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Ivan Rychlik – One of the best experts on this subject based on the ideXlab platform.

  • Whole genome sequencing and function prediction of 133 gut Anaerobes isolated from chicken caecum in pure cultures
    BMC Genomics, 2018
    Co-Authors: Matej Medvecky, Darina Cejkova, Ondrej Polansky, Daniela Karasova, Tereza Kubasova, Alois Cizek, Ivan Rychlik
    Abstract:

    Background In order to start to understand the function of individual members of gut micrmicrobiota, we cultured, sequenced and analysed bacterial Anaerobes from chicken caecum. Results Altogether 204 isolates from chicken caecum were obtained in pure cultures using Wilkins-Chalgren anaerobe agar and anaerobic growth conditions. Genomes of all the isolates were determined using the NextSeq platform and subjected to bioinformatic analysis. Among 204 sequenced isolates we identified 133 different strains belonging to seven different phyla – Firmicutes , Bacteroidetes , Actinobacteria , Proteobacteria , Verrucomicrobia , Elusimicrobia and Synergistetes . Genome sizes ranged from 1.51 Mb in Elusimicrobium minutum to 6.70 Mb in Bacteroides ovatus . Clustering based on the presence of protein coding genes showed that isolates from phyla Proteobacteria , Verrucomicrobia , Elusimicrobia and Synergistetes did not cluster with the remaining isolates. Firmicutes split into families Lactobacillaceae , Enterococcaceae , Veillonellaceae and order Clostridiales from which the Clostridium perfringens isolates formed a distinct sub-cluster. All Bacteroidetes isolates formed a separate cluster showing similar genetic composition in all isolates but distinct from the rest of the gut Anaerobes. The majority of Actinobacteria clustered closely together except for the representatives of genus Gordonibacter showing that the genome of this genus differs from the rest of Actinobacteria sequenced in this study. Representatives of Bacteroidetes commonly encoded proteins (collagenase, hemagglutinin, hemolysin, hyaluronidase, heparinases, chondroitinase, mucin-desulfating sulfatase or glutamate decarboxylase) that may enable them to interact with their host. Aerotolerance was recorded in Akkermansia and Cloacibacillus and was also common among representatives of Bacteroidetes . On the other hand, Elusimicrobium and the majority of Clostridiales were highly sensitive to air exposure despite their potential for spore formation. Conclusions Major gut micrmicrobiota members utilise different strategies for gut colonisation. High oxygen sensitivity of Firmicutes may explain their commonly reported decrease after oxidative burst during gut inflammation.

  • whole genome sequencing and function prediction of 133 gut Anaerobes isolated from chicken caecum in pure cultures
    BMC Genomics, 2018
    Co-Authors: Matej Medvecky, Darina Cejkova, Ondrej Polansky, Daniela Karasova, Tereza Kubasova, Alois Cizek, Ivan Rychlik
    Abstract:

    In order to start to understand the function of individual members of gut micrmicrobiota, we cultured, sequenced and analysed bacterial Anaerobes from chicken caecum. Altogether 204 isolates from chicken caecum were obtained in pure cultures using Wilkins-Chalgren anaerobe agar and anaerobic growth conditions. Genomes of all the isolates were determined using the NextSeq platform and subjected to bioinformatic analysis. Among 204 sequenced isolates we identified 133 different strains belonging to seven different phyla – Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Verrucomicrobia, Elusimicrobia and Synergistetes. Genome sizes ranged from 1.51 Mb in Elusimicrobium minutum to 6.70 Mb in Bacteroides ovatus. Clustering based on the presence of protein coding genes showed that isolates from phyla Proteobacteria, Verrucomicrobia, Elusimicrobia and Synergistetes did not cluster with the remaining isolates. Firmicutes split into families Lactobacillaceae, Enterococcaceae, Veillonellaceae and order Clostridiales from which the Clostridium perfringens isolates formed a distinct sub-cluster. All Bacteroidetes isolates formed a separate cluster showing similar genetic composition in all isolates but distinct from the rest of the gut Anaerobes. The majority of Actinobacteria clustered closely together except for the representatives of genus Gordonibacter showing that the genome of this genus differs from the rest of Actinobacteria sequenced in this study. Representatives of Bacteroidetes commonly encoded proteins (collagenase, hemagglutinin, hemolysin, hyaluronidase, heparinases, chondroitinase, mucin-desulfating sulfatase or glutamate decarboxylase) that may enable them to interact with their host. Aerotolerance was recorded in Akkermansia and Cloacibacillus and was also common among representatives of Bacteroidetes. On the other hand, Elusimicrobium and the majority of Clostridiales were highly sensitive to air exposure despite their potential for spore formation. Major gut micrmicrobiota members utilise different strategies for gut colonisation. High oxygen sensitivity of Firmicutes may explain their commonly reported decrease after oxidative burst during gut inflammation.

