used descriptive epidemiology and whole-genome sequencing (WGS) for a detailed outbreak investigation. Of the 2905 cases, 2776 (95.3%) were colonized, whereas from 127 (3.7%), VRE could be isolated from otherwise sterile body fluids or sites unlikely for enterococci colonization. Cases had a median age of 78 years (IQR 68–84) and 1339/2905 (46%) were female. The majority of isolates sequenced belonged to the clonal lineage ST80/CT1013 (212/397, 53%). Nosocomial transmission was observed as well as the constant import of VRE into the hospital. Extensive IPC measures were implemented and terminated the outbreak in late 2019, eventually. Our study shows that the combination of epidemiological and genomic analyses is indispensable for comprehensive outbreak investigations. The adaptation of IPC measures to these findings, their timely implementation, and strict execution also allow containment of large VRE outbreaks in hospital settings. Full article

(This article belongs to the Special Issue Nosocomial Pathogens and Antibiotic Resistance)

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10 pages, 977 KB

Open AccessEditor’s ChoiceArticle

Whole Genome Sequencing and Molecular Analysis of Carbapenemase-Producing Escherichia coli from Intestinal Carriage in Elderly Inpatients

by Maria Giufrè, Giulia Errico, Monica Monaco, Maria Del Grosso, Michela Sabbatucci, Annalisa Pantosti, Marina Cerquetti, Michela Pagnotta, Manuela Marra, Maria Carollo, Angelo Rossini, Elena Fogato, Elisabetta Cesana, Flaminia Gentiloni Silverj, Dorjan Zabzuni and Marco Tinelli

Microorganisms 2022, 10(8), 1561; https://doi.org/10.3390/microorganisms10081561 - 3 Aug 2022

Cited by 6 | Viewed by 3377

Abstract

The spread of carbapenemase-producing (CP) Enterobacterales is currently a worldwide concern, especially in the elderly. Twelve CP-E. coli isolated from rectal swabs of colonized inpatients aged ≥65 years from four hospitals in two Italian cities (Milan and Rome) were analyzed by whole [...] Read more.

The spread of carbapenemase-producing (CP) Enterobacterales is currently a worldwide concern, especially in the elderly. Twelve CP-E. coli isolated from rectal swabs of colonized inpatients aged ≥65 years from four hospitals in two Italian cities (Milan and Rome) were analyzed by whole genome sequencing (WGS) to obtain multi-locus sequence typing (MLST), identification of carbapenemase-encoding genes, resistome, plasmid content, and virulence genes. MLST analysis showed the presence of 10 unrelated lineages: ST410 (three isolates from three different hospitals in two cities) and ST12, ST38, ST69, ST95, ST131, ST189, ST648, ST1288, and ST1598 (one isolate each). Most isolates (9/12, 75%) contained a serine-β-lactamase gene (5 bla_KPC-3, 2 bla_KPC-2, and 2 bla_OXA-181), while three isolates harbored a metallo-β-lactamase gene (two bla_NDM-5 and one bla_VIM-1). In most CP-E. coli, the presence of more than one plasmid was observed, with the predominance of IncF. Several virulence genes were detected. All isolates contained genes enhancing the bacterial fitness, such as gad and terC, and all isolates but one, fimH, encoding type 1 fimbriae. In conclusion, CP-E. coli clones colonizing elderly patients showed heterogeneous genetic backgrounds. We recommend strict surveillance to monitor and prevent the spread of successful, high-risk clones in healthcare settings. Full article

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

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14 pages, 3296 KB

Open AccessEditor’s ChoiceArticle

In Vitro and In Silico Analysis of the Inhibitory Activity of EGCG-Stearate against Herpes Simplex Virus-2

by James D. Stamos, Lee H. Lee, Calvin Taylor, Tony Elias and Sandra D. Adams

Microorganisms 2022, 10(7), 1462; https://doi.org/10.3390/microorganisms10071462 - 20 Jul 2022

Cited by 12 | Viewed by 5906

Abstract

About half a billion people worldwide are infected with herpes simplex virus-2 (HSV-2). Prolonged treatment with acyclovir (ACV) and its analogs leads to the development of resistant strains. The aim of this study was to investigate the antiviral potential of epigallocatechin gallate (EGCG) [...] Read more.

About half a billion people worldwide are infected with herpes simplex virus-2 (HSV-2). Prolonged treatment with acyclovir (ACV) and its analogs leads to the development of resistant strains. The aim of this study was to investigate the antiviral potential of epigallocatechin gallate (EGCG) from Camellia sinensis and a stable analog EGCG-stearate (EGCG-S) against HSV-2 in cultured Vero cells. Cell viability and cell proliferation assays were used to determine the non-cytotoxic concentrations on cultured Vero cells. HSV-2 with a green fluorescent protein (GFP) fusion protein of VP26 virions were treated with non-cytotoxic concentrations of EGCG and EGCG-S. The effects on infectivity and mechanisms were determined by plaque assay, attachment and penetration assays, confocal microscopy, qPCR, and in silico modeling analysis. Our results demonstrate that treatment of HSV-2 virions with EGCG and EGCG-S at a concentration of 75 µM showed greater than 99.9% inhibition by inhibiting the attachment of HSV-2 virions to host cells. The bioinformatic analysis indicated high binding affinity of EGCG-S for glycoprotein D; thus EGCG-S may block fusion of HSV-2 and the cell membrane, preventing entry of HSV-2 into the cell. Full article

(This article belongs to the Special Issue Emerging Viruses and Antiviral Drugs)

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16 pages, 2522 KB

Open AccessEditor’s ChoiceArticle

Genome-Wide Study of Drug Resistant Mycobacterium tuberculosis and Its Intra-Host Evolution during Treatment

by Denis Lagutkin, Anna Panova, Anatoly Vinokurov, Alexandra Gracheva, Anastasia Samoilova and Irina Vasilyeva

Microorganisms 2022, 10(7), 1440; https://doi.org/10.3390/microorganisms10071440 - 17 Jul 2022

Cited by 15 | Viewed by 6843

Abstract

The emergence of drug resistant Mycobacterium tuberculosis (MTB) strains has become a global public health problem, while, at the same time, there has been development of new antimicrobial agents. The main goals of this study were to determine new variants associated with drug [...] Read more.

