In vitro model reveals structural and metabolic insights to the porcine caecal microbiota in response to β-mannan exposure

The gastrointestinal microbiota plays a pivotal role in shaping host physiology and health. By selectively promoting bacteria associated with improved host health, microbiota-directed fibres offer a strategy to enhance the beneficial functions of the microbiota. In this work, we developed a pH-controlled in vitro fermentation system (InVitSim) as a model to evaluate the effects of such a fibre - acetylated galactoglucomannan from Norway spruce - on the composition and functionality of porcine caecal microbial communities. We validated the experimental outcomes by comparing the response of the in vitro model to a previous in vivo feeding trial utilising the same {beta}-mannan fibres. Long-read sequencing with Oxford Nanopore, metatranscriptomics, and short-chain fatty acid measurements were undertaken to survey microbial community dynamics and functionality. Microbial communities in pigs and InVitSim responded similarly to {beta}-mannan supplementation, with taxa like Prevotella, Catenibacterium, and Faecalibacterium increasing in abundance. Intriguingly, some taxa were observed to be more affected by {beta}-mannan supplementation in InVitSim than in vivo. These taxa included several bacterial species that were not previously known to utilise {beta}-mannan, yet exhibited upregulated genes encoding carbohydrate-active enzymes involved in the degradation of this substrate. ImportanceIn this study, we establish a fermenter system able to preserve more than 70% of over 300 distinct microbial taxa identified in the porcine caecal gut. The in vitro model and the functional omic data generated from it enabled us to identify relevant microbial populations that responded to the presence of AcGGM by upregulating {beta}-mannan-specific polysaccharide utilisation loci. Our results highlight the value of in vitro approaches as a complementary tool to in vivo trials for learning about the gastrointestinal microbiomes response to dietary interventions on the host level. Description of supplementary filesO_LIIn-depth analyses for in vitro model validation and investigations. C_LIO_LICommon taxa between in vivo and in vitro systems exposed to {beta}-mannans. C_LIO_LIDifferential abundance analysis result visualisations. C_LIO_LIShort-chain fatty acid concentrations and correlation with microbial abundances. C_LI