16S rRNA sequences included in our analysis are listed in Table S1. We included the centroid sequences from the UPARSE pipeline to represent each of the OTUs assigned to the Flavonifractor genus using the UTAX algorithm with at least 40% confidence (see above). We also used blastn to search NCBI’s 16S ribosomal RNA database using OTU41 as a query. Sequences from the top hits were included. Sequences of two strains of Lachnospiraceae bacterium were included as an outgroup.

The online 16S aligner from SILVA, SINA (v1.2.11) [118], was used to align these 16S rRNA sequences. The alignment was filtered with Mothur (v.1.36.1) [119] to retain only the V4 region. A phylogenetic tree was constructed using RAxML (v7.7.8) [120] using the GTRCAT model with 100 rapid bootstraps (9 out of 39 branches had ≥50% bootstrap support values). The resulting tree was rooted with the Lachnospiraceae outgroup strains.

To generate the 16S phylogeny containing both OTUs from this study and the reference genomes, the annotated 16S rRNA genes were extracted and aligned as above, and the V4 region was retained. These alignments were used to generate a phylogenetic tree, as above, rooting the tree using Clostridium viride as an outgroup.

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