Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa
| العنوان: | Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa |
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| المؤلفون: | Thomas D.S. Sutton, Cormac Brian Fitzgerald, R. Paul Ross, Andrei V. Chaplin, Andrey N. Shkoporov, Vimalkumar Velayudhan, Colin Hill |
| المساهمون: | Science Foundation Ireland, European Regional Development Fund, SFI/12/RC/2273, SFI/14/SP APC/B3032 |
| المصدر: | BMC Genomics, Vol 19, Iss 1, Pp 1-20 (2018) BMC Genomics |
| بيانات النشر: | BMC, 2018. |
| سنة النشر: | 2018 |
| مصطلحات موضوعية: | 0301 basic medicine, Ruminococcaceae, Proteome, lcsh:QH426-470, lcsh:Biotechnology, 030106 microbiology, IBD, Faecalibacterium prausnitzii, Neotype strains, International Code of Nomenclature of Prokaryotes, Genome, Feces, 03 medical and health sciences, Species Specificity, Phylogenetics, RNA, Ribosomal, 16S, lcsh:TP248.13-248.65, Correspondence, Nomina nova, Genetics, Cluster Analysis, Humans, Microbiome, Phylogeny, Comparative genomics, Comparative Genomic Hybridization, Principal Component Analysis, Faecalibacterium moorei, biology, Phylogenetic tree, Genome shuffling, Sequence Analysis, DNA, biology.organism_classification, Gastrointestinal Microbiome, lcsh:Genetics, 030104 developmental biology, Horizontal gene transfer, Mobilome, Genome, Bacterial, Human gut microbiota, Biotechnology, Research Article |
| الوصف: | peer-reviewed Background Faecalibacterium prausnitzii is a ubiquitous member of the human gut microbiome, constituting up to 15% of the total bacteria in the human gut. Substantial evidence connects decreased levels of F. prausnitzii with the onset and progression of certain forms of inflammatory bowel disease, which has been attributed to its anti-inflammatory potential. Two phylogroups of F. prausnitzii have been identified, with a decrease in phylogroup I being a more sensitive marker of intestinal inflammation. Much of the genomic and physiological data available to date was collected using phylogroup II strains. Little analysis of F. prausnitzii genomes has been performed so far and genetic differences between phylogroups I and II are poorly understood. Results In this study we sequenced 11 additional F. prausnitzii genomes and performed comparative genomics to investigate intraspecies diversity, functional gene complement and the mobilome of 31 high-quality draft and complete genomes. We reveal a very low level of average nucleotide identity among F. prausnitzii genomes and a high level of genome plasticity. Two genomogroups can be separated based on differences in functional gene complement, albeit that this division does not fully agree with separation based on conserved gene phylogeny, highlighting the importance of horizontal gene transfer in shaping F. prausnitzii genomes. The difference between the two genomogroups is mainly in the complement of genes associated with catabolism of carbohydrates (such as a predicted sialidase gene in genomogroup I) and amino acids, as well as defense mechanisms. Conclusions Based on the combination of ANI of genomic sequences, phylogenetic analysis of core proteomes and functional differences we propose to separate the species F. prausnitzii into two new species level taxa: F. prausnitzii sensu stricto (neotype strain A2–165T = DSM 17677T = JCM 31915T) and F. moorei sp. nov. (type strain ATCC 27768T = NCIMB 13872T). This research was conducted with the financial support of Science Foundation Ireland (SFI) under Grant Number SFI/12/RC/2273, a Science Foundation Ireland’s Spokes Programme which is co-funded under the European Regional Development Fund under Grant Number SFI/14/SP APC/B3032, and a research grant from Janssen Biotech, Inc. |
| وصف الملف: | application/pdf |
| اللغة: | English |
| تدمد: | 1471-2164 |
| الوصول الحر: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::71977d6763c7f69fca1022369e97ec1bTest http://link.springer.com/article/10.1186/s12864-018-5313-6Test |
| حقوق: | OPEN |
| رقم الانضمام: | edsair.doi.dedup.....71977d6763c7f69fca1022369e97ec1b |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 14712164 |
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