A phylogenetic tree of the 73 strains in SM1 based on a multiple sequence alignment of the V3–V6 region of the 16S rRNA gene. Colored circles indicate the family-level assignment of each strain using the DADA2 assignTaxonomy function with the SILVA 138.1 database: Lachnospiraceae, blue; Bacteroidaceae, bright pink; Tannerellaceae, dark green; Rikenellaceae, light purple; Ruminococcaceae, light green; Oscillospiraceae, dark blue; Erysipelotrichaceae, orange; Akkermansiaceae, dark red. Also shown is a heatmap denoting detection (green cells) in the three replicate bioreactors after 19 days continuous culture.
