Draft Genome Sequence of Faecalimonas umbilicata JCM 30896T, an Acetate-Producing Bacterium Isolated from Human Feces.

Here, we report the draft genome sequence of Faecalimonas umbilicata JCM 30896T, an acetate-producing bacterium isolated from human feces. The genomic analysis reveals genes for acetate and vitamin B12 synthesis and will facilitate the study of the role of this strain in the human gut.

ANNOUNCEMENT

Acetate is one of the metabolic end products of anaerobic fermentation. Butyrate-producing bacteria, such as Faecalibacterium prausnitzii and Roseburia spp., can be net utilizers of acetate (1). The butyrate formed by the above-mentioned acetate-consumers has important roles in colonic health (1). Recently, we isolated a new acetate-producing bacterium, Faecalimonas umbilicata JCM 30896T, from a fecal sample from a healthy Japanese man (2). This species is a member of the family Lachnospiraceae. Anaerobic bacteria affiliated with the family Lachnospiraceae make up the majority of highly prevalent bacteria in the human intestinal tract (3). We analyzed the draft genome sequence of F. umbilicata JCM 30896T to improve our understanding of the physiology and potential health contribution of this strain in the human gut.

F. umbilicata JCM 30896T was grown on Eggerth-Gagnon agar (Merck) supplemented with 5% (vol/vol) horse blood for 4 days at 37°C under a H2-CO2-N2 (1:1:8, by volume) gas mixture. Total genomic DNA was extracted from F. umbilicata JCM 30896T using a Genomic-tip 100/G kit (Qiagen). Labiase (5.0 mg/ml; Cosmo Bio) was used to lyse bacterial cells. A whole-genome shotgun library was constructed using a SMRTbell template prep kit 1.0 (Pacific Biosciences), followed by single-molecule real-time (SMRT) sequencing conducted on the PacBio RS II sequencing system (Pacific Biosciences) by Takara. A total of 97,745 reads (311-fold coverage) with an average length of 13,372 bp were assembled de novo using Hierarchical Genome Assembly Process version 3.0 (HGAP3.0) in SMRT Analysis version 2.3.0 (4), resulting in 8 contigs with an N50 value of 1,731,485 bp. The default settings for genome assembly were used. This assembly resulted in a draft genome sequence of 3,262,821 bp with a G+C content of 41.6%. Analysis of the genome sequences was performed using the DDBJ Fast Annotation and Submission Tool (DFAST; https://dfast.nig.ac.jp/) (5). A total of 3,210 protein-coding sequences, 60 tRNAs, and 18 rRNAs were detected.

The genome of F. umbilicata JCM 30896T contained genes involved in acetate synthesis, such as formate acetyltransferase (EC 2.3.1.54), phosphotransacetylase (EC 2.3.1.8), and acetate kinase (EC 2.7.2.1). In addition, F. umbilicata JCM 30896T was predicted to possess a vitamin B12 biosynthesis pathway. Vitamin B12 is an important cofactor for a variety of enzymes. In the systematic genome assessment of B vitamin biosynthesis, vitamin B12 biosynthesis was present in 42% of the genomes of 256 common human gut bacteria (6). Furthermore, nearly half of the Firmicutes genomes (43%; 56/130) were predicted to synthesize vitamin B12 (6). Recently, true bidirectional metabolic cross-feeding dependent on vitamin B12 was observed between the mucin-degrading bacterium Akkermansia muciniphila and the butyrate-producing bacterium Eubacterium hallii (7). The production of vitamin B12 and acetate by F. umbilicata might be beneficial for growth with other bacteria lacking the vitamin B12 biosynthesis pathway, such as A. muciniphila (8), and production of butyrate by butyrate-producing bacteria, such as F. prausnitzii.

The genome sequence will facilitate further studies of the beneficial role of this strain in the human gut.

Data availability.

This whole-genome shotgun project has been deposited in DDBJ/ENA/GenBank under the accession no. BHEO00000000. The version described in this paper is the first version, BHEO01000000.