Extended Data Figure 7: Food-associated microbes and their enteric abundance over time.

a, Major bacterial and fungal taxa found in plant-based diet menu items were determined using 16S rRNA and ITS sequencing, respectively, at the species (s), genus (g) and order level (o). The majority of 16S rRNA gene sequences are Streptophyta, representing chloroplasts from the ingested plant matter. b, One of the fungi from a, Candida sp., showed a significance increase in faecal abundance on the plant-based diet (P < 0.05, Wilcoxon signed-rank test). c, Levels of bacteria and fungi associated with the animal-based diet are plotted over the plant- and animal-based diet arms. Taxa are identified on the genus (g) and species (s) level. The abundance of foodborne bacteria was near our detection limit by 16S rRNA gene sequencing; to minimize resulting measurement errors, we have plotted the fraction of samples in which bacteria are present or absent. Lactococcus lactis, Pediococcus acidilactici and Staphylococcus-associated reads all show significantly increased abundance on the animal-based diet (P < 0.05, Wilcoxon signed-rank test). Fungal concentrations were measured using ITS sequencing and are plotted in terms of log-fractional abundance. Significant increases in Penicillium-related fungi were observed, along with significant decreases in the concentration of Debaryomyces and a Candida sp. (P < 0.05, Wilcoxon signed-rank test). One possible explanation for the surprising decrease in the concentration of food-associated fungi is that the more than tenfold increase in Penicillium levels lowered the relative abundance of all other fungi, even those that increased in terms of absolute abundance.