Complete Genome Sequence of Collinsella aerofaciens Isolated from the Gut of a Healthy Indian Subject

ABSTRACT

Collinsella aerofaciens, a rod-shaped nonmotile obligate anaerobe, is the most abundant actinobacterium in the gastrointestinal tract of healthy humans. An altered abundance of C. aerofaciens may be linked with several health disorders, including irritable bowel syndrome. In the present study, we report the complete genome sequence of C. aerofaciens strain indica.

GENOME ANNOUNCEMENT

The bacterium Collinsella aerofaciens is well known for its ability to ferment a range of plant and animal origin carbohydrates and for producing H₂, ethanol, short-chain fatty acids, and lactate in the human colon (1). C. aerofaciens is the major utilizer of lactose in the human colon. Several studies demonstrated that Collinsella and Bifidobacterium can modify the host bile acids to modulate the virulence and pathogenicity of enteric pathogens (2). Recently, it was reported that an altered abundance of Collinsella may also influence host plasma cholesterol levels (3). To understand the importance of C. aerofaciens in health and disease, it is important to explore its genomic repertoire and identify functions that potentially influence host physiology.

In the present study, C. aerofaciens strain indica was isolated from a fecal sample of a healthy adult Indian subject. An approximately 500-mg fecal sample was resuspended in 1 ml of phosphate-buffered saline (PBS), diluted serially in the same buffer, and plated on a prereduced Trypticase soy agar plate (pH 7.3) supplemented with 5% (vol/vol) defibrinated sheep blood. Bacterial cells were spread over the surface of the plates using four or five glass beads (3.00 mm). Plates were incubated for 48 h at 37°C in an anaerobic workstation (Whitley DG250) filled with 80% N₂, 10% CO₂, and 10% H₂. A single colony of C. aerofaciens was grown in 5 ml of tryptic soy broth (TSB) for 48 h. Growth of the cells in TSB was monitored by spectrophotometer. C. aerofaciens cells were harvested from 2 ml of culture by centrifugation (8,000 × g for 3 min), and the genomic DNA was extracted by the THSTI method (4).

The whole-genome sequencing of C. aerofaciens was carried out by utilizing 2 different DNA sequencing platforms, those from Illumina (HiSeq 2500 system) and Oxford Nanopore Technologies (MinION). The SPAdes tool was used to assemble error-corrected long Nanopore reads and Illumina reads, which generated a single contig. The assembled complete genome sequence of C. aerofaciens was evaluated by Sanger sequencing. The complete genome of C. aerofaciens strain indica is 2,306,349 bp in length, with 60.1% GC content.

The analysis of the 2.30-Mb genome sequence of C. aerofaciens identified 1,995 genes, including 75 RNA-encoding genes. The genome has 276 subsystems and is enriched with protein (231 open reading frames [ORFs]), carbohydrate (226 ORFs), amino acid (200 ORFs), cofactor, and vitamin (102 ORFs) metabolic functions. The C. aerofaciens genome is also enriched with fatty acid, lipid, and isoprenoid metabolic functions (56 ORFs). However, the C. aerofaciens genome has several antibiotic resistance genes, such as β-lactamase, tetracycline resistance and ribosome protection functions, and multidrug resistance efflux pumps, but no gene was detected for the subcategory of virulence, pathogenicity, and disease development. The complete genome sequence of C. aerofaciens strain indica will contribute to a better understanding of the biology of the commensal and the molecular basis of its dominance in the gut of Indian subjects.

Accession number(s).

The whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number CP024160. The version described in this paper is CP024160.1.