The emergence of drug resistant Mycobacterium tuberculosis (MTB) strains has become a global public health problem, while, at the same time, there has been development of new antimicrobial agents. The main goals of this study were to determine new variants associated with drug resistance in MTB and to observe which polymorphisms emerge in MTB genomes after anti-tuberculosis treatment. We performed whole-genome sequencing of 152 MTB isolates including 70 isolates as 32 series of pre- and post-treatment MTB. Based on genotypes and phenotypic drug susceptibility, we conducted phylogenetic convergence-based genome-wide association study (GWAS) with streptomycin-, isoniazid-, rifampicin-, ethambutol-, fluoroquinolones-, and aminoglycosides-resistant MTB against susceptible ones. GWAS revealed statistically significant associations of SNPs within Rv2820c, cyp123 and indels in Rv1269c, Rv1907c, Rv1883c, Rv2407, Rv3785 genes with resistant MTB phenotypes. Comparisons of serial isolates showed that treatment induced different patterns of intra-host evolution. We found indels within Rv1435c and ppsA that were not lineage-specific. In addition, Beijing-specific polymorphisms within Rv0036c, Rv0678, Rv3433c, and dop genes were detected in post-treatment isolates. The appearance of Rv3785 frameshift insertion in 2 post-treatment strains compared to pre-treatment was also observed. We propose that the insertion within Rv3785, which was a GWAS hit, might affect cell wall biosynthesis and probably mediates a compensatory mechanism in response to treatment. These results may shed light on the mechanisms of MTB adaptation to chemotherapy and drug resistance formation. Full article

(This article belongs to the Special Issue Mycobacterium tuberculosis Infection: Control & Treatment)

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18 pages, 887 KB

Open AccessEditor’s ChoiceArticle

SARS-CoV-2 Amino Acid Mutations Detection in Greek Patients Infected in the First Wave of the Pandemic

by Niki Vassilaki, Konstantinos Papadimitriou, Anastasios Ioannidis, Nikos C. Papandreou, Raphaela S. Milona, Vassiliki A. Iconomidou and Stylianos Chatzipanagiotou

Microorganisms 2022, 10(7), 1430; https://doi.org/10.3390/microorganisms10071430 - 15 Jul 2022

Cited by 2 | Viewed by 4471

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel virus that belongs to the Coronoviridae family, emerged in December 2019, causing the COVID-19 pandemic in March 2020. Unlike previous SARS and Middle East respiratory syndrome (MERS) outbreaks, this virus has a higher transmissibility [...] Read more.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel virus that belongs to the Coronoviridae family, emerged in December 2019, causing the COVID-19 pandemic in March 2020. Unlike previous SARS and Middle East respiratory syndrome (MERS) outbreaks, this virus has a higher transmissibility rate, albeit a lower case fatality rate, which results in accumulation of a significant number of mutations and a faster evolution rate. Genomic studies on the mutation rate of the virus, as well as the identification of mutations that prevail and their impact on disease severity, are of great importance for pandemic surveillance and vaccine and drug development. Here, we aim to identify mutations on the SARS-CoV-2 viral genome and their effect on the proteins they are located in, in Greek patients infected in the first wave of the pandemic. To this end, we perform SARS-CoV-2 amplicon-based NGS sequencing on nasopharyngeal swab samples from Greek patients and bioinformatic analysis of the results. Although SARS-CoV-2 is considered genetically stable, we discover a variety of mutations on the viral genome. In detail, 18 mutations are detected in total on 10 SARS-CoV-2 isolates. The mutations are located on ORF1ab, S protein, M protein, ORF3a and ORF7a. Sixteen are also detected in patients from other regions around the world, and two are identified for the first time in the present study. Most of them result in amino acid substitutions. These substitutions are analyzed using computational tools, and the results indicate minor or major impact on the proteins’ structural stability, which could probably affect viral transmissibility and pathogenesis. The correlation of these variations with the viral load levels is examined, and their implication for disease severity and the biology of the virus are discussed. Full article

(This article belongs to the Section Virology)

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10 pages, 1519 KB

Open AccessEditor’s ChoiceArticle

Complex Trophic Interactions in an Acidophilic Microbial Community

by Guntram Weithoff and Elanor M. Bell

Microorganisms 2022, 10(7), 1340; https://doi.org/10.3390/microorganisms10071340 - 2 Jul 2022

Cited by 8 | Viewed by 3381

Abstract

Extreme habitats often harbor specific communities that differ substantially from non-extreme habitats. In many cases, these communities are characterized by archaea, bacteria and protists, whereas the number of species of metazoa and higher plants is relatively low. In extremely acidic habitats, mostly prokaryotes [...] Read more.

Extreme habitats often harbor specific communities that differ substantially from non-extreme habitats. In many cases, these communities are characterized by archaea, bacteria and protists, whereas the number of species of metazoa and higher plants is relatively low. In extremely acidic habitats, mostly prokaryotes and protists thrive, and only very few metazoa thrive, for example, rotifers. Since many studies have investigated the physiology and ecology of individual species, there is still a gap in research on direct, trophic interactions among extremophiles. To fill this gap, we experimentally studied the trophic interactions between a predatory protist (Actinophrys sol, Heliozoa) and its prey, the rotifers Elosa woralli and Cephalodella sp., the ciliate Urosomoida sp. and the mixotrophic protist Chlamydomonas acidophila (a green phytoflagellate, Chlorophyta). We found substantial predation pressure on all animal prey. High densities of Chlamydomonas acidophila reduced the predation impact on the rotifers by interfering with the feeding behaviour of A. sol. These trophic relations represent a natural case of intraguild predation, with Chlamydomonas acidophila being the common prey and the rotifers/ciliate and A. sol being the intraguild prey and predator, respectively. We further studied this intraguild predation along a resource gradient using Cephalodella sp. as the intraguild prey. The interactions among the three species led to an increase in relative rotifer abundance with increasing resource (Chlamydomonas) densities. By applying a series of laboratory experiments, we revealed the complexity of trophic interactions within a natural extremophilic community. Full article

(This article belongs to the Special Issue Extremophilic Microorganisms and Their Communities)

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15 pages, 2915 KB

Open AccessEditor’s ChoiceArticle

Edwardsiella ictaluri T3SS Effector EseN Modulates Expression of Host Genes Involved in the Immune Response

by Lidiya P. Dubytska, Ranjan Koirala, Azhia Sanchez and Ronald Thune

Microorganisms 2022, 10(7), 1334; https://doi.org/10.3390/microorganisms10071334 - 1 Jul 2022

Cited by 12 | Viewed by 4543

Abstract

The type III secretion system (T3SS) effector EseN is encoded on the Edwardsiella ictaluri chromosome and is homologous to a family of T3SS effector proteins with phosphothreonine lyase activity. Previously we demonstrated that E. ictaluri invasion activates extracellular signal-regulated kinases 1 and 2 [...] Read more.