Laetitia Pieulle – One of the best experts on this subject based on the ideXlab platform.

  • Biochemical Function, Molecular Structure and Evolution of an Atypical Thioredoxin Reductase from Desulfovibrio vulgaris
    Frontiers in Microbiology, 2017
    Co-Authors: Odile Valette, Tam T. T. Tran, Christine Cavazza, Elodie Caudeville, Gaël Brasseur, Alain Dolla, Emmanuel Talla, Laetitia Pieulle
    Abstract:

    Thioredoxin reductase (TR) regulates the intracellular redox environment by reducing thioredoxin (Trx). In Anaerobes, recent findings indicate that the Trx redox network is implicated in the global redox regulation of metabolism but also actively participates in protecting cells against O2. In the anaerobe Desulfovibrio vulgaris Hildenborough (DvH), there is an intriguing redundancy of the Trx system which includes a classical system using NADPH as electron source, a non-canonical system using NADH and an isolated TR (DvTRi). The functionality of DvTRi was questioned due to its lack of reactivity with DvTrxs. Structural analysis shows that DvTRi is a NAD(P)H-independent TR but its reducer needs still to be identified. Moreover, DvTRi reduced by an artificial electron source is able to reduce in turn DvTrx1 and complexation experiments demonstrate a direct interaction between DvTRi and DvTrx1. The deletion mutant tri exhibits a higher sensitivity to disulfide stress and the gene tri is upregulated by O2 exposure. Having DvTRi in addition to DvTR1 as electron source for reducing DvTrx1 must be an asset to combat oxidative stress. Large-scale phylogenomics analyses show that TRi homologs are confined within the Anaerobes. All TRi proteins displayed a conserved TQ/NGK motif instead of the HRRD motif, which is selective for the binding of the 2′-phosphate group of NADPH. The evolutionary history of TRs indicates that tr1 is the common gene ancestor in prokaryotes, affected by both gene duplications and horizontal gene events, therefore leading to the appearance of TRi through subfunctionalization over the evolutionary time.

Matej Medvecky – One of the best experts on this subject based on the ideXlab platform.

  • Whole genome sequencing and function prediction of 133 gut Anaerobes isolated from chicken caecum in pure cultures
    BMC Genomics, 2018
    Co-Authors: Matej Medvecky, Darina Cejkova, Ondrej Polansky, Daniela Karasova, Tereza Kubasova, Alois Cizek, Ivan Rychlik
    Abstract:

    Background In order to start to understand the function of individual members of gut microbiota, we cultured, sequenced and analysed bacterial Anaerobes from chicken caecum. Results Altogether 204 isolates from chicken caecum were obtained in pure cultures using Wilkins-Chalgren anaerobe agar and anaerobic growth conditions. Genomes of all the isolates were determined using the NextSeq platform and subjected to bioinformatic analysis. Among 204 sequenced isolates we identified 133 different strains belonging to seven different phyla – Firmicutes , Bacteroidetes , Actinobacteria , Proteobacteria , Verrucomicrobia , Elusimicrobia and Synergistetes . Genome sizes ranged from 1.51 Mb in Elusimicrobium minutum to 6.70 Mb in Bacteroides ovatus . Clustering based on the presence of protein coding genes showed that isolates from phyla Proteobacteria , Verrucomicrobia , Elusimicrobia and Synergistetes did not cluster with the remaining isolates. Firmicutes split into families Lactobacillaceae , Enterococcaceae , Veillonellaceae and order Clostridiales from which the Clostridium perfringens isolates formed a distinct sub-cluster. All Bacteroidetes isolates formed a separate cluster showing similar genetic composition in all isolates but distinct from the rest of the gut Anaerobes. The majority of Actinobacteria clustered closely together except for the representatives of genus Gordonibacter showing that the genome of this genus differs from the rest of Actinobacteria sequenced in this study. Representatives of Bacteroidetes commonly encoded proteins (collagenase, hemagglutinin, hemolysin, hyaluronidase, heparinases, chondroitinase, mucin-desulfating sulfatase or glutamate decarboxylase) that may enable them to interact with their host. Aerotolerance was recorded in Akkermansia and Cloacibacillus and was also common among representatives of Bacteroidetes . On the other hand, Elusimicrobium and the majority of Clostridiales were highly sensitive to air exposure despite their potential for spore formation. Conclusions Major gut microbiota members utilise different strategies for gut colonisation. High oxygen sensitivity of Firmicutes may explain their commonly reported decrease after oxidative burst during gut inflammation.

