Murine gut microbial metagenomes for understanding bacterial strain engraftment

Raw metagenomic data for the publication "Experimental evaluation of ecological principles to understand and modulate the outcome of bacterial strain competition in gut microbiomes." We performed systematic experiments in gnotobiotic mice to test the applicability of coexistence theory to the stable establishment of gut microbes and to determine if such information can be utilized to stably modulate the gut microbiota at the strain level. We selected two species of gut bacteria, Akkermansia muciniphila and Bacteroides vulgatus, based on their importance in modulating host metabolism and immunity. To study niche occupancy and intraspecific competition under close-to-natural but strictly controlled conditions, we utilized gnotobiotic mice colonized with complex microbiomes with and without A. muciniphila and B. vulgatus. We specifically tested (i) to what degree the absence of a species determines colonization, (ii) if colonization can be prevented or altered by prior introduction of another strain of a species, and (iii) the effect of colonization order on coexistence between strains of the same species. Finally, we applied the information gained from these experiments to design a subtractive antibiotic strategy with the aim of removing an A. muciniphila strain from an assembled community and replacing it with a different strain.