Draft Genome Sequence of the Spore-Forming Probiotic Strain Bacillus coagulans Unique IS-2.

ITALIC! Bacillus coagulansUnique IS-2 is a potential spore-forming probiotic that is commercially available on the market. The draft genome sequence presented here provides deep insight into the beneficial features of this strain for its safe use as a probiotic for various human and animal health applications.

GENOME ANNOUNCEMENT

Among the lactic acid bacteria (LAB), spore formers have gained much attention due to their ability to withstand adverse conditions during production, downstream processing, storage, and gastric transit (1, 2). Their high survival rates under hostile conditions make them the primary choice of probiotic candidates to consume either as oral medications or for incorporation into functional foods. Bacillus coagulans Unique IS-2 has been isolated from healthy human feces (3) and has obtained a “no objection” rating from the U.S. FDA to its generally regarded as safe (GRAS) status. B. coagulans Unique IS-2 is a nontoxic, safe spore-forming probiotic, which has shown therapeutic effect in clinical disorders, like hypercholesterolemia (4), bacterial vaginosis (5), and acute diarrhea (6), and in the treatment of functional abdominal pain in children (7). Furthermore, in vitro studies have indicated the efficacy of this strain to withstand high temperatures, its gastric tolerance, and its ability to metabolize an array of sugars (3).

Here, we report the draft genome sequence of B. coagulans Unique IS-2 in order to unravel the genetic blueprint that confers its probiotic traits and safe use.

Whole-genome sequencing was performed using the Illumina MiSeq platform at the Institute of Microbial Technology (IMTECH), Chandigarh, India. The Illumina sequencing libraries were prepared using the Nextera XT sample preparation kit with dual indexing adaptors. A total of 971,128,104 paired-end reads were obtained, providing 282-fold coverage depth of the genome. Among them, 43,446,692 Illumina reads were de novo assembled using CLC Genomics Workbench 7.5. The assembled genome sequence was annotated by the RAST annotation pipeline Web server (8, 9) and by NCBI Prokaryotic Genome Annotation Pipeline (PGAP) version 2.9. rRNAs and tRNAs were annotated using RNAmmer (10) and tRNAscan-SE (11), respectively. The genome analysis was performed using the Artemis genome viewer (12).

The draft genome sequence assembled to 143 contigs composed of 3,446,692 bp, with an average G+C content of 46.4%. The genome contains a total of 3,870 protein-coding sequences (CDSs), including 80 tRNAs and 3 rRNAs, with a coding percentage of 84.2% and 1.12 gene density per kilobase. The genome consists of clustered regularly interspaced short palindromic repeat (CRISPR) cassettes and two putative bacteriocin operons.

Furthermore, SEED metabolic analysis revealed 2,638 functional genes (434 subsystems), of which the highest number accounted for central carbohydrate metabolism (501 genes, including xylose, sucrose, maltose, and maltodextrin and chitin utilization), amino acids and derivatives (361 genes), protein metabolism (240 genes), cofactors and vitamins (197 genes), RNA metabolism (142 genes), sporulation and dormancy (92 genes), and stress response (84 genes).

Generation of the complete genetic blueprint of B. coagulans Unique IS-2 revealed many interesting probiotic traits and shed light on the molecular mechanism at the base of its probiotic and beneficial properties, widening its horizons as a safe probiotic for extensive use in food and pharmaceutical preparations.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession no. JZDH00000000. The version described in this paper is version JZDH01000000.