The type III secretion system (T3SS) effector EseN is encoded on the Edwardsiella ictaluri chromosome and is homologous to a family of T3SS effector proteins with phosphothreonine lyase activity. Previously we demonstrated that E. ictaluri invasion activates extracellular signal-regulated kinases 1 and 2 (ERK1/2) early in the infection, which are subsequently inactivated by EseN. Comparative transcriptomic analysis showed a total of 753 significant differentially expressed genes in head-kidney-derived macrophages (HKDM) infected with an EseN mutant (∆EseN) compared to HKDM infected with wild-type (WT) strains. This data strongly indicates classical activation of macrophages (the M1 phenotype) in response to E. ictaluri infection and a significant role for EseN in the manipulation of this process. Our data also indicates that E. ictaluri EseN is involved in the modulation of pathways involved in the immune response to infection and expression of several transcription factors, including NF-κβ (c-rel and relB), creb3L4, socs6 and foxo3a. Regulation of transcription factors leads to regulation of proinflammatory interleukins (IL-8, IL-12a, IL-15, IL-6) and cyclooxygenase-2 (COX-2) expression. Inhibition of COX-2 mRNA by WT E. ictaluri leads to decreased production of prostaglandin E2 (PGE2), which is the product of COX-2 activity. Collectively, our results indicate that E. ictaluri EseN is an important player in the modulation of host immune responses to E.ictaluri infection. Full article

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

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16 pages, 1249 KB

Open AccessEditor’s ChoiceArticle

Ingenious Action of Vibrio cholerae Neuraminidase Recruiting Additional GM1 Cholera Toxin Receptors for Primary Human Colon Epithelial Cells

by Johanna Detzner, Charlotte Püttmann, Gottfried Pohlentz and Johannes Müthing

Microorganisms 2022, 10(6), 1255; https://doi.org/10.3390/microorganisms10061255 - 20 Jun 2022

Cited by 3 | Viewed by 3675

Abstract

For five decades it has been known that the pentamer of B subunits (choleragenoid) of the cholera toxin (CT) of Vibrio cholerae binds with high preference to the ganglioside GM1 (II³Neu5Ac-Gg4Cer). However, the exact structures of CT-binding GM1 lipoforms of primary [...] Read more.

For five decades it has been known that the pentamer of B subunits (choleragenoid) of the cholera toxin (CT) of Vibrio cholerae binds with high preference to the ganglioside GM1 (II³Neu5Ac-Gg4Cer). However, the exact structures of CT-binding GM1 lipoforms of primary human colon epithelial cells (pHCoEpiCs) have not yet been described in detail. The same holds true for generating further GM1 receptor molecules from higher sialylated gangliosides with a GM1 core through the neuraminidase of V. cholerae. To avoid the artificial incorporation of exogenous gangliosides from animal serum harboring GM1 and higher sialylated ganglio-series gangliosides, pHCoEpiCs were cultured in serum-free medium. Thin-layer chromatography overlay binding assays using a choleragenoid combined with electrospray ionization mass spectrometry revealed GM1 lipoforms with sphingosine (d18:1) as the sole sphingoid base linked to C14:0, C16:0, C18:0 or C20:0 fatty acyl chains forming the ceramide (Cer) moieties of the main choleragenoid-binding GM1 species. Desialylation of GD1a (IV³Neu5Ac,II³Neu5Ac-Gg4Cer) and GT1b (IV³Neu5Ac,II³(Neu5Ac)₂-Gg4Cer) of pHCoEpiCs by V. cholerae neuraminidase was observed. GD1a-derived GM1 species with stable sphingosine (d18:1) and saturated fatty acyl chains varying in chain length from C16:0 up to C22:0 could be identified, indicating the ingenious interplay between CT and the neuraminidase of V. cholerae recruiting additional GM1 receptors of pHCoEpiCs. Full article

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

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10 pages, 302 KB

Open AccessEditor’s ChoiceArticle

Mating Interactions between Schistosoma bovis and S. mansoni and Compatibility of Their F1 Progeny with Biomphalaria glabrata and Bulinus truncatus

by Amos Mathias Onyekwere, Alejandra De Elias-Escribano, Julien Kincaid-Smith, Sarah Dametto, Jean-François Allienne, Anne Rognon, Maria Dolores Bargues and Jérôme Boissier

Microorganisms 2022, 10(6), 1251; https://doi.org/10.3390/microorganisms10061251 - 19 Jun 2022

Cited by 8 | Viewed by 4482

Abstract

Contrary to the majority of other Trematoda, Schistosoma species are gonochoric. Consequently, in endemic areas where several schistosome species overlap and can co-infect the same definitive host, there may be frequent opportunities for interspecific pairing. Our experimental study provides novel insight on the [...] Read more.

Contrary to the majority of other Trematoda, Schistosoma species are gonochoric. Consequently, in endemic areas where several schistosome species overlap and can co-infect the same definitive host, there may be frequent opportunities for interspecific pairing. Our experimental study provides novel insight on the pairing behavior between Schistosoma bovis and S. mansoni in mixed infections in mice. We used six mate choice experiments to assess mating interactions between the two schistosome species. We show that mating between the two Schistosoma species is not random and that S. mansoni exhibits greater mate recognition compared to S. bovis. We also performed reciprocal crosses (male S. mansoni × female S. bovis) and (female S. mansoni × male S. bovis) that produce active swimming miracidia. These miracidia were genotyped by ITS2 sequencing and proposed for mollusc infection. Molecular analyses show that all the miracidia are parthenogenetically produced (i.e., their harbor the mother ITS2 genotype) and as a consequence can only infect the mollusc of the maternal species. Offspring produced by male S. mansoni × female S. bovis pairing can only infect Bulinus truncatus whereas offspring produced by female S. mansoni × male S. bovis can only infect Biomphalaria glabrata snails. Evolutionary and epidemiological consequences are discussed. Full article

(This article belongs to the Section Parasitology)

12 pages, 571 KB

Open AccessEditor’s ChoiceArticle

Influence on Soybean Aphid by the Tripartite Interaction between Soybean, a Rhizobium Bacterium, and an Arbuscular Mycorrhizal Fungus

by Élisée Emmanuel Dabré, Mohamed Hijri and Colin Favret

Microorganisms 2022, 10(6), 1196; https://doi.org/10.3390/microorganisms10061196 - 11 Jun 2022

Cited by 19 | Viewed by 4922

Abstract

The inoculation of arbuscular mycorrhizal (AM) fungi and rhizobia in legumes has been proven to increase plant growth and yield. To date, studies of the effects of these interactions on phytophagous insects have shown them to be context-dependent depending on the inoculant strain, [...] Read more.

