Draft genome and description of Merdibacter massiliensis gen.nov., sp. nov., a new bacterium genus isolated from the human ileum

Hussein Anani,Rita Abou Abdallah,Nisrine Chelkha,Pierre-Edouard Fournier,Davide Ricaboni,Anthony Fontanini,Morgane Mailhe,Didier Raoult

doi:10.1038/s41598-019-44343-8

Abstract

We used phenotypic, genomic and phylogenetic information following the taxono-genomics approach to demonstrate that strain Marseille–P3254, isolated from an ileal sample of a 76-year old woman who underwent upper and lower digestive tract endoscopy for esophagitis and colonic polyp, is representative of a novel bacterial genus within the family Erysipelotrichaceae in the phylum Firmicutes. It is an anaerobic Gram-negative bacterium without catalase and oxidase activities. The genome of strain Marseille–P3254 is 2,468,496-bp long with a 40.1% G + C content. This new bacterium is most closely related to Eubacterium dolichum, with which it shares 90.7% 16S rRNA sequence similarity. In addition, genomic comparison using the digital DNA–DNA hybridization and OrthoANI analyses between the novel organism and the E. dolichum type strain revealed identities of 25.2 and 68.91%, respectively. The major fatty acids were C16: 0, C18: 1n9 and C18: 0. Based on these data, we propose the creation of the new genus Merdibacter gen. nov., with strain Marseille-P3254T (=CSUR P3254 = DSM 103534) being the type strain of the new species Merdibacter massiliensis gen. nov., sp. nov.

Highlights

A thorough knowledge of the gut microbiota composition appears essential to understand many aspects of health and diseases in humans
NR_113409), the phylogenetically closest bacterium with standing in nomenclature (Fig. 1). As this value is lower than the 95% threshold defined by Stackebrandt and Ebers for delineating a new genus, strain Marseille-P3254 was considered as representative of a putatively new genus within the family Erysipelotrichaceae in the phylum Firmicutes
Using the taxono-genomics concept combining the genomic and phenotypic properties of a putative new taxa[15], we have characterized a new bacterial species representing a new genus within the family Erysipelotrichaceae in a human ileal specimen

Summary

Introduction

A thorough knowledge of the gut microbiota composition appears essential to understand many aspects of health and diseases in humans. Culturomics, a new approach to study and decipher the human microbiota, based on the diversification of culture conditions and complementary to 16S rRNA metagenomics, has enabled the culture of more than 500 new bacterial species to date[1,2,3]. Most of these new species were characterized using the taxono-genomics strategy that combines phenotypic characteristics and whole genome sequencing analysis[4]. Sp., nov., strain Marseille-P3254 (red) relative to other closely related bacterial taxa within the family Erysipelotrichaceae as well as members of the family Eubacteriaceae.

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Conclusion