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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

Principal components analysis (PCA) of relative abundances.PCA was used to compare variation of relative OTU abundances within and between liquid (L) and solid (S) rumen samples from groups R, A, RA and AA. Variation in individual samples is shown. Red = group R (LR and SR), blue = group A (LA and SA), green = group RA (LRA and SRA) and black = group AA (LAA and SAA). Individual animals are indicated by numbers (e.g. LRA55 and SRA55 are animal number 55, liquid and solid respectively, treatment group RA).
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pone.0133234.g002: Principal components analysis (PCA) of relative abundances.PCA was used to compare variation of relative OTU abundances within and between liquid (L) and solid (S) rumen samples from groups R, A, RA and AA. Variation in individual samples is shown. Red = group R (LR and SR), blue = group A (LA and SA), green = group RA (LRA and SRA) and black = group AA (LAA and SAA). Individual animals are indicated by numbers (e.g. LRA55 and SRA55 are animal number 55, liquid and solid respectively, treatment group RA).

Mentions: Principal components analysis (PCA) of relative abundances of OTUs from groups R, A, RA and AA OTUs showed that, apart from 2 animals (A2 and A17), group R separated from group A in the first and second principal components for both liquid and solid fractions (Fig 2). We are uncertain why rumen microbe profiles of A2 and A17 were more similar to group R than group A as their intakes and weight increase were not unusually low for group A. The slaughter weights and carcass weights of animals A2 and A17 were the lowest and third lowest respectively in group A but still higher than the group R average. Animals A1, A4 and A15 also had low group A slaughter and carcass weights and yet their microbiome profiles were very different to those of group R. Comparison of relative abundances of OTUs detected in group R with those in group A showed that 58% (solid fraction) and 55% (liquid fraction) of the OTUs were significantly different (FDR<0.05) between these two groups (S1 Table). So it is clear that feed restriction caused large changes in the composition of the rumen microbiome.


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)

Principal components analysis (PCA) of relative abundances.PCA was used to compare variation of relative OTU abundances within and between liquid (L) and solid (S) rumen samples from groups R, A, RA and AA. Variation in individual samples is shown. Red = group R (LR and SR), blue = group A (LA and SA), green = group RA (LRA and SRA) and black = group AA (LAA and SAA). Individual animals are indicated by numbers (e.g. LRA55 and SRA55 are animal number 55, liquid and solid respectively, treatment group RA).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4520551&req=5

pone.0133234.g002: Principal components analysis (PCA) of relative abundances.PCA was used to compare variation of relative OTU abundances within and between liquid (L) and solid (S) rumen samples from groups R, A, RA and AA. Variation in individual samples is shown. Red = group R (LR and SR), blue = group A (LA and SA), green = group RA (LRA and SRA) and black = group AA (LAA and SAA). Individual animals are indicated by numbers (e.g. LRA55 and SRA55 are animal number 55, liquid and solid respectively, treatment group RA).
Mentions: Principal components analysis (PCA) of relative abundances of OTUs from groups R, A, RA and AA OTUs showed that, apart from 2 animals (A2 and A17), group R separated from group A in the first and second principal components for both liquid and solid fractions (Fig 2). We are uncertain why rumen microbe profiles of A2 and A17 were more similar to group R than group A as their intakes and weight increase were not unusually low for group A. The slaughter weights and carcass weights of animals A2 and A17 were the lowest and third lowest respectively in group A but still higher than the group R average. Animals A1, A4 and A15 also had low group A slaughter and carcass weights and yet their microbiome profiles were very different to those of group R. Comparison of relative abundances of OTUs detected in group R with those in group A showed that 58% (solid fraction) and 55% (liquid fraction) of the OTUs were significantly different (FDR<0.05) between these two groups (S1 Table). So it is clear that feed restriction caused large changes in the composition of the rumen microbiome.

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