Diet Alters Both the Structure and Taxonomy of the Ovine Gut Microbial Ecosystem

Abstract

We surveyed the ruminal metagenomes of 16 sheep under two different diets using Illumina pair-end DNA sequencing of raw microbial DNA extracted from rumen samples. The resulting sequence data were bioinformatically mapped to known prokaryotic 16S rDNA sequences to identify the taxa present in the samples and then analysed for the presence of potentially new taxa. Strikingly, the majority of the microbial individuals found did not map to known taxa from 16S sequence databases. We used a novel statistical modelling approach to compare the taxonomic distributions between animals fed a forage-based diet and those fed concentrated grains. With this model, we found significant differences between the two groups both in the dominant taxa present in the rumen and in the overall shape of the taxa abundance curves. In general, forage-fed animals have a more diverse microbial ecosystem, whereas the concentrate-fed animals have ruminal systems more heavily dominated by a few taxa. As expected, organisms from methanogenic groups are more prevalent in forage-fed animals. Finally, all of these differences appear to be grounded in an underlying common input of new microbial individuals into the rumen environment, with common organisms from one feed group being present in the other, but at much lower abundance.

Colony Location and Captivity Influence the Gut Microbial Community Composition of the Australian Sea Lion (Neophoca cinerea)

“…While differences in phylum abundances between the two groups were not statistically significant, qualitative differences were observed at the OTU level. Dietary resources have been shown to exert a strong influence on microbial community compositions of both terrestrial and marine mammals (5,47,48). Recent studies observing the influence of diet on gut microbiota of fish and mammalian livestock species have shown that animals that forage manifest greater microbial diversity than those fed from artificial or concentrate sources (47)(48)(49).…”

“…Dietary resources have been shown to exert a strong influence on microbial community compositions of both terrestrial and marine mammals (5,47,48). Recent studies observing the influence of diet on gut microbiota of fish and mammalian livestock species have shown that animals that forage manifest greater microbial diversity than those fed from artificial or concentrate sources (47)(48)(49). The varied diet of wild Australian sea lions includes a number of species with chitinous body parts, including small crustaceans, rock lobster, and cephalopods such as cuttlefish, octopus, and squid (27,28).…”

The players may change but the game remains: network analyses of ruminal microbiomes suggest taxonomic differences mask functional similarity

“…Our final database contained 27 290 sequences. In our previous work ( 37 ), we also used the EMIRGE package ( 38 ) to identify novel 16S rDNA genes in the samples. However, using EMIRGE or attempting to assemble the sequence reads, while it might uncover further taxonomic diversity in the samples, will also bias the counting of microbial individuals in complex ways that would undermine the comparisons we planned.…”

Linseed Oil Supplementation of Lambs’ Diet in Early Life Leads to Persistent Changes in Rumen Microbiome Structure

“…A range of approaches such as increasing feed quality, increasing the ratio of concentrate to forage feed, using rumen modifiers such as defaunation or methanogenesis inhibitors (e.g., mevastatin), using production-enhancing agents such as ionophores and using lipids or fatty acids as dietary supplements have been investigated as a means of manipulating the rumen microbiome to achieve specific outcomes ( Boadi et al, 2004 ; Knapp et al, 2014 ; Caro et al, 2016 ). Although these strategies have yielded varying levels of success, diet has been repeatedly shown to strongly influence rumen microbial structure ( de Menezes et al, 2011 ; Ellison et al, 2014 ; Cobellis et al, 2016 ). For example, Petri et al (2013) reported significant differences in rumen bacterial community structure in mature cattle fed a forage diet versus those on a high concentrate diet while Kocherginskaya et al (2001) described differences in bacterial community composition in cattle fed hay diets compared to those fed corn diets.…”