GitHub repository: data, results, and analysis pipeline.

Project: "In vitro modelling of the structure and metabolism of the porcine caecal microbiota in response to β-mannan exposure" (FigShare link).

Item description: GitHub repository containing processed data, result files, and the analysis pipeline in the form of an R Markdown report.

Abstract: The intestinal microbiota plays a pivotal role in host health. Prebiotics and microbiota-directed fibres that target health-promoting microbes can potentially enhance the beneficial effects of the microbiota. β-mannans are fibres that may be utilised by a selection of beneficial bacteria, such as Roseburia, Faecalibacterium, and Prevotella species. Here, we conducted an in vitro fermentation experiment using porcine caecal material from an in vivo feeding trial with the inclusion of acetylated galactoglucomannan (AcGGM) from Norway spruce. We validated the effect of AcGGM on population abundance changes in the in vitro microbial community by comparison to an in vivo community. Functional data were obtained using metatranscriptomics to investigate gene expression of mannan-degrading enzymes during growth on AcGGM, and measurements of produced short-chain fatty acids. The in vitro fermentation identified several AcGGM-utilising taxa that significantly increased in abundance when grown on the substrate, while the same taxa were not observed to be more abundant in AcGGM-fed pigs. These taxa included several species with upregulated genes for mannan degradation that were previously unknown to utilise β-mannan.