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Metagenomic analysis of the rumen microbiome in wheat-induced frothy bloat among steers
Frothy bloat is a serious metabolic disorder that causes reduced performance or mortality in stocker cattle grazing hard red winter wheat forage in the Southern Great Plains. We hypothesized a dysbiosis to develop in the rumen microbiome of stocker cattle when grazed on high quality winter wheat pasture that predisposes them to frothy bloat risk. In this study, rumen contents were harvested from six cannulated steers (mean BW 450 lb; three with bloat score ‘2’ and three with bloat score ‘0’), extracted for genomic DNA and subjected for shotgun sequencing on 454/Roche platform. Approximately 1.5 million reads were sequenced, assembled and assigned for phylogenetic and functional annotations. Differences in microbial communities between bloated and non-bloated steers were analyzed using Mixed procedure of SAS. Bacteria predominated up to 84% of the sequences while archaea contributed to nearly 5% of the sequences. The abundance of archaea tended to be higher in bloated animals (P<0.12) dominated by Methanobrevibacter. Predominant bacterial phyla were Firmicutes(65%), Actinobacteria(13%), Bacteroidetes(10%) and Proteobacteria(6%). Firmicutes were largely represented by Eubacteriaceae, Ruminococcaceae, Lachnospiraceae and Eubacteriaceae. However, only a few genera from Firmicutes such as Butyrivibrio and Lactobacillus showed differences (P<0.05) between both groups. Bacteroidetes showed distinct differences between both groups with lineages from Prevotellaceae to be higher (P<0.05) in bloated animals while non-bloated animals had higher (P<0.05) abundance of Porphyromonadaceae, and Bacteroidaceae members. Actinobacteria was dominated by Coriobacteriaceae lineages which tended to be higher (P<0.12) in non-bloated steers. Functional annotations of assembled reads to KEGG database revealed the abundance of several metabolic pathways, with carbohydrate and protein metabolism well represented. Among the carbohydrate metabolism, utilization of monosaccharides was higher (P<0.05) in bloated animals while disaccharide degradation tended to be higher (P<0.12) in non-bloated animals. Assignment of contigs to CaZy database revealed the distribution of Glycosyl Hydrolases across all samples showing the presence of a core microbiome associated with fiber digestion. Principle component analysis based on phylogenetic and functional assignments both revealed the tendency to cluster microbial communities by the incidence of bloat, however validation will require greater sample numbers. It can be concluded that the rumen microbial community structure and metabolic potential are substantially altered under moderate frothy bloat conditions.
Keywords: Rumen microbiome, Frothy bloat, metagenomics, wheat forage