Metagenomic and Meta-Transcriptomic Analysis Reveal the Colonization and Expression Profile of Probiotic Strains in Humans and Animals

In humans and animals, probiotics are widely accepted as crucial for host health and growth. The investigation of the probiotic colonization and expression of probiotics in the host is beneficial for proper usage of probiotics and isolation of indigenous probiotics. In this study, we analyzed commonly used probiotic strains in the intestines/rumen of humans and animals by analyzing metagenomic and paired meta-transcriptomic data from the gut or rumen microbiome of humans (n = 13), pigs (n = 6), chickens (n = 6), cattle (n = 14), sheep (n = 10), and mice (n = 8). First, we generated an expression profile based on 192 selected representative probiotic strains from a published database. A total of 58 probiotic strains were not detected in any samples, while 3 strains were presented and expressed in all individuals. Overall, the probiotic expression of probiotics as detected by meta-transcriptome was significantly higher than the relative abundance of probiotic as detected by metagenomics in cattle, sheep, mice, and humans; however, this difference was not significant in pigs and chickens. In total, 17 (cattle), 21 (sheep), 22 (pig), 14 (chicken), 13 (mouse), and 3 (human) probiotic strains were identified as probiotic strains with significantly higher expression levels [Fold Change (FC) ≥ 2, False Discovery Rate (FDR) ≤ 0.05]. Among them, Clostridium butyricum TOA was found to be significantly expressed in the rumen or gut of all host species. In addition, network analysis based on the expression of probiotics as detected by meta-transcriptomics revealed that several probiotic strains were significantly negatively linked with Salmonella spp., Mycoplasma spp., and Escherichia coli. The results in this study provide a useful reference for developing indigenous probiotics.