<i>Bifidobacterium longum</i> subsp. <i>infantis</i> as widespread bacteriocin gene clusters carrier stands out among the <i>Bifidobacterium</i>

Abstract

<i>Bifidobacterium</i> is the dominant genus, particularly in the intestinal tract niche of healthy breast-fed infants, and many of these strains have been proven to elicit positive effects on infant development. In addition to its effective antimicrobial activity against detrimental microorganisms, it helps to improve the intestinal microbiota balance. The isolation and identification of bacteriocins from <i>Bifidobacterium</i> have been limited since the mid-1980s, leading to an underestimation of its ability for bacteriocin production. Here, we employed a silicon-based search strategy to mine 354 putative bacteriocin gene clusters (BGCs), most of which have never been reported, from the genomes of 759 <i>Bifidobacterium</i> strains distributed across 9 species. Consistent with previous reports, most <i>Bifidobacterium</i> strains did not carry or carry only a single BGC; however, <i>Bifidobacterium longum</i> subsp. <i>infantis</i>, in contrast to other <i>Bifidobacterium</i> species, carried numerous BGCs, including lanthipeptides, lasso peptides, thiopeptides, and class IId bacteriocins. The antimicrobial activity of the crude bacteriocins and transcription analysis confirmed its potential for bacteriocin biosynthesis. Additionally, we investigated the association of bacteriocins with the phylogenetic positions of their homologs from other genera and niches. In conclusion, this study re-examines a few <i>Bifidobacterium</i> species traditionally regarded as a poor source of bacteriocins. These bacteriocin genes impart a competitive advantage to <i>Bifidobacterium</i> in colonizing the infant intestinal tract. IMPORTANCE Development of the human gut microbiota commences from birth, with bifidobacteria being among the first colonizers of the newborn intestinal tract and dominating it for a considerable period. To date, the genetic basis for the successful adaptation of bifidobacteria to this particular niche remains unclear since studies have mainly focused on glycoside hydrolase and adhesion-related genes. Bacteriocins are competitive factors that help producers maintain colonization advantages without destroying the niche balance; however, they have rarely been reported in <i>Bifidobacterium</i>. The advancement in sequencing methods and bacteriocin databases enables the use of a silicon-based search strategy for the comprehensive and rapid re-evaluation of the bacteriocin distribution of <i>Bifidobacterium</i>. Our study revealed that <i>B. infantis</i> carries abundant bacteriocin biosynthetic gene clusters for the first time, presenting new evidence regarding the competitive interactions of <i>Bifidobacterium</i> in the infant intestinal tract.