The inoculation of arbuscular mycorrhizal (AM) fungi and rhizobia in legumes has been proven to increase plant growth and yield. To date, studies of the effects of these interactions on phytophagous insects have shown them to be context-dependent depending on the inoculant strain, the plant, and the insect species. Here, we document how a symbiosis involving an AM fungus, Rhizophagus irregularis; a rhizobium, Bradyrhizobium japonicum; and soybean, Glycine max, influences the soybean aphid, Aphis glycines. Soybean co-inoculated with the AM fungus–rhizobium pair increased the plant’s biomass, nodulation, mycorrhizal colonization, nitrogen, and carbon concentrations, but decreased phosphorus concentration. Similar effects were observed with rhizobium alone, with the exception that root biomass was unaffected. With AM fungus alone, we only observed an increase in mycorrhizal colonization and phosphorus concentration. The aphids experienced an increased reproductive rate with the double inoculation, followed by rhizobium alone, whereas no effect was observed with the AM fungus. The size of individual aphids was not affected. Furthermore, we found positive correlation between nitrogen concentration and aphid population density. Our results confirm that co-inoculation of two symbionts can enhance both plant and phytophagous insect performance beyond what either symbiont can contribute alone. Full article

(This article belongs to the Special Issue Microbial-Based Plant Biostimulants)

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19 pages, 7292 KB

Open AccessEditor’s ChoiceArticle

Complete Genome Analysis of Rhodococcus opacus S8 Capable of Degrading Alkanes and Producing Biosurfactant Reveals Its Genetic Adaptation for Crude Oil Decomposition

by Yanina Delegan, Kirill Petrikov, Ekaterina Frantsuzova, Natalia Rudenko, Viktor Solomentsev, Nataliya Suzina, Vasili Travkin and Inna P. Solyanikova

Microorganisms 2022, 10(6), 1172; https://doi.org/10.3390/microorganisms10061172 - 7 Jun 2022

Cited by 11 | Viewed by 5311

Abstract

Microorganisms capable of decomposing hydrophobic substrates in cold climates are of considerable interest both in terms of studying adaptive reactions to low temperatures and in terms of their application in biotechnologies for cleaning up oil spills in a crude-oil polluted soil. The aim [...] Read more.

Microorganisms capable of decomposing hydrophobic substrates in cold climates are of considerable interest both in terms of studying adaptive reactions to low temperatures and in terms of their application in biotechnologies for cleaning up oil spills in a crude-oil polluted soil. The aim of this work was to investigate the genome of Rhodococcus opacus S8 and explore behavior traits of this strain grown in the presence of hexadecane. The genome size of strain S8 is 8.78 Mb, of which the chromosome size is 7.75 Mb. The S8 strain contains 2 circular plasmids of 135 kb and 105 kb and a linear plasmid with a size of 788 kb. The analysis of the genome revealed the presence of genes responsible for the degradation of alkanes and synthesis of biosurfactants. The peculiarities of morphology of microbial cells when interacting with a hydrophobic substrate were revealed. An adaptive mechanism responsible in the absence of oxygen for maintaining the process of degradation of hexadecane is discussed. The data obtained show that the strain S8 has great potential to be used in biotechnologies. Full article

(This article belongs to the Section Environmental Microbiology)

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19 pages, 1579 KB

Open AccessEditor’s ChoiceArticle

Microbial Interrelationships across Sites of Breastfeeding Mothers and Infants at 6 Weeks Postpartum

by Erin C. Davis, Mei Wang and Sharon M. Donovan

Microorganisms 2022, 10(6), 1155; https://doi.org/10.3390/microorganisms10061155 - 2 Jun 2022

Cited by 15 | Viewed by 4174

Abstract

Infancy is a critical life stage for the establishment of the gut microbiome. Human milk contains a unique microbial ecosystem that serves as a continuous source of commensal bacteria for the infant. However, the origin of the human milk microbiota, how it is [...] Read more.

Infancy is a critical life stage for the establishment of the gut microbiome. Human milk contains a unique microbial ecosystem that serves as a continuous source of commensal bacteria for the infant. However, the origin of the human milk microbiota, how it is influenced by breastfeeding exclusivity, and its role in infant gut microbiota assembly are not clear. To interrogate these questions, we examined the relationships among fecal, oral, breast skin, and human milk microbiota of 33 exclusively breastfeeding (EBF) and mixed-feeding (MF; human milk + infant formula) mother–infant pairs at 6 weeks postpartum. Here, we show that MF infants have a significantly more diverse oral microbiome comprised of lower relative abundances of Streptococcus and Gemella and higher abundances of Veillonella. Using both SourceTracker2 and FEAST, we demonstrate breast skin and infant saliva as the principal contributing sources to the human milk microbiota. Of the sampled sites, human milk and maternal stool were predicted to contribute the largest fraction to the infant fecal microbiome, but the majority of the community was estimated to arise from unknown sources. Lastly, we identified twenty-one significant co-occurrence relationships between bacteria in human milk and on other maternal and infant body sites. These results demonstrate several unique microbial interrelationships between breastfeeding dyads, providing insight into potential mechanisms of microbial assembly in early life. Full article

(This article belongs to the Special Issue Novel Insights into the Infant Gut Microbiome and Host–Microbe Interactions)

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10 pages, 1043 KB

Open AccessEditor’s ChoiceArticle

Fecal Microbiome Differences in Angus Steers with Differing Feed Efficiencies during the Feedlot-Finishing Phase

by Jeferson M. Lourenco, Christina B. Welch, Taylor R. Krause, Michael A. Wieczorek, Francis L. Fluharty, Michael J. Rothrock, T. Dean Pringle and Todd R. Callaway

Microorganisms 2022, 10(6), 1128; https://doi.org/10.3390/microorganisms10061128 - 31 May 2022

Cited by 18 | Viewed by 4058

Abstract

The gastrointestinal microbiota of cattle is important for feedstuff degradation and feed efficiency determination. This study evaluated the fecal microbiome of Angus steers with distinct feed efficiencies during the feedlot-finishing phase. Angus steers (n = 65), fed a feedlot-finishing diet for 82 [...] Read more.

The gastrointestinal microbiota of cattle is important for feedstuff degradation and feed efficiency determination. This study evaluated the fecal microbiome of Angus steers with distinct feed efficiencies during the feedlot-finishing phase. Angus steers (n = 65), fed a feedlot-finishing diet for 82 days, had growth performance metrics evaluated. Steers were ranked based upon residual feed intake (RFI), and the 5 lowest RFI (most efficient) and 5 highest RFI (least efficient) steers were selected for evaluation. Fecal samples were collected on 0-d and 82-d of the finishing period and microbial DNA was extracted and evaluated by 16S rRNA gene sequencing. During the feedlot trial, inefficient steers had decreased (p = 0.02) Ruminococcaceae populations and increased (p = 0.01) Clostridiaceae populations. Conversely, efficient steers had increased Peptostreptococcaceae (p = 0.03) and Turicibacteraceae (p = 0.01), and a trend for decreased Proteobacteria abundance (p = 0.096). Efficient steers had increased microbial richness and diversity during the feedlot period, which likely resulted in increased fiber-degrading enzymes in their hindgut, allowing them to extract more energy from the feed. Results suggest that cattle with better feed efficiency have greater diversity of hindgut microorganisms, resulting in more enzymes available for digestion, and improving energy harvest in the gut of efficient cattle. Full article

(This article belongs to the Special Issue The Microbial Population of the Gastrointestinal Tract of Animals: Impacts on Host Physiology)

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17 pages, 13160 KB

Open AccessEditor’s ChoiceArticle

Differential Viral Genome Diversity of Healthy and RSS-Affected Broiler Flocks

by Jakub Kubacki, Weihong Qi and Cornel Fraefel

Microorganisms 2022, 10(6), 1092; https://doi.org/10.3390/microorganisms10061092 - 25 May 2022

Cited by 18 | Viewed by 3946

Abstract

The intestinal virus community contributes to health and disease. Runting and stunting syndrome (RSS) is associated with enteric viruses and leads to economic losses in the poultry industry. However, many viruses that potentially cause this syndrome have also been identified in healthy animals. [...] Read more.

