Diversity and functions of the sheep faecal microbiota: a multi‐omic characterization

Abstract

SummaryLittle is currently known on the microbial populations colonizing the sheep large intestine, despite their expected key role in host metabolism, physiology and immunity. This study reports the first characterization of the sheep faecal microbiota composition and functions, obtained through the application of a multi‐omic strategy. An optimized protocol was first devised for DNA extraction and amplification from sheep stool samples. Then, 16S rDNA sequencing, shotgun metagenomics and shotgun metaproteomics were applied to unravel taxonomy, genetic potential and actively expressed functions and pathways respectively. Under a taxonomic perspective, the sheep faecal microbiota appeared globally comparable to that of other ruminants, with Firmicutes being the main phylum. In functional terms, we detected 2097 gene and 441 protein families, finding that the sheep faecal microbiota was primarily involved in catabolism. We investigated carbohydrate transport and degradation activities and identified phylum‐specific pathways, such as methanogenesis for Euryarchaeota and acetogenesis for Firmicutes. Furthermore, our approach enabled the identification of proteins expressed by the eukaryotic component of the microbiota. Taken together, these findings unveil structure and role of the distal gut microbiota in sheep, and open the way to further studies aimed at elucidating its connections with management and dietary variables in sheep farming.

Bighorn sheep gut microbiomes associate with genetic and spatial structure across a metapopulation

“…Geographic, genetic, & environmental distance analyses. To assess how microbiome similarity correlated with geographic/genetic distances and environmental variables, we used the lmer function in the lme4 package to run linear mixed-effects models comparing pairwise weighted unifrac and Jaccard (presence/absence) distances with (1) pairwise individual-level geographic distances and Rousset's a, and (2) pairwise differences in population-level traits (heterozygosity, elevation, NDVI, and rainfall) as fixed effects, and population memberships as random effects 53 . To test our hypotheses, we compared increasingly reduced versions of models 1(a), 1(b), 2(a), and 2(b) for both weighted unifrac and Jaccard distances using sequential chi-squared tests and confirmed our model selection results by comparing AIC and BIC values (See Supplementary Table S4 for model selection details).…”

The Sarda Sheep Host Fecal Proteome

“…IgA is essential in maintaining a homeostatic relationship with the resident microbiota, and its production appears to be carefully regulated by the host to shape gut microbiota composition and functions; moreover, its expression can be related to the presence of eukaryotic parasites in the gut (we found sequences from Haemonchus spp. in the metagenome from the same sheep analyzed in this study).…”

“…Recently, we reported the first characterization of the sheep fecal microbiota, obtained by using a multi‐meta‐omic approach . Here, the mass spectra generated in the context of that study were reanalyzed using a host‐specific database in order to gain insights into the host fecal proteome of healthy sheep.…”

“…Details about sheep, fecal samples, sample preparation, and LC‐MS/MS analysis are reported in our sheep fecal microbiota study . Briefly, fecal samples were collected from the rectal ampulla of five lactating Sarda sheep, which were apparently healthy, free‐grazing and fed a limited amount of commercial feed.…”

Variation in gut bacterial composition is associated with Haemonchus contortus parasite infection of sheep

“…Over the past 15 years there has been an explosive growth in analysis of microbial populations through genetic amplification and detection technologies; with the hope that research in this field can translate to improved health. To date, much of the work conducted has been in humans [5][6][7], though numerous studies have investigated the microbial composition of the digestive tract of other animals, including production animals [8][9][10]. The importance of microbes in the digestive tract of animals has long been appreciated, particularly their role in the digestion of cellulose in ruminants.…”