Fig. 3: Identified RiPP families are present and transcribed in the healthy human microbiome.

a The data represents RiPP precursor families’ prevalence and average abundance across six human body sites. Each dot signifies a family, with bioactive ones in red and unknown ones in black. Blue numbers denote the count of bioactive and total families per site. Dark grey number in the brackets indicates the number of RiPPs that are present in at least 50% of individuals at each body site. b The Sankey diagram illustrates the distribution of RiPP families in the healthy human microbiome, categorizing them as either niche-specific (present in one site) or cross-niche (present in more than one site), and further differentiating them as genus/species-specific or genus/species-cross. c The t-SNE plot showcases the distinct profiles of RiPP precursor families in different body sites. The clustering of RiPP families within each body site indicates conservation. Each dot on the plot represents one metagenome sample. d Predicted activity of RiPP families. The scale represents the proportion of each predicted activity (upper) or uncharacterized RiPP families (bottom). The number in brackets indicates the count and percentage of the RiPP family relative to all families. The term “multiple” indicates multi-functional RiPPs. Different colors are used to highlight the connections between RiPP types and their predicted activities. e Presence and transcription of all RiPP classes in 281 paired metagenomic and metatranscriptomic data from fecal samples of healthy individuals. The pie charts present the percentage of transcribed RiPP families in each class that predicted bioactivity (red) or unknown (grey).