Reclassification of <i>Shigella</i> species as later heterotypic synonyms of <i>Escherichia coli</i> in the Genome Taxonomy Database

Parks, Donovan H.; Chuvochina, Maria; Reeves, Peter R.; Beatson, Scott A.; Hugenholtz, Philip

doi:10.1101/2021.09.22.461432

Cited by 14 publications

(12 citation statements)

References 54 publications

(81 reference statements)

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“…The putative proinflammatory genera examined in these comparisons included Helicobacter , Alistipes , Rikenellaceae RC9 gut group, Parasutterella , Desulfovibrio , Odoribacter , Chlamydia , Rhodospirillale Uncultured, Rikenellaceae , Rikenella , Rodentibacter , and Escherichia-Shigella (ie, closely related to Escherichia coli ). 18 Overall, this shows that circadian rhythm disruption leads to a relatively higher relative abundance of putative proinflammatory bacteria after exposure to DSS.…”

Section: Resultsmentioning

confidence: 85%

Colonic Epithelial Circadian Disruption Worsens Dextran Sulfate Sodium–Induced Colitis

Jochum

Engen

Shaikh

et al. 2022

Inflammatory Bowel Diseases

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Background Disruption of central circadian rhythms likely mediated by changes in microbiota and a decrease in gut-derived metabolites like short chain fatty acids (SCFAs) negatively impacts colonic barrier homeostasis. We aimed to explore the effects of isolated peripheral colonic circadian disruption on the colonic barrier in a mouse model of colitis and explore the mechanisms, including intestinal microbiota community structure and function. Methods Colon epithelial cell circadian rhythms were conditionally genetically disrupted in mice: TS4Cre-BMAL1lox (cBMAL1KO) with TS4Cre as control animals. Colitis was induced through 5 days of 2% dextran sulfate sodium (DSS). Disease activity index and intestinal barrier were assessed, as were fecal microbiota and metabolites. Results Colitis symptoms were worse in mice with peripheral circadian disruption (cBMAL1KO). Specifically, the disease activity index and intestinal permeability were significantly higher in circadian-disrupted mice compared with control animals (TS4Cre) (P < .05). The worsening of colitis appears to be mediated, in part, through JAK (Janus kinase)-mediated STAT3 (signal transducer and activator of transcription 3), which was significantly elevated in circadian-disrupted (cBMAL1KO) mice treated with DSS (P < .05). Circadian-disrupted (cBMAL1KO) mice also had decreased SCFA metabolite concentrations and decreased relative abundances of SCFA-producing bacteria in their stool when compared with control animals (TS4Cre). Conclusions Disruption of intestinal circadian rhythms in colonic epithelial cells promoted more severe colitis, increased inflammatory mediators (STAT3 [signal transducer and activator of transcription 3]), and decreased gut microbiota–derived SCFAs compared with DSS alone. Further investigation elucidating the molecular mechanisms behind these findings could provide novel circadian directed targets and strategies in the treatment of inflammatory bowel disease.

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Section: Resultsmentioning

confidence: 85%

Colonic Epithelial Circadian Disruption Worsens Dextran Sulfate Sodium–Induced Colitis

Jochum

Engen

Shaikh

et al. 2022

Inflammatory Bowel Diseases

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“…For example, several Eubacterium rectale isolates were recently reclassified as Agathbacter rectalis based on phenotypic, chemotaxonomic and multiple-marker phylogenetic results. 76 Moreover, Parks et al 77 developed the genome taxonomy database (GTDB), which aims to establish a standardized microbial taxonomy based on genome phylogeny. In this database, an average nucleotide identity (ANI)-based approach was adopted to reclassify species, which resulted in the reclassification of several E. coli strains to Shigella species.…”

