The raw sequencing reads used to generate the Flavonifractor sp. 54 genome assembly were downloaded from the NCBI SRA database (accession number ERR1022445). These reads were aligned back to the reference genome using bwa mem. The coverage of the annotated 16S rRNA gene relative to median coverage of the reference genome was determined and used to estimate the number of copies of this locus in the strain, approximately four copies. Further, Pilon (version 1.22) [136] was used to confirm there is no variation among the four copies of the gene.

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