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Description of Mediterraneibacter massiliensis, gen. nov., sp. nov., a new genus isolated from the gut microbiota of an obese patient and reclassification of Ruminococcus faecis, Ruminococcus lactaris, Ruminococcus torques, Ruminococcus gnavus and Clostridium glycyrrhizinilyticum as Mediterraneibacter faecis comb. nov., Mediterraneibacter lactaris comb. nov., Mediterraneibacter torques comb. nov., Mediterraneibacter gnavus comb. nov. and Mediterraneibacter glycyrrhizinilyticus comb. nov.

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A Correction to this article was published on 28 September 2018

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Abstract

An anaerobic isolate, strain AT7T, was cultivated from a stool sample of a morbidly obese French woman using a microbial culturomics approach. The 16S rRNA gene sequence analysis showed that strain AT7T exhibited 96% nucleotide sequence similarity with Ruminococcus torques strain JCM 6553T (= ATCC 27756T = VPI B2-51T), currently the closest related species with a validly published name. The strain was observed to be a Gram-stain positive, non-motile, asporogenous and coccobacillary-shaped bacterium. It was found to be catalase positive and oxidase negative. Its major fatty acids were identified as C16:0 (54%) and C18:1n9 (30%). The draft genome of strain AT7T is 3,069,882 bp long with 42.4% G+C content. 2925 genes were predicted, including 2867 protein-coding genes and 58 RNAs. Based on phenotypic, biochemical, phylogenetic and genomic evidence, we propose the creation of the new genus Mediterraneibacter and species, Mediterraneibacter massiliensis, that contains strain AT7T (= CSUR P2086T = DSM 100837T), and the reclassification of Ruminococcus faecis, Ruminococcus lactaris, Ruminococcus torques, Ruminococcus gnavus, Clostridium glycyrrhizinilyticum as Mediterraneibacter faecis comb. nov., with type strain Eg2T (= KCTC 5757T = JCM15917T), Mediterraneibacter lactaris comb. nov., with type strain ATCC 29176T (= VPI X6-29T), Mediterraneibacter torques comb. nov., with type strain ATCC 27756T (= VPI B2-51T), Mediterraneibacter gnavus comb. nov., with type strain ATCC 29149T (= VPI C7-9T) and Mediterraneibacter glycyrrhizinilyticus comb. nov., with type strain ZM35T (= JCM 13368T = DSM 17593T), respectively.

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Change history

  • 28 September 2018

    Subsequent to the publication of the above article, it has been noticed that the designation of the type strain is not correct. The strain referred to throughout the article as strain AT7T should be designated as strain Marseille-P2086T (= CSUR P2086T = DSM 100837T). The corrected for protologue for the species Mediterraneibacter massiliensis, represented by strain Marseille-P2086T as type strain, is given below.

Abbreviations

AGIOS:

Average of genomic identity of orthologous gene sequences

COG:

Clusters of orthologous groups

CSUR:

Collection de souches de l’Unité des Rickettsies

DDH:

DNA–DNA hybridization

DSM:

Deutsche Sammlung von Mikroorganismen

EUCAST:

European Committee on antimicrobial susceptibility testing

FAME:

Fatty acid methyl ester

GC/MS:

Gas chromatography/mass spectrometry

GGDC:

Genome-to-genome distance calculator

IUPAC:

International Union of Pure and Applied Chemistry

ORF:

Open reading frame

MALDI-TOF:

Matrix-assisted laser-desorption/ionization time-of-flight

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Acknowledgements

The authors thank the Xegen Company (www.xegen.fr) for automating the genomic annotation process and Magdalen LARDIERE for English correction.

Funding

This study was funded by the « Fondation Méditerranée Infection» and the French National Research Agency under the program “Investissements d’avenir” with the reference ANR-10-IAHU-03.

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Authors and Affiliations

  1. Aix Marseille Univ, IRD, MEPHI, IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France

    Amadou Hamidou Togo, Nicholas Armstrong, Grégory Dubourg, Magali Richez, Jeremy Delerce, Anthony Levasseur, Didier Raoult & Matthieu Million

  2. Aix Marseille Univ, IRD, VITROME, IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France

    Awa Diop, Fadi Bittar, Noémie Labas & Pierre-Edouard Fournier

  3. NORT “Nutrition, Obesity and Risk of Thrombosis”, INSERM1062, INRA1260, Aix Marseille Université, 13385, Marseille, France

    Marie Maraninchi & René Valero

  4. CHU Hôpital de la Conception, Service Nutrition, Maladies Métaboliques et Endocrinologie, APHM, 13385, Marseille, France

    René Valero

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  1. Amadou Hamidou Togo
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  14. Matthieu Million
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Contributions

AHT isolated the bacterium, performed the phenotypic characterization, drafted the manuscript; AD performed the genomic analyses and drafted manuscript. FB and P-EF helped in data interpretation, drafted the manuscript and reference checking, MM and RV take care of the patient and provide samples; NA, GD, NL and MR performed genome sequencing and chemotaxonomic analysis; JD, AL performed comprehensive genomic analysis; DR designed and directed the project; MM drafted manuscript, checked the references and acted as corresponding author.

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Correspondence to Matthieu Million.

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Togo, A.H., Diop, A., Bittar, F. et al. Description of Mediterraneibacter massiliensis, gen. nov., sp. nov., a new genus isolated from the gut microbiota of an obese patient and reclassification of Ruminococcus faecis, Ruminococcus lactaris, Ruminococcus torques, Ruminococcus gnavus and Clostridium glycyrrhizinilyticum as Mediterraneibacter faecis comb. nov., Mediterraneibacter lactaris comb. nov., Mediterraneibacter torques comb. nov., Mediterraneibacter gnavus comb. nov. and Mediterraneibacter glycyrrhizinilyticus comb. nov.. Antonie van Leeuwenhoek 111, 2107–2128 (2018). https://doi.org/10.1007/s10482-018-1104-y

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  • DOI: https://doi.org/10.1007/s10482-018-1104-y

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