The intestinal virus community contributes to health and disease. Runting and stunting syndrome (RSS) is associated with enteric viruses and leads to economic losses in the poultry industry. However, many viruses that potentially cause this syndrome have also been identified in healthy animals. To determine the difference in the virome of healthy and diseased broilers, samples from 11 healthy and 17 affected broiler flocks were collected at two time points and analyzed by Next-Generation Sequencing. Virus genomes of Parvoviridae, Astroviridae, Picornaviridae, Caliciviridae, Reoviridae, Adenoviridae, Coronaviridae, and Smacoviridae were identified at various days of poultry production. De novo sequence analysis revealed 288 full or partial avian virus genomes, of which 97 belonged to the novel genus Chaphamaparvovirus. This study expands the knowledge of the diversity of enteric viruses in healthy and RSS-affected broiler flocks and questions the association of some viruses with the diseases. Full article

(This article belongs to the Special Issue Viral Metagenomic Analysis in Animals)

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17 pages, 1765 KB

Open AccessEditor’s ChoiceArticle

Fungal Diversity in Two Wastewater Treatment Plants in North Italy

by Simone Buratti, Carolina Elena Girometta, Rebecca Michela Baiguera, Barbara Barucco, Marco Bernardi, Giuseppe De Girolamo, Maura Malgaretti, Desdemona Oliva, Anna Maria Picco and Elena Savino

Microorganisms 2022, 10(6), 1096; https://doi.org/10.3390/microorganisms10061096 - 25 May 2022

Cited by 25 | Viewed by 4354

Abstract

In urban wastewater treatment plants, bacteria lead the biological component of the depuration process, but the microbial community is also rich in fungi (mainly molds, yeasts and pseudo-yeasts), whose taxonomical diversity and relative frequency depend on several factors, e.g., quality of wastewater input, [...] Read more.

In urban wastewater treatment plants, bacteria lead the biological component of the depuration process, but the microbial community is also rich in fungi (mainly molds, yeasts and pseudo-yeasts), whose taxonomical diversity and relative frequency depend on several factors, e.g., quality of wastewater input, climate, seasonality, and depuration stage. By joining morphological and molecular identification, we investigated the fungal diversity in two different plants for the urban wastewater treatment in the suburbs of the two major cities in Lombardia, the core of industrial and commercial activities in Italy. This study presents a comparison of the fungal diversity across the depuration stages by applying the concepts of α-, β- and ζ-diversity. Eurotiales (mainly with Aspergillus and Penicillium), Trichosporonales (Trichosporon sensu lato), Saccharomycetales (mainly with Geotrichum) and Hypocreales (mainly with Fusarium and Trichoderma) are the most represented fungal orders and genera in all the stages and both the plants. The two plants show different trends in α-, β- and ζ-diversity, despite the fact that they all share a crash during the secondary sedimentation and turnover across the depuration stages. This study provides an insight on which taxa potentially contribute to each depuration stage and/or keep viable propagules in sludges after the collection from the external environment. Full article

(This article belongs to the Special Issue Fungal Biodiversity for Bioremediation)

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16 pages, 1882 KB

Open AccessEditor’s ChoiceArticle

Enhanced Immunogenicity of Inactivated Dengue Vaccines by Novel Polysaccharide-Based Adjuvants in Mice

by Shuenn-Jue Wu, Dan Ewing, Appavu K. Sundaram, Hua-Wei Chen, Zhaodong Liang, Ying Cheng, Vihasi Jani, Peifang Sun, Gregory D. Gromowski, Rafael A. De La Barrera, Megan A. Schilling, Nikolai Petrovsky, Kevin R. Porter and Maya Williams

Microorganisms 2022, 10(5), 1034; https://doi.org/10.3390/microorganisms10051034 - 16 May 2022

Cited by 6 | Viewed by 5434

Abstract

Dengue fever, caused by any of four dengue viruses (DENV1-4), is a major global burden. Currently, there is no effective vaccine that prevents infection in dengue naïve populations. We tested the ability of two novel adjuvants (Advax-PEI and Advax-2), using aluminum hydroxide (alum) [...] Read more.

Dengue fever, caused by any of four dengue viruses (DENV1-4), is a major global burden. Currently, there is no effective vaccine that prevents infection in dengue naïve populations. We tested the ability of two novel adjuvants (Advax-PEI and Advax-2), using aluminum hydroxide (alum) as control, to enhance the immunogenicity of formalin- or psoralen-inactivated (PIV or PsIV) DENV2 vaccines in mice. Mice were vaccinated on days 0 and 30, and serum samples were collected on days 30, 60, 90, and 101. Neutralizing antibodies were determined by microneutralization (MN) assays, and the geometric mean 50% MN (MN₅₀) titers were calculated. For the PIV groups, after one dose MN₅₀ titers were higher in the novel adjuvant groups compared to the alum control, while MN₅₀ titers were comparable between the adjuvant groups after the second dose. For the PsIV groups, both novel adjuvants induced higher MN₅₀ titers than the alum control after the second dose. Spleen cells were collected on days 45 and 101 for enzyme-linked immunospot (ELISPOT) for IFNγ and IL4. Both PIV and PsIV groups elicited different degrees of IFNγ and IL4 responses. Overall, Advax-2 gave the best responses just ahead of Advax-PEI. Given Advax-2’s extensive human experience in other vaccine applications, it will be pursued for further development. Full article

(This article belongs to the Special Issue Arboviruses)

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15 pages, 1036 KB

Open AccessEditor’s ChoiceArticle

Fungi Can Be More Effective than Bacteria for the Bioremediation of Marine Sediments Highly Contaminated with Heavy Metals

by Filippo Dell’Anno, Eugenio Rastelli, Emanuela Buschi, Giulio Barone, Francesca Beolchini and Antonio Dell’Anno

Microorganisms 2022, 10(5), 993; https://doi.org/10.3390/microorganisms10050993 - 9 May 2022

Cited by 53 | Viewed by 9031

Abstract

The contamination of coastal marine sediments with heavy metals (HMs) is a widespread phenomenon that requires effective remediation actions. Bioremediation based on the use of bacteria is an economically and environmentally sustainable effective strategy for reducing HM contamination and/or toxicity in marine sediments. [...] Read more.

