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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.

McCabe MS, Cormican P, Keogh K, O'Connor A, O'Hara E, Palladino RA, Kenny DA, Waters SM - PLoS ONE (2015)

Bottom Line: 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).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.

View Article: PubMed Central - PubMed

Affiliation: Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, County Meath, Ireland.

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.

No MeSH data available.


Related in: MedlinePlus

Correlation analysis of OTU-M7 and OTU-M10 with OTU-S3004.Scatter plot analysis of percentage relative abundances (% rel. ab.), in all liquid and solid fraction samples, of OTU-M7 (Methanobrevibacter gottschalkii clade) and OTU-M10 (Methanobrevibacter ruminantium clade) plotted against OTU-S3004. Power regression (blue dashed line) showed the highest R2 values (shown on each scatter plot) in all comparisons apart from OTU-M10 (liquid) vs. OTU-S3004 (liquid) for which a polynomial regression showed the highest R2 value.
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pone.0133234.g009: Correlation analysis of OTU-M7 and OTU-M10 with OTU-S3004.Scatter plot analysis of percentage relative abundances (% rel. ab.), in all liquid and solid fraction samples, of OTU-M7 (Methanobrevibacter gottschalkii clade) and OTU-M10 (Methanobrevibacter ruminantium clade) plotted against OTU-S3004. Power regression (blue dashed line) showed the highest R2 values (shown on each scatter plot) in all comparisons apart from OTU-M10 (liquid) vs. OTU-S3004 (liquid) for which a polynomial regression showed the highest R2 value.

Mentions: To determine if OTU-S3004 might be specifically associated with OTU-M7, we looked at correlations between OTU-M7 and OTUs that showed the top 20 largest significant (FDR<0.05) changes in relative abundance between group R and group A (Tables 3 and 4). For this, the only negative correlation with OTU-M7 was with OTU-S3004 in the liquid fraction (ρ = -0.72, P value = <1x10-20). We also looked at correlations between the relative abundance of all of the Succinivibrionacae-assigned OTUs and all of the archaea-assigned OTUs (S4 Table). By far the strongest negative correlation in the liquid fraction was between OTU-M7 and OTU-S3004 (S4 Table). The only strong (i.e. ρ <-0.70) negative correlations in the solid fractions were between OTU-T26 and OTUs-S3008, S3010, and S3016 (S4 Table) which were low in relative abundance. Prevotella and R. flavefaciens-assigned OTUs also showed large decreases in group R (Fig 8) and significant negative Spearman correlations with M7 in both solid and liquid fractions (S5 and S6 Tables), but the relative abundance of these OTUs was low (<1%) and the level of significance and strength of correlation was far lower than for OTU-S3004. We also conducted scatter plot analysis to look at the relationship between the relative abundances of OTU-S3004 and the two dominant methanogen OTUs (OTUM7 and OTU-M10) (Fig 9). There was no obvious relationship between OTU-S3004 and OTU-M10 but there was a clear relationship between OTU-M7 and OTU-S3004 which was particularly strong for the liquid fraction samples and showed a power type regression. So there appeared to be a specific inverse relationship between the Methanobrevibacter gottschalkii clade, but not the Methanobrevibacter ruminantium clade, and OTU-S3004 in all of the liquid fraction samples. To our knowledge, a strong inverse relationship between this highly abundant putative Succinivibrionaceae and Methanobrevibacter gottschalkii clade in the rumen of cattle has not been previously reported and warrants further study.


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.

McCabe MS, Cormican P, Keogh K, O'Connor A, O'Hara E, Palladino RA, Kenny DA, Waters SM - PLoS ONE (2015)

Correlation analysis of OTU-M7 and OTU-M10 with OTU-S3004.Scatter plot analysis of percentage relative abundances (% rel. ab.), in all liquid and solid fraction samples, of OTU-M7 (Methanobrevibacter gottschalkii clade) and OTU-M10 (Methanobrevibacter ruminantium clade) plotted against OTU-S3004. Power regression (blue dashed line) showed the highest R2 values (shown on each scatter plot) in all comparisons apart from OTU-M10 (liquid) vs. OTU-S3004 (liquid) for which a polynomial regression showed the highest R2 value.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4520551&req=5

pone.0133234.g009: Correlation analysis of OTU-M7 and OTU-M10 with OTU-S3004.Scatter plot analysis of percentage relative abundances (% rel. ab.), in all liquid and solid fraction samples, of OTU-M7 (Methanobrevibacter gottschalkii clade) and OTU-M10 (Methanobrevibacter ruminantium clade) plotted against OTU-S3004. Power regression (blue dashed line) showed the highest R2 values (shown on each scatter plot) in all comparisons apart from OTU-M10 (liquid) vs. OTU-S3004 (liquid) for which a polynomial regression showed the highest R2 value.
Mentions: To determine if OTU-S3004 might be specifically associated with OTU-M7, we looked at correlations between OTU-M7 and OTUs that showed the top 20 largest significant (FDR<0.05) changes in relative abundance between group R and group A (Tables 3 and 4). For this, the only negative correlation with OTU-M7 was with OTU-S3004 in the liquid fraction (ρ = -0.72, P value = <1x10-20). We also looked at correlations between the relative abundance of all of the Succinivibrionacae-assigned OTUs and all of the archaea-assigned OTUs (S4 Table). By far the strongest negative correlation in the liquid fraction was between OTU-M7 and OTU-S3004 (S4 Table). The only strong (i.e. ρ <-0.70) negative correlations in the solid fractions were between OTU-T26 and OTUs-S3008, S3010, and S3016 (S4 Table) which were low in relative abundance. Prevotella and R. flavefaciens-assigned OTUs also showed large decreases in group R (Fig 8) and significant negative Spearman correlations with M7 in both solid and liquid fractions (S5 and S6 Tables), but the relative abundance of these OTUs was low (<1%) and the level of significance and strength of correlation was far lower than for OTU-S3004. We also conducted scatter plot analysis to look at the relationship between the relative abundances of OTU-S3004 and the two dominant methanogen OTUs (OTUM7 and OTU-M10) (Fig 9). There was no obvious relationship between OTU-S3004 and OTU-M10 but there was a clear relationship between OTU-M7 and OTU-S3004 which was particularly strong for the liquid fraction samples and showed a power type regression. So there appeared to be a specific inverse relationship between the Methanobrevibacter gottschalkii clade, but not the Methanobrevibacter ruminantium clade, and OTU-S3004 in all of the liquid fraction samples. To our knowledge, a strong inverse relationship between this highly abundant putative Succinivibrionaceae and Methanobrevibacter gottschalkii clade in the rumen of cattle has not been previously reported and warrants further study.

Bottom Line: 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).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.

View Article: PubMed Central - PubMed

Affiliation: Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, County Meath, Ireland.

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.

No MeSH data available.


Related in: MedlinePlus