Fig. 3

Engraftment of germ-free mice with a defined community of human Clostridia and Erysipelotrichia isolates. a Placement of the members of a defined microbial community (strains 1, 3, 6, 7, 8, 9, 13, 14, 15, 16, 18, 21, 26, 27, 28, and 29) on a maximum likelihood phylogeny built from the alignments of 11 total single copy 30S and 50S ribosomal proteins, which were concatenated together for a total alignment length of 1822 amino acids. The tree encompasses 66 taxa, three of which being Alicyclobacillus species belonging to the class Bacilli that were included as an outgroup. Strain 4 from the defined microbial community was excluded from analysis because NCBI flagged its deposited genomic sequence as chimeric, containing sequences from two strains belonging to the same species, Hungatella hathewayi. Sequences that did not belong to strains within the defined microbial community were obtained from [26]. 150 non-parametric bootstraps were performed to determine confidence of branch placements (white triangle at a node indicate above 70% confidence). b Germ-free mice were engrafted with a community of 14 Clostridia and 3 Erysipelotrichia isolates and microbiota profiling performed on colon contents obtained five days later