Whole genome sequencing and functional analysis of porcine-borne Bacillus coagulans LYBC06

Bacillus coagulans LYBC06 strain with lactate-producing capacity was isolated from mucosal tissue of the digestive tract of a fattening pig. The resequencing of the LYBC06 strain revealed that the overall genome was less variable, with a genome-wide heterozygous ratio of 0.042 %, total SNP locus variants 0.4273% of the entire genome, total InDel mutations 0.0182%, total increased and decreased CNV copies 0.0031% and total SV annotated variants 0.0083% of the entire genome. The mutated genes were mainly involved in the growth of the strain, regulation of energy metabolism, and production of proteases and lactate. The whole genome of LYBC06 strain was sequenced with the length of 3385106 bp, GC content of 46.86% and 4092 coding genes (85.96% of coding). Functional annotation of the proteins encoding genes showed that the growth process of LYBC06 strain involved several metabolic pathway transformation processes of various substances, and many encoding genes were involved in the resistance to macrolides, polypeptides and tetracyclines. The basic characteristics of the genome of LYBC06 strain were relatively similar to those of other Bacillus coagulans, and the collinearity between several Bacillus coagulans strains was relatively good. Bacterial growth, gene expression of lactate dehydrogenase and lactate production in LYBC06 strain were largely synchronized, and the maximum amount of lactate could be produced up to 92 g/L at 16 h culture during the logarithmic growth phase, in which the LdhL1 gene played an important role in the production of lactate in LYBC06 strain.

Automated summary

Bacillus coagulans LYBC06 strain with lactate-producing capacity was isolated from a fattening pig's digestive tract. Resequencing revealed a less variable genome with a heterozygous ratio of 0.042%, SNP variants of 0.4273% and InDel mutations of 0.0182%. Mutated genes were involved in strain growth, energy metabolism regulation, and production of proteases and lactate. The LYBC06 strain had similar characteristics to other Bacillus coagulans strains and the production of lactate was associated with the LdhL1 gene.