Complete genome sequence of Bacillus coagulans CACC834 isolated from canine.

Bacillus coagulans CACC 834 was isolated from canine feces, and its potential probiotic properties were characterized by functional genome analysis. Whole-genome sequencing of B. coagulans CACC 834 was performed using the PacBio RSII platforms. The complete genome assembly consisted of one circular chromosome (3.1 Mb) with guanine (G) + cytosine (C) content of 47.1%. Annotation revealed 3,181 protein-coding sequences (CDSs), 30 rRNAs, and 83 tRNAs. Gene associated 11% of the genes were involved in replication, recombination, and repair. We also annotated various stress-related, acid resistance, bile salt resistance and adhesion-related domains in this strain, which likely provide support in exerting probiotic action by survival under gastrointestinal tract. These results add to our comprehensive understanding of B. coagulans and suggest potential mammal-related industrial applications. © Copyright 2021 Korean Society of Animal Science and Technology.

Bacillus coagulans strains are gram-positive, spore-forming, and produce lactic acid, which possesses the capacity to balance intestinal gut microbiota, ultimately promoting the growth of animals and improving immunity [1,2]. In addition, B. coagulans is resistant to high temperatures because of its probiotic activity, modulates and strengthens the immune system to protect against infections, and minimizes inflammation-related tissue damage [3].

We isolated B. coagulans CACC 834 (KACC 22145) from the feces of a female 3-year-old Boston terrier in Korea. The samples were incubated under anaerobic conditions at 37°C [4].

Whole-genome sequencing was performed using the Pacific Biosciences (PacBio) RS II Single Molecule Real Time (SMRT) platform with a 20 kb SMRTbellTM template library at ChunLab. The reads were assembled using the PacBio SMAR Analysis 2.3.0. [5].

The sequences were annotated using the combined results of the automatic National Center for Biotechnology Information (NCBI) Prokaryotic Genome Annotation Pipeline (PGAP) and Rapid Annotations using Subsystems Technology (RAST) [6].

The complete genome of B. coagulans CACC 834 was composed of a 3,077,319 bp circular chromosome with 47.1% guanine (G) + cytosine (C) content. The genome contained 3,181 protein-coding sequences (CDS), 30 rRNAs, and 83 tRNAs (Table 1). The genome features of B. coagulans CACC 834 are summarized in Fig. 1. Among these CDS, 2,909 genes were classified into 20 clusters of orthologous groups (COG) functional categories (Fig. 1B). More than 41% of genes were involved in transport and metabolism, including amino acid, carbohydrate, inorganic ion, nucleotide, coenzyme, and lipid. Interestingly, 11% of the genes were involved in replication, recombination, and repair (Fig. 1B).

Table 1.

Genome overview of Bacillus coagulas CACC834

Feature	Values
Genome size (bp)	3,077,319
No. of contigs	1
GC content	47.1%
Protein-coding genes (CDSs)	684
rRNA	30
tRNA	83
plasmid	0
Genbank Acession No.	CP076597

Fig. 1.

Genome features of Bacillus coagulans CACC834.

(A) Circular genome maps of B. coagulans CACC834 chromosome. Circles from the outside to the center denote rRNA and tRNA gene, reverse strand CDS, forward strand CDS, GC skew, and GC content. (B) Genome number of COG categorie. CDS, protein-coding genes; COG, clusters of orthologous group; G, guanine; C, cytosine.

The genome of B. coagulans CACC 834 possessed hsp20, hsp60, dnaK, dnaJ and grpE operons, encoding enzymes and proteins for heat shock. Also, B. coagulans CACC 834 has heat shock induced genes, such as clpB, clpP, mcsB, and repair-related genes, such as recA and uvrABC. The expression of these genes is expected to help promote cell recovery from heat shock by limiting damage caused by stress [7-9]. Furthermore, B. coagulans CACC 834 carried genes known to be involved in lactate synthesis, adhesion, acid resistance, and bile resistance (Table 2).

Table 2.

Predicted genes involved in probiotic potency in B. coagulans CACC834

Predicted function	B. coagulans CACC834
	Predicted genes	Start position	End position	Length (bp)
Lactate synthesis	ldh	1,433,259	1,434,242	984
Adhesion protein	EpsD	393,741	394,838	1,098
	FliD	724,445	726,531	2,088
Acid resistance-related
Protection or repair of macromolecules	dnaK	1,737,678	1,737,546	1,827
	dnaJ	1,736,410	1,737,546	1,137
	grpE	1,739,540	1,740,202	663
	recA	125,046	1,226,113	1,068
	uvrABC	765,135	767,135	2,001
	clpB	108,312	110,762	2,451
	clpP	793,689	794,279	591
	mcsB	108,312	110,762	2,451
Fatty acid synthesis	fabF	870,816	871,754	1,242
	fabH	871,824	873,065	939
	fadD	260,088	261,242	1,155
	fabI	903,131	903,910	780
Acid shock response	aspS	1,804,625	180,696	1,773
Metabolic rearrangements	alsD	2,318,874	2,319,623	750
Gylcine betain ABC transport system	opuCC	467,919	468,833	915
Bile salt resistance	bass	1,090,675	1,091,145	471

This study on complete genome sequence of B. coagulans CACC 834 may increase our understanding of the probiotic effects in host healthcare and extend its potential application as an industrial strain.

The complete genome of B. coagulans strain CACC 834 determined in this study has been deposited in the NCBI GenBank database under accession number CP076597.