Complete Genome Sequence of Faecalibacterium prausnitzii Isolated from the Gut of a Healthy Indian Adult

ABSTRACT

Faecalibacterium prausnitzii is the most abundant (~4%) member of the phylum Firmicutes found in the colon of healthy humans. It is a strict anaerobe and plays an important role in intestinal homeostasis. Here, we report the complete genome sequence of F. prausnitzii strain Indica.

GENOME ANNOUNCEMENT

Faecalibacterium prausnitzii, a non-spore-forming and nonmotile bacterium closely related to members of Clostridium cluster IV, inhabits the colon of healthy humans and plays an important role in host physiology by modulating gut immunity and inflammation and by providing several metabolic functions to humans (1). Depletion of F. prausnitzii and reduced diversity of gut microbiota are often associated with the frequent incidence, prevalence, and severity of inflammatory bowel disease (2–4) and undernutrition (5). To understand the contribution of F. prausnitzii in host physiology, it is important to isolate commensal strains from different parts of the world and explore their genomic repertoire.

In the present study, we isolated F. prausnitzii strain Indica from the fecal sample of a healthy adult Indian subject. A fresh fecal sample was directly resuspended in prereduced phosphate-buffered saline, diluted, and plated on a trypticase soy agar plate (pH 7.0) supplemented with 5% (vol/vol) defibrinated sheep blood and 0.5 g/liter l-cysteine-HCl and 33 mM potassium acetate. Plates were incubated for 48 h at 37°C in an anaerobic workstation (Whitley DG250) filled with 80% N₂, 10% CO₂, and 10% H₂. The genomic DNA of F. prausnitzii was extracted by a Translational Health Science and Technology Institute (THSTI) method after 48 h of incubation in rich medium under anaerobic growth conditions (6).

The complete genome sequencing of F. prausnitzii was done using Illumina (HiSeq 2500 System) and Oxford Nanopore Technologies (MinION) DNA sequencing platforms. Error-corrected long Nanopore and Illumina reads were used for the hybrid assembly with the SPAdes tool, which generated a single contig. The assembly was evaluated using Sanger sequencing. The assembled genome of F. prausnitzii strain Indica is 2,868,932 bp in length and has a GC content of 56.9%.

Analysis of the 2.86-Mb genome sequence of F. prausnitzii revealed 2,707 coding sequences, including 77 RNAs encoding genes. The genome is highly enriched with carbohydrate metabolic functions (215 genes). In addition to genes encoding central carbohydrate metabolism (63 genes), the F. prausnitzii genome contains a large number of genes encoding monosaccharide (50 genes), disaccharide and oligosaccharide (56 genes), and polysaccharide (9 genes) utilization functions. More than 14 genes in the F. prausnitzii genome are linked to fermentation functions that can efficiently ferment dietary carbohydrates into short-chain fatty acids, such as formate, acetate, propionate, butyrate, and mixed acids. Moreover, the genome of F. prausnitzii encodes several cofactors, vitamins, prosthetic groups, and functions for pigment biosynthesis (109 genes). Surprisingly, we also observed that the F. prausnitzii genome harbors 51 genes that can encode resistance against several antibiotics, including beta-lactams, fluoroquinolones, tetracyclines, aminoglycosides, and macrolides. Several efflux pumps (the major facilitator superfamily, the resistance-nodulation-cell division family, the small multidrug resistance family, the multidrug and toxic compound extrusion family, and the ATP-binding cassette family) encoding genes present in the genome of F. prausnitzii can contribute to antibiotic resistance and detoxification of xenobiotic compounds. The complete genome sequence of F. prausnitzii strain Indica will contribute to a better understanding of the biology of this commensal strain and the molecular basis of its dominance in the gut of Indian subjects.

Accession number(s).

This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number CP023819. The version described in this paper is the first version, CP023819.1.