Illumina MiSeq Phylogenetic Amplicon Sequencing Shows a Large Reduction of an Uncharacterised Succinivibrionaceae and an Increase of the Methanobrevibacter gottschalkii Clade in Feed Restricted Cattle

Abstract

Periodic feed restriction is used in cattle production to reduce feed costs. When normal feed levels are resumed, cattle catch up to a normal weight by an acceleration of normal growth rate, known as compensatory growth, which is not yet fully understood. Illumina Miseq Phylogenetic marker amplicon sequencing of DNA extracted from rumen contents of 55 bulls showed that restriction of feed (70% concentrate, 30% grass silage) for 125 days, to levels that caused a 60% reduction of growth rate, resulted in a large increase of relative abundance of Methanobrevibacter gottschalkii clade (designated as OTU-M7), and a large reduction of an uncharacterised Succinivibrionaceae species (designated as OTU-S3004). There was a strong negative Spearman correlation (ρ = -0.72, P = <1x10-20) between relative abundances of OTU-3004 and OTU-M7 in the liquid rumen fraction. There was also a significant increase in acetate:propionate ratio (A:P) in feed restricted animals that showed a negative Spearman correlation (ρ = -0.69, P = <1x10-20) with the relative abundance of OTU-S3004 in the rumen liquid fraction but not the solid fraction, and a strong positive Spearman correlation with OTU-M7 in the rumen liquid (ρ = 0.74, P = <1x10-20) and solid (ρ = 0.69, P = <1x10-20) fractions. Reduced A:P ratios in the rumen are associated with increased feed efficiency and reduced production of methane which has a global warming potential (GWP 100 years) of 28. Succinivibrionaceae growth in the rumen was previously suggested to reduce methane emissions as some members of this family utilise hydrogen, which is also utilised by methanogens for methanogenesis, to generate succinate which is converted to propionate. Relative abundance of OTU-S3004 showed a positive Spearman correlation with propionate (ρ = 0.41, P = <0.01) but not acetate in the liquid rumen fraction.

Plane of nutrition affects the phylogenetic diversity and relative abundance of transcriptionally active methanogens in the bovine rumen

“…This was consistent with a decrease in ruminal propionate and attendant increased acetate:propionate (A:P) ratio, an indication of greater methanogenesis in these animals 5 . Following two months of re-alimentation, the volatile fatty acid ratios of ruminal digesta from previously feed restricted animals mirrored that of their non-restricted contemporaries, while a reversal in the relative abundance of 16S DNA from the Methanobrevibacter gottschalkii clade and the putative Succinivibrionaceae 16S DNA 5 was also observed.…”

“…This observation was positively correlated with a dramatic decrease (from 30% to less than 1%) in the relative abundance of a single bacterial 16S DNA sequence which could only be identified confidently as an uncultured Proteobacteria species and appeared to be related to the family Succinivibrionaceae 5 . As some Succinivibrionaceae species utilise hydrogen 13 we hypothesized that the aforementioned putative Succinivibrionaceae species was in competition for substrate, possibly hydrogen, with the Methanobrevibacter gottschalkii clade 5 in feed restricted animals. This was consistent with a decrease in ruminal propionate and attendant increased acetate:propionate (A:P) ratio, an indication of greater methanogenesis in these animals 5 .…”

“…Feed restricted animals have been previously shown to have slower passage rate of feed through the rumen 9,10 which has previously been correlated with increased CH 4 emissions per unit of feed from ruminants 9,11,12 . We previously found that feed-restricted animals had increased relative abundance of 16S DNA from the Methanobrevibacter gottschalkii clade 5 . This observation was positively correlated with a dramatic decrease (from 30% to less than 1%) in the relative abundance of a single bacterial 16S DNA sequence which could only be identified confidently as an uncultured Proteobacteria species and appeared to be related to the family Succinivibrionaceae 5 .…”

“…We previously found that feed-restricted animals had increased relative abundance of 16S DNA from the Methanobrevibacter gottschalkii clade 5 . This observation was positively correlated with a dramatic decrease (from 30% to less than 1%) in the relative abundance of a single bacterial 16S DNA sequence which could only be identified confidently as an uncultured Proteobacteria species and appeared to be related to the family Succinivibrionaceae 5 . As some Succinivibrionaceae species utilise hydrogen 13 we hypothesized that the aforementioned putative Succinivibrionaceae species was in competition for substrate, possibly hydrogen, with the Methanobrevibacter gottschalkii clade 5 in feed restricted animals.…”

“…As some Succinivibrionaceae species utilise hydrogen 13 we hypothesized that the aforementioned putative Succinivibrionaceae species was in competition for substrate, possibly hydrogen, with the Methanobrevibacter gottschalkii clade 5 in feed restricted animals. This was consistent with a decrease in ruminal propionate and attendant increased acetate:propionate (A:P) ratio, an indication of greater methanogenesis in these animals 5 . Following two months of re-alimentation, the volatile fatty acid ratios of ruminal digesta from previously feed restricted animals mirrored that of their non-restricted contemporaries, while a reversal in the relative abundance of 16S DNA from the Methanobrevibacter gottschalkii clade and the putative Succinivibrionaceae 16S DNA 5 was also observed.…”