The contamination of coastal marine sediments with heavy metals (HMs) is a widespread phenomenon that requires effective remediation actions. Bioremediation based on the use of bacteria is an economically and environmentally sustainable effective strategy for reducing HM contamination and/or toxicity in marine sediments. However, information on the efficiency of marine-derived fungi for HM decontamination of marine sediments is still largely lacking, despite evidence of the performance of terrestrial fungal strains on other contaminated matrixes (e.g., soils, freshwater sediments, industrial wastes). Here, we carried out for the first time an array of parallel laboratory experiments by using different combinations of chemical and microbial amendments (including acidophilic autotrophic and heterotrophic bacteria, as well as filamentous marine fungi) for the bioremediation of highly HM-contaminated sediments of the Portman Bay (NW Mediterranean Sea), an area largely affected by long-term historical discharges of mine tailings. Our results indicate that the bioleaching performance of metals from the sediment is based on the addition of fungi (Aspergillus niger and Trichoderma sp.), either alone or in combination with autotrophic bacteria, was higher when compared to other treatments. In particular, fungal addition allowed obtaining bioleaching yields for As eight times higher than those by chemical treatments and double compared with the addition of bacteria alone. Moreover, in our study, the fungal addition was the only treatment allowing effective bioleaching of otherwise not mobile fractions of Zn and Cd, thus overtaking bacterial treatments. We found that the lower the sediment pH reached by the experimental conditions, as in the case of fungal addition, the higher the solubilization yield of metals, suggesting that the specific metabolic features of A. niger and Trichoderma sp. enable lowering sediment pH and enhance HM bioleaching. Overall, our findings indicate that fungi can be more effective than acidophilic autotrophic and heterotrophic bacteria in HM bioleaching, and as such, their use can represent a promising and efficient strategy for the bioremediation of marine sediments highly contaminated with heavy metals. Full article

(This article belongs to the Section Environmental Microbiology)

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9 pages, 1969 KB

Open AccessEditor’s ChoiceArticle

Changes in Invasive Neisseria meningitidis and Haemophilus influenzae Infections in France during the COVID-19 Pandemic

by Ala-Eddine Deghmane and Muhamed-Kheir Taha

Microorganisms 2022, 10(5), 907; https://doi.org/10.3390/microorganisms10050907 - 26 Apr 2022

Cited by 42 | Viewed by 6259

Abstract

BackgroundSince the appearance of COVID-19 in January 2020, invasive bacterial infections have decreased significantly worldwide. However, alterations in age and sex distributions, clinical forms, phenotypes, and genotypes of isolates have not been analyzed. Our goal is to present and discuss these data [...] Read more.

BackgroundSince the appearance of COVID-19 in January 2020, invasive bacterial infections have decreased significantly worldwide. However, alterations in age and sex distributions, clinical forms, phenotypes, and genotypes of isolates have not been analyzed. Our goal is to present and discuss these data considering the current COVID-19 pandemic situation. Methods: The data of the national reference center for meningococci and Haemophilus influenzae in France were mined to examine the above aspects of invasive bacterial infection before (2018–2019) and after (2020–2021) the COVID-19 pandemic. Detailed epidemiological, clinical, and microbiological data were collected, and whole genome sequencing was carried out on meningococcal isolates (n = 1466). Results: In addition to the overall decline in the number of cases, various changes in age, sex, and phenotypes of isolates were also noted. As for N. meningitidis, more cases were observed in adults, as well as more invasive pneumopathies. Furthermore, fewer hyperinvasive meningococcal genotypes have circulated since COVID-19 emerged. The situation has been different for H. influenzae, as the number of invasive cases among adults decreased due to a reduction in non-typeable isolates. In contrast, cases due to serotypeable isolates, particularly serotypes a and b, increased in children <5 years-old. Conclusions: It is possible that measures implemented to stop COVID-19 may have reduced the circulation of N. meningitidis and H. influenzae isolates, but to a variable extent. This may be due to differences in circulation between these two species according to age groups. Vaccination schedules against these two species may have also influenced the evolution of these invasive bacterial infections since the emergence of the COVID-19 pandemic. Full article

(This article belongs to the Special Issue The COVID-19 Pandemic and Bacterial Infections: Microbiological and Clinical Aspects)

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23 pages, 1114 KB

Open AccessEditor’s ChoiceArticle

Comparative Genomics Applied to Systematically Assess Pathogenicity Potential in Shiga Toxin-Producing Escherichia coli O145:H28

by Michelle Qiu Carter, Nicole Laniohan, Chien-Chi Lo and Patrick S. G. Chain

Microorganisms 2022, 10(5), 866; https://doi.org/10.3390/microorganisms10050866 - 21 Apr 2022

Cited by 7 | Viewed by 4266

Abstract

Shiga toxin-producing Escherichia coli (STEC) O145:H28 can cause severe disease in humans and is a predominant serotype in STEC O145 environmental isolates. Here, comparative genomics was applied to a set of clinical and environmental strains to systematically evaluate the pathogenicity potential in environmental [...] Read more.

Shiga toxin-producing Escherichia coli (STEC) O145:H28 can cause severe disease in humans and is a predominant serotype in STEC O145 environmental isolates. Here, comparative genomics was applied to a set of clinical and environmental strains to systematically evaluate the pathogenicity potential in environmental strains. While the core genes-based tree separated all O145:H28 strains from the non O145:H28 reference strains, it failed to segregate environmental strains from the clinical. In contrast, the accessory genes-based tree placed all clinical strains in the same clade regardless of their genotypes or serotypes, apart from the environmental strains. Loss-of-function mutations were common in the virulence genes examined, with a high frequency in genes related to adherence, autotransporters, and the type three secretion system. Distinct differences in pathogenicity islands LEE, OI-122, and OI-57, the acid fitness island, and the tellurite resistance island were detected between the O145:H28 and reference strains. A great amount of genetic variation was detected in O145:H28, which was mainly attributed to deletions, insertions, and gene acquisition at several chromosomal “hot spots”. Our study demonstrated a distinct virulence gene repertoire among the STEC O145:H28 strains originating from the same geographical region and revealed unforeseen contributions of loss-of-function mutations to virulence evolution and genetic diversification in STEC. Full article

(This article belongs to the Special Issue Know Your Enemy: Improved Understanding, Detection, Control, and Therapy for Shiga Toxin-Producing Escherichia coli Infection)

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12 pages, 763 KB

Open AccessEditor’s ChoiceArticle

Road Salt versus Urban Snow Effects on Lake Microbial Communities

by Isabelle B. Fournier, Connie Lovejoy and Warwick F. Vincent

Microorganisms 2022, 10(4), 803; https://doi.org/10.3390/microorganisms10040803 - 12 Apr 2022

Cited by 11 | Viewed by 3656

Abstract

Freshwater salinization is an ongoing concern for north temperate lakes; however, little is known about its impacts on microbial communities, particularly for bacteria. We tested the hypotheses that road de-icing salt induces changes in the microbial community structure of lake plankton, and that [...] Read more.