  • whole genome sequencing and function prediction of 133 gut Anaerobes isolated from chicken caecum in pure cultures
    BMC Genomics, 2018
    Co-Authors: Matej Medvecky, Darina Cejkova, Ondrej Polansky, Daniela Karasova, Tereza Kubasova, Alois Cizek, Ivan Rychlik
    Abstract:

    In order to start to understand the function of individual members of gut microbiota, we cultured, sequenced and analysed bacterial Anaerobes from chicken caecum. Altogether 204 isolates from chicken caecum were obtained in pure cultures using Wilkins-Chalgren anaerobe agar and anaerobic growth conditions. Genomes of all the isolates were determined using the NextSeq platform and subjected to bioinformatic analysis. Among 204 sequenced isolates we identified 133 different strains belonging to seven different phyla – Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Verrucomicrobia, Elusimicrobia and Synergistetes. Genome sizes ranged from 1.51 Mb in Elusimicrobium minutum to 6.70 Mb in Bacteroides ovatus. Clustering based on the presence of protein coding genes showed that isolates from phyla Proteobacteria, Verrucomicrobia, Elusimicrobia and Synergistetes did not cluster with the remaining isolates. Firmicutes split into families Lactobacillaceae, Enterococcaceae, Veillonellaceae and order Clostridiales from which the Clostridium perfringens isolates formed a distinct sub-cluster. All Bacteroidetes isolates formed a separate cluster showing similar genetic composition in all isolates but distinct from the rest of the gut Anaerobes. The majority of Actinobacteria clustered closely together except for the representatives of genus Gordonibacter showing that the genome of this genus differs from the rest of Actinobacteria sequenced in this study. Representatives of Bacteroidetes commonly encoded proteins (collagenase, hemagglutinin, hemolysin, hyaluronidase, heparinases, chondroitinase, mucin-desulfating sulfatase or glutamate decarboxylase) that may enable them to interact with their host. Aerotolerance was recorded in Akkermansia and Cloacibacillus and was also common among representatives of Bacteroidetes. On the other hand, Elusimicrobium and the majority of Clostridiales were highly sensitive to air exposure despite their potential for spore formation. Major gut microbiota members utilise different strategies for gut colonisation. High oxygen sensitivity of Firmicutes may explain their commonly reported decrease after oxidative burst during gut inflammation.

Joseph E. Rubin – One of the best experts on this subject based on the ideXlab platform.

  • Antimicrobial Resistance in Clostridium and Brachyspira spp. and Other Anaerobes.
    Microbiology spectrum, 2018
    Co-Authors: Marie Archambault, Joseph E. Rubin
    Abstract:

    This article describes the antimicrobial resistance to date of the most frequently encountered anaerobic bacterial pathogens of animals. The different sections show that antimicrobial resistance can vary depending on the antimicrobial, the anaerobe, and the resistance mechanism. The variability in antimicrobial resistance patterns is also associated with other factors such as geographic region and local antimicrobial usage. On occasion, the same resistance gene was observed in many Anaerobes, whereas some were limited to certain Anaerobes. This article focuses on antimicrobial resistance data of veterinary origin.

Solange Oliveira – One of the best experts on this subject based on the ideXlab platform.

  • structure of a dioxygen reduction enzyme from desulfovibrio gigas
    Nature Structural & Molecular Biology, 2000
    Co-Authors: Carlos Frazao, Solange Oliveira, Gabriela G F Silva, Claudio M Gomes, Pedro M Matias, Ricardo Coelho, L C Sieker, S Macedo, Ming Y Liu
    Abstract:

    Desulfovibrio gigas is a strict anaerobe that contains a well-characterized metabolic pathway that enables it to survive transient contacts with oxygen. The terminal enzyme in this pathway, rubredoxin:oxygen oxidoreductase (ROO) reduces oxygen to water in a direct and safe way. The 2.5 A resolution crystal structure of ROO shows that each monomer of this homodimeric enzyme consists of a novel combination of two domains, a flavodoxin-like domain and a Zn-β-lactamase-like domain that contains a di-iron center for dioxygen reduction. This is the first structure of a member of a superfamily of enzymes widespread in strict and facultative Anaerobes, indicating its broad physiological significance.