Interactions between gut commensal bacteria and polysaccharides derived from algae and legumes: identification of metabolites produced and pathways involved.

UNLABELLED: Diet is a key driver of gut microbiome functions, largely via microbial fermentation of dietary fibers. We investigated how 15 human gut commensals from Bacteroidota, Bacillota, and Actinomycetota metabolize structurally distinct poly-/oligosaccharides from algae (Ulva lactuca, Saccharina latissima, Undaria pinnatifida) and chickpeas (Cicer arietinum). In low-nutrient, carbon-defined cultures, we quantified growth (ΔOD), acidification (ΔpH), and short-chain fatty acids (SCFAs). Then, we conducted untargeted liquid chromatography-high-resolution mass spectrometry (LC-HRMS) metabolomics and RNA sequencing on eight representative strains. Chickpea raffinose-family oligosaccharides (RFOs) broadly stimulated growth, fermentation, and SCFA production across phyla, whereas algal polysaccharide use was restricted to specific Bacteroidota species. Metabolomics revealed phylum- and strain-resolved signatures and bioactive molecules beyond SCFAs, including tryptophan derivatives (for example, indolelactic acid), γ-aminobutyric acid (GABA), and micronutrient-related compounds (for example, riboflavin), whose abundance depended on both taxon and substrate. Transcriptomic analysis in the presence of raffinose indicated coordinated activation of carbohydrate-active enzymes (CAZymes), specialized transport systems (SusC/D, TonB, or ATP-binding cassette [ABC] transporters), and transcriptional regulators (for example, LacI), consistent with substrate-responsive carbohydrate gene clusters. Bacteroidota exhibited the largest CAZyme mobilization and transcriptional remodeling, while Bacillota and Actinomycetota showed targeted responses consistent with narrower substrate scopes.

CONCLUSIONS

Fiber structure mechanistically links to selective microbial functions. Pulses-derived RFOs elicit broad, phylum-specific metabolic programs, and algae polysaccharides engage a limited set of Bacteroidota specialists. This integrative framework (growth, SCFAs, metabolomics, transcriptomics) refines how discrete fiber types can be matched to microbial capacities, informing precision-nutrition strategies that leverage sustainable fibers (pulses, algae) to promote health-relevant metabolites and targeted microbiome modulation.