Dysgonomonas massiliensis sp. nov., a new species isolated from the human gut and its taxonogenomic description
Culturomics has allowed the isolation of a significant number of new bacterial species from the human gut microbiota and proved to be a valuable complement to culture-independent techniques. Using this culture-based approach, a new bacterial species has been isolated from a stool sample of a 39-year-old healthy Pygmy male and described using the taxonogenomic strategy. Cells of strain Marseille-P4356T are Gram-stain negative cocci. The strain grows optimally at 37 °C and is catalase positive but oxidase negative. Its 16S rRNA gene sequence exhibited 92.96% sequence similarity with Dysgonomonas gadei strain JCM 16698T (NR_113134.1), currently its phylogenetically closest species that has been validly named. The genome of strain Marseille-P4356T is 3,472,011 bp long with 37.3 mol% G+C content. Phenotypic, biochemical, proteomic, genomic and phylogenetic analyses, clearly demonstrate that strain Marseille-P4356T (= CCUG 71356T = CSUR P4356T) represents a new species within the genus Dysgonomonas, for which we propose the name Dysgonomonas massiliensis sp. nov.
KeywordsCulturomics Taxono-genomics Pygmy Dysgonomonas massiliensis Gut microbiota
This study was supported by IHU Méditerranée Infection, Marseille, France and by the French Government under the «Investissements d’avenir» (Investments for the Future) program managed by the Agence Nationale de la Recherche (ANR, fr: National Agency for Research), (reference: Méditerranée Infection 10-IAHU- 03). This work was supported by Région Provence Alpes Côte d’Azur and European funding FEDER PRIMI.
MB: Isolated, described and wrote the manuscript; MDMF: helped in the taxonogenomics description, GD: critical analysis of the work and wrote the manuscript, ET: Genomic analysis, MR: helped in the taxonogenomics description, JD: genomic analysis, AL: helped in the genomic analyses, ZD: writing an critical analysis of the manuscript, DR: designed the project, helped in writing, reviewing and critical analysis; FC: study design, data analysis and writing the manuscript.
Compliance with ethical standards
Conflict of interest
The authors declare no conflict of interest.
- Hofstad T, Olsen I, Eribe ER et al (2000) Dysgonomonas gen. nov. to accommodate Dysgonomonas gadei sp. nov., an organism isolated from a human gall bladder, and Dysgonomonas capnocytophagoides (formerly CDC group DF-3). Int J Syst Evol Microbiol 50:2189–2195. https://doi.org/10.1099/00207713-50-6-2189 CrossRefGoogle Scholar
- Murray PR, Rosenthal KS, Pfaller MA (2013) Medical microbiology, with student consult online Access, 7. Medical Microbiology. Elsevier Health SciencesGoogle Scholar
- Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512–526. https://doi.org/10.1093/oxfordjournals.molbev.a040023 Google Scholar
- Tateno Y, Takezaki N, Nei M (1994) Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site. Mol Biol Evol 11:261–277. https://doi.org/10.1093/oxfordjournals.molbev.a040108 Google Scholar
- Wallace PL, Hollis DG, Weaver RE, Moss CW (1989) Characterization of CDC group DF-3 by cellular fatty acid analysis. J Clin Microbiol 27:735–737Google Scholar