Whole-genome-based phylogeny supports the objections against the reclassification of Eubacterium rectale to Agathobacter rectalis

Zuo, Guanghong; Hao, Bailin

doi:10.1099/ijsem.0.001047

Cited by 6 publications

(5 citation statements)

References 6 publications

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“…Of note, the isolate branches close to Agathobacter spp., including the well-known butyrate producing species formerly named Eubacterium rectale. Despite the urgent need to revisit the taxonomy of Eubacterium spp., the placement of E. rectale within the genus Agathobacter and the status of this genus in general have been disputed, despite being still a valid name [147][148][149][150] . Hence, it is sound to propose that the isolate belongs to the genus Roseburia.…”

Section: Methodsmentioning

confidence: 99%

A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity

et al. 2020

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Our knowledge about the gut microbiota of pigs is still scarce, despite the importance of these animals for biomedical research and agriculture. Here, we present a collection of cultured bacteria from the pig gut, including 110 species across 40 families and nine phyla. We provide taxonomic descriptions for 22 novel species and 16 genera. Meta-analysis of 16S rRNA amplicon sequence data and metagenome-assembled genomes reveal prevalent and pig-specific species within Lactobacillus, Streptococcus, Clostridium, Desulfovibrio, Enterococcus, Fusobacterium, and several new genera described in this study. Potentially interesting functions discovered in these organisms include a fucosyltransferase encoded in the genome of the novel species Clostridium porci, and prevalent gene clusters for biosynthesis of sactipeptide-like peptides. Many strains deconjugate primary bile acids in in vitro assays, and a Clostridium scindens strain produces secondary bile acids via dehydroxylation. In addition, cells of the novel species Bullifex porci are coccoidal or spherical under the culture conditions tested, in contrast with the usual helical shape of other members of the family Spirochaetaceae. The strain collection, called ‘Pig intestinal bacterial collection’ (PiBAC), is publicly available at www.dsmz.de/pibac and opens new avenues for functional studies of the pig gut microbiota.

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Section: Methodsmentioning

confidence: 99%

A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity

et al. 2020

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“…In silico comparison of gene sequences of known Lachnospiraceae flagellins derived from mouse cecal bacteria to flagellin sequences of the human microbiome in the Gen-Bank database identified 4 Roseburia species (intestinalis, hominis, inulinivorans, and faecis) and Eubacterium rectale (also classified as Agathobacter rectale in the Lachnospiraceae family 22,23 ), which had high homology in the aminoand carboxy-domains to previously defined flagellins from mouse Lachnospiraceae and clustered together phylogenetically (Supplementary Figure 1). These 5 species had a total of 23 flagellins, with 2-6 per bacterium, similar to the murine-origin Lachnospiraceae strains, with 3-8 flagellins per bacterial strain (https://www.ncbi.nlm.nih.gov/ bioproject/175997).…”

Section: Human-derived Lachnospiraceae Flagellins Are Immunodominant Antigens In Crohn's Diseasementioning

confidence: 99%

Human Microbiota Flagellins Drive Adaptive Immune Responses in Crohn’s Disease

et al. 2021

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BACKGROUND AND AIMS: Crohn's disease and ulcerative colitis are characterized by dysregulated adaptive immune responses to the microbiota in genetically susceptible individuals, but the specificity of these responses remains largely undefined. Therefore, we developed a microbiota antigen microarray to characterize microbial antibody reactivity, particularly to human-derived microbiota flagellins, in inflammatory bowel disease. METHODS: Sera from healthy volunteers (n ¼ 87) at the University of Alabama at Birmingham and from patients recruited from the Kirklin Clinic of University of Alabama at Birmingham Hospital, including patients with Crohn's disease (n ¼ 152) and ulcerative colitis (n ¼ 170), were

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“…are present in the oral cavity, the intestinal tract and the environment [47]. Eubacterium (and also Agathobacter rectalis [48,49]) rectale was present in 57.7% of negative CDI samples and 14.8% of positive CDI samples. Anaerostipes spp.…”

Section: Discussionmentioning

confidence: 99%

Gut Microbiota Associated with Clostridioides difficile Carriage in Three Clinical Groups (Inflammatory Bowel Disease, C. difficile Infection and Healthcare Workers) in Hospital Field

Martinez,

Crevecoeur,

Thirion

et al. 2023

Microorganisms

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Clostridioides difficile is an anaerobic spore-forming Gram-positive bacterium. C. difficile carriage and 16S rDNA profiling were studied in three clinical groups at three different sampling times: inflammatory bowel disease (IBD) patients, C. difficile infection (CDI) patients and healthcare workers (HCWs). Diversity analysis was realized in the three clinical groups, the positive and negative C. difficile carriage groups and the three analysis periods. Concerning the three clinical groups, β-diversity tests showed significant differences between them, especially between the HCW group and IBD group and between IBD patients and CDI patients. The Simpson index (evenness) showed a significant difference between two clinical groups (HCWs and IBD). Several genera were significantly different in the IBD patient group (Sutterella, Agathobacter) and in the CDI patient group (Enterococcus, Clostridioides). Concerning the positive and negative C. difficile carriage groups, β-diversity tests showed significant differences. Shannon, Simpson and InvSimpson indexes showed significant differences between the two groups. Several genera had significantly different relative prevalences in the negative group (Agathobacter, Sutterella, Anaerostipes, Oscillospira) and the positive group (Enterococcus, Enterobacteriaceae_ge and Enterobacterales_ge). A microbiota footprint was detected in C. difficile-positive carriers. More experiments are needed to test this microbiota footprint to see its impact on C. difficile infection.

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Whole-genome-based phylogeny supports the objections against the reclassification of Eubacterium rectale to Agathobacter rectalis

Cited by 6 publications

References 6 publications

A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity

A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity

Human Microbiota Flagellins Drive Adaptive Immune Responses in Crohn’s Disease

Gut Microbiota Associated with Clostridioides difficile Carriage in Three Clinical Groups (Inflammatory Bowel Disease, C. difficile Infection and Healthcare Workers) in Hospital Field

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