zoo microbiome

Functionality of intestinal microbiota depends on diet and gut physiology; how these factors contribute to the occurrence of specific microbiota activities has not been completely revealed. Microbial pdu and cbi-cob-hem clusters encode the key enzyme glycerol/diol dehydratase (PduCDE) that mediates the transformation of dietary nutrients glycerol to 1,3-propanediol and 1,2-propanediol to propionate, and enzymes for cobalamin synthesis, a co-factor and shared good of microbial communities. We aimed to investigate whether Pdu related traits of intestinal microbiota are associated with diet and gut physiology via genetic and metabolic biomarkers. We analyzed fecal samples of 55 species (n=104) from Mammalia and Aves class using a novel approach combining metagenomics with quantification of genetic biomarkers in fecal samples and metabolic biomarkers during in vitro fermentation. Microbial diversity was evaluated via phylogenetic analysis of MAGs assembled from metagenomic sequencing of animal fecal samples and discovered > 1800 novel metagenomes of unknown species . Occurence and activity of pdu/cbi-cob-hem was identified as a common feature of animal microbiota while few taxa (58/5040 metagenomic assembled genomes) harbored pdu operon. Higher amounts of 1,3-propanediol and propionate produced by hindgut-fermenting carnivores/omnivores in vitro were consistent with higher diversity and abundance of pdu/cbi-cob-hem profile in microbial communities. This trait-based study suggests gut physiology and diet direct the potential of gut microbiota to utilize glycerol/1,2-propanediol and to produce cobalamin with a higher occurrence in hindgut fermenters. Our approach combining metagenomics with phenotypic analysis enabled the prediction of a common function in animal fecal microbiota by metabolic and genetic biomarkers.