Description and genomic characterization of Massiliimalia massiliensis gen. nov., sp. nov., and Massiliimalia timonensis gen. nov., sp. nov., two new members of the family Ruminococcaceae isolated from the human gut
Using the culturomics approach, we isolated two strains, Marseille-P2963 and Marseille-P3753, from the intestinal microbiota of a 19-year-old healthy Saudi Arabian Bedouin male and from a 32-year-old healthy Senegalese male faecal transplant donor. Here, we studied their phenotypic, phylogenetic and genomic characteristics. Both strains were phylogenetically related, but different from Ruminococcus species. Bacterial cells were anaerobic, rod-shaped, non-spore-forming and not motile, with neither catalase nor oxidase activities. Their growth temperatures ranged from 28 to 45 °C, with an optimal growth at 37 °C. The genomes are 2,842,720 bp- and 2,707,061 bp-long respectively. The G + C contents are 47.18% and 46.90%, respectively. Based on these characteristics, we propose the creation of a new genus within the family Ruminococcaceae named Massiliimalia gen. nov., that contains the new species Massiliimalia massiliensis gen. nov., sp. nov., and Massiliimalia timonensis gen. nov., sp. nov. Strains Marseille-P2963T (= CSUR P2963 = DSM 106837) and Marseille-P3753T (= CSUR P3753 = CCUG 71632) are their type strains, respectively.
KeywordsCulturomics Gut Massiliimalia massiliensis Massiliimalia timonensis Taxono-genomics
Average of genomic identity of orthologous gene sequences
Average nucleotide identity
Culture Collection, University of Gothenburg
Clusters of Orthologous Groups
Collection de Souches de l’Unité des Rickettsies
Deutsche Sammlung von Mikroorganismen und Zellkulturen
Fatty acid methyl ester
Gas chromatography/mass spectrometry
Genome-to-Genome Distance Calculator
High-scoring segment pairs
- MALDI-TOF MS
Matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry
Mega base pairs
Short chain fatty acid
The authors thank the Xegen Company (www.xegen.fr) for automating the genomic annotation process and Magdalen LARDIERE for English correction.
PA isolated for the first time the strain Marseille-P3753, performed its phenotypic characterization and wrote the manuscript; SIT isolated for the first time the strain Marseille-P2963 and performed its phenotypic characterization; ND, JCL and GD have actively participated in the laboratory project in which both strains were isolated; CA have performed the first correction of the manuscript; ET performed the genomes sequencing of both strains; MR performed for both strains fatty acid methyl ester analysis and measurements of short chain fatty acids; FDP performed for both strains the necessary work in electron microscopy for have the electron micrographs; DR designed and directed the project; PEF corrected the manuscript, verified the accuracy of the Latin name “Massiliimalia” and acted as the corresponding author.
This study was supported by “Fondation Méditerranée Infection” 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 also supported by Région Provence Alpes Côte d’Azur and European funding FEDER PRIMI.
Compliance with ethical standards
See Materials and Methods.
Conflict of interest
The authors declare no conflict of interest.
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