Generating a fucose permease deletion mutant in Bifidobacterium longum subspecies infantis ATCC 15697

An improved temperature-sensitive shuttle vector system for scarless gene deletion in human-gut-associated Bifidobacterium species

Bifidobacterium is a prevalent bacterial taxon in the human gut that comprises over 10 (sub)species. Previous studies suggest that these species use evolutionarily distinct strategies for symbiosis with their hosts. However, the underlying species-specific mechanisms remain unclear due to the lack of efficient gene knockout systems applicable across different species. Here, we developed improved temperature-sensitive shuttle vectors by introducing Ser139Trp into the replication protein RepB. We then used temperature-sensitive plasmids to construct a double-crossover-mediated scarless gene deletion system. The system was employed for targeted gene deletion in Bifidobacterium longum subsp. longum, B. longum subsp. infantis, Bifidobacterium breve, Bifidobacterium adolescentis, Bifidobacterium kashiwanohense, and Bifidobacterium pseudocatenulatum. Deletion of genes involved in capsular polysaccharide biosynthesis, aromatic lactic acid production, and sugar utilization resulted in the expected phenotypic changes in the respective (sub)species. The temperature-sensitive plasmids developed in this study will aid in deciphering the evolutionary traits of the human-gut-associated Bifidobacterium species.

Milk fat globule membrane protects Bifidobacterium longum ssp. infantis ATCC 15697 against bile stress by modifying global transcriptional responses

The milk fat globule membrane (MFGM) can protect probiotic bacteria from bile stress. However, its potential mechanism has not been reported. In this study, the viability, morphology and gene transcriptional response of Bifidobacterium longum ssp. infantis ATCC 15697 (BI_15697) stressed by bile salts with or without MFGM were investigated. It was shown that MFGM alleviated the reduction in BI_15697 population induced by 0.2% porcine bile stress and restored the population to the control levels. MFGM ameliorated the shrunken, fragmented appearance and irregular morphology of BI_15697 and maintained cell integrity disrupted by bile stress. RNA-sequencing results showed that MFGM increased transport of glucose and raffinose and decreased that of branched-chain amino acids (BCAA) in the presence of bile salts. MFGM stimulated the expression of genes involved in the synthesis of raffinose in galactose metabolism and the metabolism of BCAA, suggesting that MFGM stimulated the accumulation of raffinose and BCAA in the presence of bile. In addition, MFGM stimulated the expression of 2 bile efflux transporters under bile stress. Together, the multifactorial response helps BI_15697 excrete bile salts and maintain cellular integrity in response to bile stress. This study proposes a mechanism for the protection of BI_15697 against bile salt stress by MFGM, thereby providing a molecular basis for its application in incorporation of probiotics.

Priority effects shape the structure of infant-type Bifidobacterium communities on human milk oligosaccharides

Bifidobacteria are among the first colonizers of the infant gut, and human milk oligosaccharides (HMOs) in breastmilk are instrumental for the formation of a bifidobacteria-rich microbiota. However, little is known about the assembly of bifidobacterial communities. Here, by applying assembly theory to a community of four representative infant-gut associated Bifidobacterium species that employ varied strategies for HMO consumption, we show that arrival order and sugar consumption phenotypes significantly affected community formation. Bifidobacterium bifidum and Bifidobacterium longum subsp. infantis, two avid HMO consumers, dominate through inhibitory priority effects. On the other hand, Bifidobacterium breve, a species with limited HMO-utilization ability, can benefit from facilitative priority effects and dominates by utilizing fucose, an HMO degradant not utilized by the other bifidobacterial species. Analysis of publicly available breastfed infant faecal metagenome data showed that the observed trends for B. breve were consistent with our in vitro data, suggesting that priority effects may have contributed to its dominance. Our study highlights the importance and history dependency of initial community assembly and its implications for the maturation trajectory of the infant gut microbiota.