Freshwater salinization is an ongoing concern for north temperate lakes; however, little is known about its impacts on microbial communities, particularly for bacteria. We tested the hypotheses that road de-icing salt induces changes in the microbial community structure of lake plankton, and that changes due to chloride would differ from those due to urban snowmelt because of additional chemicals in the snowmelt. In a laboratory incubator experiment, an overwintering plankton community in lake water was exposed for two weeks to either NaCl or municipal road snow with the same level of chloride. Microbial community structure as determined by 16S (prokaryotes) and 18S (eukaryotes) rRNA transcript analysis showed changes in response to the chloride-only enrichment, with some rare taxa becoming more prominent. Consistent with our hypothesis, the salt and the snow treatments induced different community changes. These results indicate that ecotoxicology assays based on a single salt addition may not reflect the in situ effects of salt-contaminated urban snow, and that the combined chemical effects of urban snowmelt require direct testing. Full article

(This article belongs to the Section Environmental Microbiology)

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8 pages, 362 KB

Open AccessEditor’s ChoiceArticle

Outbreak of MRSA in a Gynecology/Obstetrics Department during the COVID-19 Pandemic: A Cautionary Tale

by Mareike Möllers, Marie-Kristin von Wahlde, Franziska Schuler, Alexander Mellmann, Christian Böing, Vera Schwierzeck, Julia Sophie Schneider and Stefanie Kampmeier

Microorganisms 2022, 10(4), 689; https://doi.org/10.3390/microorganisms10040689 - 23 Mar 2022

Cited by 13 | Viewed by 5886

Abstract

Since March 2020, the COVID-19 pandemic forced hospitals worldwide to intensify their infection control measures to prevent health care-associated transmission of SARS-CoV-2. The correct use of personal protective equipment, especially the application of masks, was quickly identified as priority to reduce transmission with [...] Read more.

Since March 2020, the COVID-19 pandemic forced hospitals worldwide to intensify their infection control measures to prevent health care-associated transmission of SARS-CoV-2. The correct use of personal protective equipment, especially the application of masks, was quickly identified as priority to reduce transmission with this pathogen. Here, we report a nosocomial cluster of methicillin-resistant Staphylococcus aureus (MRSA) that occurred during the COVID-19 pandemic in a gynecology/obstetrics department, despite these intensified contact precautions. Five MRSA originating from clinical samples after surgical intervention led to an outbreak investigation. Firstly, this included environmental sampling of the operation theatre (OT) and, secondly, a point prevalence screening of patients and health care workers (HCW). All detected MRSA were subjected to whole genome sequencing (WGS) and isolate relatedness was determined using core genome multilocus sequence typing (cgMLST). WGS revealed one MRSA cluster with genetically closely related five patient and two HCW isolates differing in a single cgMLST allele at maximum. The outbreak was terminated after implementation of infection control bundle strategies. Although contact precaution measures, which are also part of MRSA prevention bundle strategies, were intensified during the COVID-19 pandemic, this MRSA outbreak could take place. This illustrates the importance of adherence to classical infection prevention strategies. Full article

(This article belongs to the Special Issue Antimicrobial Resistance and Outbreaks Due to Multidrug-resistant Bacteria in Hospitalized COVID-19 Patients)

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15 pages, 1240 KB

Open AccessEditor’s ChoiceArticle

Colonization of Dogs and Their Owners with Staphylococcus aureus and Staphylococcus pseudintermedius in Households, Veterinary Practices, and Healthcare Facilities

by Christiane Cuny, Franziska Layer-Nicolaou, Robert Weber, Robin Köck and Wolfgang Witte

Microorganisms 2022, 10(4), 677; https://doi.org/10.3390/microorganisms10040677 - 22 Mar 2022

Cited by 51 | Viewed by 6675

Abstract

There are uncertainties with respect to the transmission of methicillin-susceptible and methicillin-resistant Staphylococcus aureus (MSSA and MRSA) and Staphylococcus pseudintermedius between dogs and humans. In this study, we investigated concomitant nasal colonization of dogs and humans in three cohorts. Cohort I, households owning [...] Read more.

There are uncertainties with respect to the transmission of methicillin-susceptible and methicillin-resistant Staphylococcus aureus (MSSA and MRSA) and Staphylococcus pseudintermedius between dogs and humans. In this study, we investigated concomitant nasal colonization of dogs and humans in three cohorts. Cohort I, households owning dogs: In 42 of 84 households, 66 humans (36.9%) and 10 dogs (8.9%) carried S. aureus. MRSA, attributed to sequence type (ST) 22 and ST130, were detected in two (1.1%) of the humans but in none of the dogs. Typing by means of spa-typing and whole-genome sequencing (WGS) indicated eight transmissions of S. aureus between humans and dogs in 8 of 42 (19.0%) households with human S. aureus carriers, whereas in 11 of 38 (29.0%) households with ≥two persons and S. aureus colonization of humans, 15 human-to-human transmissions were observed (p = 0.43). S. pseudintermedius was isolated from 42 dogs (37.5%), but from only one human (0.6%). In this case, WGS-based typing indicated strong relatedness of this isolate with a canine isolate from the same household. Cohort II, dogs and their owners visiting a veterinary practice: Among 17 humans and 17 dogs attending a veterinary practice, MSSA was detected in three humans and two dogs, and S. pseudintermedius in only six dogs. Cohort III, dogs used for animal-assisted interventions in human healthcare facilities and their owners: MSSA was obtained in 1 of 59 dogs (1.7%) and in 17 of 60 (28.3%) of the dog owners, while S. pseudintermedius was isolated from seven (12%) dogs and one (1.7%) human owner. We conclude that the risk of exchanging S. aureus/MRSA between humans and dogs is higher than that for S. pseudintermedius. Full article

(This article belongs to the Special Issue Multi-Drug Resistant (MDR) Gram-Positive Bacterial Infections)

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13 pages, 2502 KB

Open AccessEditor’s ChoiceArticle

Typing of the Gut Microbiota Community in Japanese Subjects

by Tomohisa Takagi, Ryo Inoue, Akira Oshima, Hiroshi Sakazume, Kenta Ogawa, Tomo Tominaga, Yoichi Mihara, Takeshi Sugaya, Katsura Mizushima, Kazuhiko Uchiyama, Yoshito Itoh and Yuji Naito

Microorganisms 2022, 10(3), 664; https://doi.org/10.3390/microorganisms10030664 - 20 Mar 2022

Cited by 46 | Viewed by 15728

Abstract

Gut microbiota are involved in both host health and disease and can be stratified based on bacteriological composition. However, gut microbiota clustering data are limited for Asians. In this study, fecal microbiota of 1803 Japanese subjects, including 283 healthy individuals, were analyzed by [...] Read more.

