In vivo human and swine gut microbiomes

Gut microbiota can have important metabolic functions that impact host health, and in vitro models offer an important avenue for studying how bacteria interact to transform dietary inputs into metabolites and proteins that affect the host. However, establishing such models with high microbiota recovery and long-term stability remains a significant challenge. Here we developed an in vitro intestinal model (X-Gutor) through a continuous optimization strategy based on integrating microbial source tracking, metagenomics and short-chain fatty acid (SCFAs) analysis to monitor temporal changes in gut community profiles, gene-encoded function and metabolism. A gut metabolism database (GutDB) was devised to enable efficient metabolic profiling and interaction demultiplexing of gut microbiota. The resulting X-Gutor models for human and swine gut microbiota recovered 96.27 ± 4.92% and 90.48 ± 5.95%, respectively, of the original set of species and maintained this level of diversity for 4 months. The X-Gutor model was able to recapitulate Prevotella as a major population in both human and swine gut microbiota that has complex growth-niche-based interactions with Bacteroides, Lactobacillus and Succinivibrio species, as a function of diet/redox-potential, pH and biofilm-matrix. The X-Gutor model can serve as an important in vitro discovery platform for exploration of gut microbiota responses to diet, therapeutics and probiotics.