Dysgonomonas massiliensis sp. nov., a new species isolated from the human gut and its taxonogenomic description

  • Melhem Bilen
  • Maxime Descartes Mbogning Fonkou
  • Grégory Dubourg
  • Enora Tomei
  • Magali Richez
  • Jérémy Delerce
  • Anthony Levasseur
  • Ziad Daoud
  • Didier Raoult
  • Frédéric CadoretEmail author
Original Paper


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.


Culturomics 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.

Authors’ contribution

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.

Supplementary material

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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Melhem Bilen
    • 1
    • 2
  • Maxime Descartes Mbogning Fonkou
    • 1
  • Grégory Dubourg
    • 1
  • Enora Tomei
    • 1
  • Magali Richez
    • 1
  • Jérémy Delerce
    • 1
  • Anthony Levasseur
    • 1
  • Ziad Daoud
    • 2
  • Didier Raoult
    • 1
    • 3
  • Frédéric Cadoret
    • 1
    Email author
  1. 1.IRD, APHM, MEPHI, IHU-Méditerranée InfectionAix Marseille UniversitéMarseilleFrance
  2. 2.Clinical Microbiology Department, Faculty of Medicine and Medical SciencesUniversity of BalamandAmiounLebanon
  3. 3.Special Infectious Agents Unit, King Fahd Medical Research CenterKing Abdulaziz UniversityJeddahSaudi Arabia

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