Section: Discussionmentioning

confidence: 99%

Integrative multiomics analysis reveals host-microbe-metabolite interplays associated with the aging process in Singaporeans

et al. 2022

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The age-associated alterations in microbiomes vary across populations due to the influence of genetics and lifestyles. To the best of our knowledge, the microbial changes associated with aging have not yet been investigated in Singapore adults. We conducted shotgun metagenomic sequencing of fecal and saliva samples, as well as fecal metabolomics to characterize the gut and oral microbial communities of 62 healthy adult male Singaporeans, including 32 young subjects (age, 23.1 ± 1.4 years) and 30 elderly subjects (age, 69.0 ± 3.5 years). We identified 8 gut and 13 oral species that were differentially abundant in elderly compared to young subjects. By combining the gut and oral microbiomes, 25 age-associated oral-gut species connections were identified. Moreover, oral bacteria Acidaminococcus intestine and Flavonifractor plautii were less prevalent/abundant in elderly gut samples than in young gut samples, whereas Collinsella aerofaciens and Roseburia hominis showed the opposite trends. These results indicate the varied gut-oral communications with aging. Subsequently, we expanded the association studies on microbiome, metabolome and host phenotypic parameters. In particular, Eubacterium eligens increased in elderly compared to young subjects, and was positively correlated with triglycerides, which implies that the potential role of E. eligens in lipid metabolism is altered during the aging process. Our results demonstrated aging-associated changes in the gut and oral microbiomes, as well as the connections between metabolites and host-microbe interactions, thereby deepening the understanding of alterations in the human microbiome during the aging process in a Singapore population.

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“…( 2020 ) suggested including the four species of Shigella within the genus Escherichia , creating E. sonnei, E. boydii, E flexneri, and E. dysenteriae. However, based on DNA similarity threshold that they routinely use to define species, these newly named Escherichia species should remain within E. coli ( Parks et al 2021 ).…”

Section: Discussionmentioning

confidence: 99%

“…To accommodate the burgeoning numbers of sequenced strains in all taxa, the Genome Taxonomy Database (GTDB; gtdb.ecogenomic.org/) recommended the application of a genome-wide identity threshold (analogous to ANI) to define bacterial species ( Parks et al 2018 ). Imposing their metrics, strains currently classified as E. coli would be split into six species— E. coli , E. coli _E, Escherichia ruysiae , Escherichia marmotae, Escherichia sp001660175 , and Escherichia sp005843885 —with the majority consigned to E. coli ( Parks et al 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Escherichia Coli: What Is and Which Are?

Cobo-Simón

Hart

Ochman

2022

Molecular Biology and Evolution

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Escherichia coli have served as important model organisms for over a century—used to elucidate key aspects of genetics, evolution, molecular biology, and pathogenesis. However, defining which strains actually belong to this species is erratic and unstable due to shifts in the characters and criteria used to distinguish bacterial species. Additionally, many isolates designated as E. coli are genetically more closely related to strains of Shigella than to other E. coli, creating a situation in which the entire genus of Shigella and its four species are encompassed within the single species E. coli. We evaluated all complete genomes assigned to E. coli and its closest relatives according to the Biological Species Concept (BSC), using evidence of reproductive isolation and gene flow (i.e., homologous recombination in the case of asexual bacteria) to ascertain species boundaries. The BSC establishes a uniform, consistent and objective principle that allows species-level classification across all Domains of Life and does not rely on either phenotypic or genotypic similarity to a defined type-specimen for species membership. Analyzing a total of 1887 sequenced genomes and comparing our results to other genome-based classification methods, we found few barriers to gene flow among the strains, clades, phylogroups or species within E. coli and Shigella. Due to the utility in recognizing which strains constitute a true biological species, we designate genomes that form a genetic cohesive group as members of E. coliBIO.

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Reclassification of Shigella species as later heterotypic synonyms of Escherichia coli in the Genome Taxonomy Database

Cited by 14 publications

References 54 publications

Colonic Epithelial Circadian Disruption Worsens Dextran Sulfate Sodium–Induced Colitis

Colonic Epithelial Circadian Disruption Worsens Dextran Sulfate Sodium–Induced Colitis

Integrative multiomics analysis reveals host-microbe-metabolite interplays associated with the aging process in Singaporeans

Escherichia Coli: What Is and Which Are?

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