Identification of prophages in Bacillus licheniformis in sauce-flavor baijiu fermentation

Abstract:

[Background] Phages are an important part of microbial community, but the classification and presence of them in traditional baijiu fermentation are still unclear. [Objective] By exploring prophage regions in the genomes of Bacillus licheniformis in public databases and in sauce-flavor baijiu fermentation, we intend to clarify the classification and infection of prophages in key functional strains in traditional sauce-flavor baijiu fermentation. [Methods] With culture-independent (bacterial whole genome analysis) and culture-dependent (strain screening and specific PCR) techniques, the classification and presence of prophages in B. licheniformis from different natural habitats and sauce-flavor baijiu fermentation were analyzed. [Results] The whole genome analysis of bacteria detected 165 prophages in genomes of 30 B. licheniformis strains from different habitats, of which 63.6% (105/165) had intact sequences. A total of 97.1% of the prophages in the B. licheniformis belonged to Siphoviridae, and 2.9% Myoviridae. The functions of 53.0% genes of the intact prophages were unknown. Seven integrated prophage regions were detected in sauce-flavor baijiu-derived B. licheniformis MT-B06, of which 57.1% (4/7) were intact prophage regions. Co-infection of multiple prophages was detected in B. licheniformis from sauce-flavor baijiu fermentation. There was horizontal gene transfer of CotD family spore coat protein gene on the bacterial genome to the prophage. In the 26 sauce-flavor baijiu-derived B. licheniformis strains, 69.2% (18/26) were detected positive of prophage-encoded major capsid protein gene, and 100.0% (26/26) positive of prophage-encoded CotD family spore coat protein gene. [Conclusion] High level of prophage integration was found in B. licheniformis from different natural habitats and sauce-flavor baijiu fermentation. Horizontal gene transfer of CotD family spore coat protein gene from host to the prophage of B. licheniformis in sauce-flavor baijiu fermentation was widely observed. This study is the first time to explore the classification and presence of bacteriophages in traditional baijiu fermentation, which helps to deepen the understanding of bacteriophage-host interaction in the fermenting microbial community.