Fig. 6: The ucd operon is prevalent in metagenomes and actively transcribed in urolithin C-metabolizing human fecal samples.

a Prevalence of ucd operon (at least one gene) and of a uroC-metabolizing species (at least one species) in fecal metagenomes from the CuratedMetagenomicData R package. Only studies with ≥ 200 participants are depicted. All 86 studies are available in Supplementary Fig. 17.b Summary of urolithin concentrations in human fecal slurries (n = 10 healthy donors) incubated with 100 μM uroC for 48 h. Data are represented as mean ± SEM (n = 3 experimental replicates). Participants (5 female, 5 male) were aged 21–43 years with BMI between 18.1–26.3. c Summary of urolithin concentrations in fecal slurries (n = 10 healthy donors) incubated with 100 μM uroC for 48 h. The presence of uroC-metabolizing species and of the ucd operon is denoted above the graph if the bacterium or operon was detected in the uroC-treated fecal slurry (Supplementary Fig. 18b, f, g). Data are representative of 1 replicate for each donor where DNA and RNA were also extracted from fecal slurries. d, e ucd gene-specific RT-PCR on fecal microbiota communities from 10 healthy donors using the primer set described in Fig. 2h. Samples are matched to the urolithin metabolism data in (c) and 16S rRNA sequencing in Supplementary Fig. 18a–e (all from 1 replicate for each donor). 1% agarose gel of amplicons derived from (d) uroC-metabolizing and (e) non-metabolizing fecal slurries. Bands corresponding to the E. bolteae ucd operon (~ 3.6 kb) are labeled with red arrows. The no template control (NTC) is the same for (d, e). See Supplementary Fig. 18h, i for the no reverse transcriptase control PCR reactions on the same samples. Source data are provided as a Source data file.