Hugonella massiliensis gen. nov., sp. nov., genome sequence, and description of a new strictly anaerobic bacterium isolated from the human gut

Abstract

The human gut is composed of a large diversity of microorganisms, which have been poorly described. Here, using culturomics, a new concept based on the variation in culture conditions and MALDI-TOF MS identification, we proceed to explore the microbial diversity of the complex ecosystem of the human gut. Using this approach, we isolated strain AT8^T (=CSUR P2118 = DSM 101782) from stool specimens collected from a 51-year-old obese French woman. Strain AT8^T is a strictly anaerobic, nonmotile, nonspore-forming gram-positive coccus that do not exhibit catalase and oxidase activities. 16S rDNA-based identification of strain AT8^T demonstrated 92% gene sequence similarity with Eggerthella lenta DSM 2243, the phylogenetically closed validly named type species. Here, we present a set of features for the strain AT8^T and the description of its complete genome sequence and annotation. The 2,091,845 bp long genome has a G+C content of 63.46% and encodes1,849 predicted genes; 1,781 were protein-coding genes, and 68 were RNAs. On the basis of the characteristics reported here, we propose the creation of a new bacterial genus Hugonella gen. nov., belonging to the Eggerthellaceae family and including Hugonella massiliensis gen. nov., sp. nov., strain AT8^T as the type strain.

Keywords: Hugonella massiliensis sp. nov.; culturomics; obesity; taxonogenomic.

Figure 1

Phylogenetic tree highlighting the position of Hugonella massiliensis strain AT8^T relative to other close strains. Sequences were aligned using Muscle v3.8.31 with default parameters and phylogenetic inferences were obtained using neighbor‐joining method with 500 bootstrap replicates, within MEGA6 software. The scale bar represents a 0.1% nucleotide sequence divergence

Figure 2

Gel view comparing Hugonella massiliensis strain AT8^T to other closely related species. The gel view displays the raw spectra of strain AT8^T of loaded spectrum files arranged in a pseudo‐gel like look. The x‐axis records the m/z value. The left y‐axis displays the running spectrum number originating from subsequent spectra loading. The peak intensity is expressed by a gray scale scheme code. The right y‐axis indicates the relation between the color of a peak and its intensity, in arbitrary units. Displayed species are indicated on the left

Figure 3

Graphical circular map of the chromosome. From outside to the center: Genes on the forward strand colored by Clusters of Orthologous Groups (COG) categories (only gene assigned to COG), genes on the reverse strand colored by COG categories (only gene assigned to COG), RNA genes (tRNAs green, rRNAs red), G+C content, and G+C skew

Figure 4

Distribution of functional classes of predicted genes according to the clusters of orthologous groups of proteins of Hugonella massiliensis strain AT8^T and other close related species