A metabolite-dependent mechanism by which Bifidobacterium animalis subsp. lactis promotes Bacteroides colonization

Combining sequence-based approaches with anaerobic microbiology and modelling to understand gut microbial communities.

Gut micro-organisms possess biochemical capabilities that far exceed those of their mammalian hosts, particularly in the ability to gain energy from the breakdown of diet-derived plant material (fibre). This article reviews investigations into gut microbial communities conducted by Harry Flint and his research group. First, extracellular cellulosome and amylosome enzyme complexes were found to mediate the breakdown of plant cell walls and resistant starch by specialised Firmicutes bacteria, both in the human colon and in the rumen. In contrast, Bacteroidetes (Bacteroides, Prevotella spp.) rely on their ability to capture soluble carbohydrates. Human dietary studies examining the impact of fibre sources upon microbiota composition and metabolism identified 'diet-responsive' species. In addition, dominant species of butyrate-producing bacteria, including a subset able to convert lactate to butyrate, were isolated from healthy human volunteers. Most produce butyrate from carbohydrates via butyryl-CoA:acetate CoA-transferase, with uptake of external acetate, while lactate conversion is associated with a highly inducible gene cluster (lct). In pH-controlled chemostat studies, mildly acid pH depressed growth of propionate-producing Bacteroidetes, but favoured butyrate production by Firmicutes. This may explain why % butyrate among SCFA increases with total faecal SCFA concentration in human studies. Although lactate is normally consumed by lactate-utilising bacteria, destabilisation of the microbial community associated with lactate accumulation can result in radically altered microbiota and metabolite profiles. A theoretical model based on microbial functional groups (MFG) was developed to better understand community dynamics. Consequences for nutritional research of our expanding knowledge of the microbial ecology of the human gut are considered.

Coculture of Collinsella aerofaciens and Bacteroides thetaiotaomicron under bile acid stress reveals vitamin B6 exchange

Although bile acid-mediated microbiome-host interactions are known to shape gut microbial composition and function, the mechanisms by which bile acid stress influences microbial metabolic interactions remain poorly understood. Here, we investigated the interaction between two key gut microbes, Bacteroides thetaiotaomicron and Collinsella aerofaciens, under deoxycholic acid (DCA) stress. In anaerobic coculture, C. aerofaciens mitigated the inhibitory effects of DCA on B. thetaiotaomicron, primarily through DCA uptake from the medium, as confirmed by DCA quantification. Proteomic analysis showed that DCA broadly disrupted amino acid and vitamin metabolism, particularly in B. thetaiotaomicron. In contrast, coculture promoted widespread metabolic activation in C. aerofaciens, including enhanced vitamin B6 metabolism and increased production of citrulline and ornithine. These findings suggest that metabolic cooperation enhances resistance to bile acid stress and may contribute to gut microbiome resilience, with potential relevance to liver- and bile acid-related disorders.

Surfactin-like lipopeptides contribute to interference competition of Bacillus velezensis against the marine Flavobacteriaceae in phycosphere.

This study demonstrates that Bacillus velezensis SPE2, a low-abundance isolate from the phycosphere of dinoflagellate, exhibits a wide degree of antagonistic activity against multiple marine Flavobacteriaceae strains, a dominant taxonomic group across the phycosphere of diverse phytoplankton species.

A gut symbiotic filamentous fungus reprograms host metabolism and the microbiota to confer radioprotection.

The gut mycobiome is increasingly linked to host physiology, yet functional insights are dominated by yeasts, leaving the roles of filamentous fungi largely unexplored. Here, we identify Mucor racemosus as a gut-resident symbiotic filamentous fungus that establishes intestinal colonization via both hyphal and spore forms. M. racemosus confers radioprotection through an integrated metabolic program coupling direct host support with microbiota-mediated amplification. The fungus produces L-glutamate, L-aspartate, and DL-lysine, which are transferred to the host to enhance DNA damage repair in radiation-exposed intestinal epithelial cells. In parallel, M. racemosus-derived methylthioadenosine remodels the gut bacterial community by enriching Limosilactobacillus reuteri and reprogramming sulfur metabolism to generate radioprotective methionine. This coordinated fungal-bacterial metabolic axis reinforces intestinal radiotolerance. Consistent with this mechanism, dietary administration of M. racemosus-fermented cheese confers radioprotection in vivo. Together, these findings establish gut filamentous fungi as active metabolic organizers of host-microbiota interactions.

Metabolic strategies of Enterobacteriaceae gut colonization.

Microbiome-mediated Biotransformation of Human Lactoferrin (effera®) Enhances Epithelial Barrier Function in an Ex Vivo Adult Model