Gut microbiota are involved in both host health and disease and can be stratified based on bacteriological composition. However, gut microbiota clustering data are limited for Asians. In this study, fecal microbiota of 1803 Japanese subjects, including 283 healthy individuals, were analyzed by 16S rRNA sequencing and clustered using two models. The association of various diseases with each community type was also assessed. Five and fifteen communities were identified using partitioning around medoids (PAM) and the Dirichlet multinominal mixtures model, respectively. Bacteria exhibiting characteristically high abundance among the PAM-identified types were of the family Ruminococcaceae (Type A) and genera Bacteroides, Blautia, and Faecalibacterium (Type B); Bacteroides, Fusobacterium, and Proteus (Type C); and Bifidobacterium (Type D), and Prevotella (Type E). The most noteworthy community found in the Japanese subjects was the Bifidobacterium-rich community. The odds ratio based on type E, which had the largest population of healthy subjects, revealed that other types (especially types A, C, and D) were highly associated with various diseases, including inflammatory bowel disease, functional gastrointestinal disorder, and lifestyle-related diseases. Gut microbiota community typing reproducibly identified organisms that may represent enterotypes peculiar to Japanese individuals and that are partly different from those of indivuals from Western countries. Full article

(This article belongs to the Special Issue State-of-the-Art Gut Microbiota Research in Asia)

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15 pages, 15221 KB

Open AccessEditor’s ChoiceArticle

Localization of the Swainsonine-Producing Chaetothyriales Symbiont in the Seed and Shoot Apical Meristem in Its Host Ipomoea carnea

by Marwa Neyaz, Dale R. Gardner, Rebecca Creamer and Daniel Cook

Microorganisms 2022, 10(3), 545; https://doi.org/10.3390/microorganisms10030545 - 2 Mar 2022

Cited by 12 | Viewed by 4172

Abstract

Several species of fungi from the orders Chaetothyriales and Pleosporales have been reported to produce swainsonine and be associated as symbionts with plants of the Convolvulaceae and Fabaceae, respectively. An endosymbiont belonging to the Chaetothyriales produces swainsonine and grows as an epibiont on [...] Read more.

Several species of fungi from the orders Chaetothyriales and Pleosporales have been reported to produce swainsonine and be associated as symbionts with plants of the Convolvulaceae and Fabaceae, respectively. An endosymbiont belonging to the Chaetothyriales produces swainsonine and grows as an epibiont on the adaxial leaf surfaces of Ipomoea carnea, but how the symbiont passes through plant growth and development is unknown. Herein, different types of microscopy were used to localize the symbiont in seeds and in cross sections of plant parts. The symbiont was found in several tissues including the hilum, the sclereids, and the hypocotyl of seeds. In five-day old seedlings and mature plants, the symbiont was found in the shoot apical meristem (SAM) and the adaxial surface of immature folded leaves. The mycelia generally formed a close association with peltate glandular trichomes. This report provides further data explaining the relationship between the seed transmitted Chaetothyriales symbiont and Ipomoea carnea. These results provide a possible explanation for how this symbiont, and others like Periglandula may persist and are transmitted over time. Full article

(This article belongs to the Section Plant Microbe Interactions)

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17 pages, 2412 KB

Open AccessEditor’s ChoiceArticle

Persistent Cutaneous Leishmania major Infection Promotes Infection-Adapted Myelopoiesis

by Fabio Luiz Bandeira Ferreira, Olivier Séguin, Albert Descoteaux and Krista M. Heinonen

Microorganisms 2022, 10(3), 535; https://doi.org/10.3390/microorganisms10030535 - 28 Feb 2022

Cited by 8 | Viewed by 5161

Abstract

Hematopoietic stem/progenitor cells (HSPC) are responsible for the generation of most immune cells throughout the lifespan of the organism. Inflammation can activate bone marrow HSPCs, leading to enhanced myelopoiesis to replace cells, such as neutrophils, which are attracted to inflamed tissues. We have [...] Read more.

Hematopoietic stem/progenitor cells (HSPC) are responsible for the generation of most immune cells throughout the lifespan of the organism. Inflammation can activate bone marrow HSPCs, leading to enhanced myelopoiesis to replace cells, such as neutrophils, which are attracted to inflamed tissues. We have previously shown that HSPC activation promotes parasite persistence and expansion in experimental visceral leishmaniasis through the increased production of permissive monocytes. However, it is not clear if the presence of the parasite in the bone marrow was required for infection-adapted myelopoiesis. We therefore hypothesized that persistent forms of Leishmania major (cutaneous leishmaniasis) could also activate HSPCs and myeloid precursors in the C57Bl/6 mouse model of intradermal infection in the ear. The accrued influx of myeloid cells to the lesion site corresponded to an increase in myeloid-biased HSPCs in the bone marrow and spleen in mice infected with a persistent strain of L. major, together with an increase in monocytes and monocyte-derived myeloid cells in the spleen. Analysis of the bone marrow cytokine and chemokine environment revealed an attenuated type I and type II interferon response in the mice infected with the persistent strain compared to the self-healing strain, while both strains induced a rapid upregulation of myelopoietic cytokines, such as IL-1β and GM-CSF. These results demonstrate that an active infection in the bone marrow is not necessary for the induction of infection-adapted myelopoiesis, and underline the importance of considering alterations to the bone marrow output when analyzing in vivo host-pathogen interactions. Full article

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

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14 pages, 5628 KB

Open AccessEditor’s ChoiceArticle

Unamplified, Long-Read Metagenomic Sequencing Approach to Close Endosymbiont Genomes of Low-Biomass Insect Populations

by Joseph R. Petrone, Alam Muñoz-Beristain, Paula Rios Glusberger, Jordan T. Russell and Eric W. Triplett

Microorganisms 2022, 10(3), 513; https://doi.org/10.3390/microorganisms10030513 - 26 Feb 2022

Cited by 6 | Viewed by 6215

Abstract

With the current advancements in DNA sequencing technology, the limiting factor in long-read metagenomic assemblies is now the quantity and quality of input DNA. Although these requirements can be met through the use of axenic bacterial cultures or large amounts of biological material, [...] Read more.

With the current advancements in DNA sequencing technology, the limiting factor in long-read metagenomic assemblies is now the quantity and quality of input DNA. Although these requirements can be met through the use of axenic bacterial cultures or large amounts of biological material, insect systems that contain unculturable bacteria or that contain a low amount of available DNA cannot fully utilize the benefits of third-generation sequencing. The citrus greening disease insect vector Diaphorina citri is an example that exhibits both of these limitations. Although endosymbiont genomes have mostly been closed after the short-read sequencing of amplified template DNA, creating de novo long-read genomes from the unamplified DNA of an insect population may benefit communities using bioinformatics to study insect pathosystems. Here all four genomes of the infected D. citri microbiome were sequenced to closure using unamplified template DNA and two long-read sequencing technologies. Avoiding amplification bias and using long reads to assemble the bacterial genomes allowed for the circularization of the Wolbachia endosymbiont of Diaphorina citri for the first time and paralleled the annotation context of all four reference genomes without utilizing a traditional hybrid assembly. The strategies detailed here are suitable for the sequencing of other insect systems for which the input DNA, time, and cost are an issue. Full article

(This article belongs to the Section Environmental Microbiology)

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