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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

Difference between diversity of OTUs in rumens of restricted and ad libitum treatment groupsLR = Liquid Restricted (n = 14), SR = Solid Restricted (n = 14), LA = Liquid Ad lib (n = 13), SA = Solid Ad lib (n = 13). Line plot (top panel) shows an increase in group R relative to the other groups, in the average number of OTUs for which the relative abundance <0.1%. Box and whisker plot shows median, quartiles and maximum and minimum values of the sums of the number of OTUs identified within in each sample. P-values are BH-corrected and derived from Wilcoxon pairwise comparisons of number of OTUs between different treatment groups.
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pone.0133234.g003: Difference between diversity of OTUs in rumens of restricted and ad libitum treatment groupsLR = Liquid Restricted (n = 14), SR = Solid Restricted (n = 14), LA = Liquid Ad lib (n = 13), SA = Solid Ad lib (n = 13). Line plot (top panel) shows an increase in group R relative to the other groups, in the average number of OTUs for which the relative abundance <0.1%. Box and whisker plot shows median, quartiles and maximum and minimum values of the sums of the number of OTUs identified within in each sample. P-values are BH-corrected and derived from Wilcoxon pairwise comparisons of number of OTUs between different treatment groups.

Mentions: The diversity of prokaryotic OTUs was also greatly increased in group R compared to groups A, RA and AA (Fig 3). This increased diversity was probably due to the slower passage rate in group R which would have allowed the slower growing microbes to become established. There have been numerous studies spanning several decades on the effects of feed restriction on rumen fermentation activity and these generally show that as long as maintenance requirements are met, as was the case in group R, there is a negative relationship between level of feed intake and digestability. This is mostly attributed to slower passage rate of feed and increased particle retention time in the rumen when intake decreases [28, 29] but could also be due to increased microbial diversity. If the increased microbial diversity in the rumen persisted for the early part of the post-restriction period, this may have contributed to improved fermentation of the ad libitum diet in the group RA (compensating) animals compared to the group AA animals. Unfortunately we only took samples for DNA extraction and VFA analysis at 55 days post-restriction so it was not possible to determine how many days post-restriction that it took for the rumen microbiota to revert to the ad libitum state in group RA animals.


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)

Difference between diversity of OTUs in rumens of restricted and ad libitum treatment groupsLR = Liquid Restricted (n = 14), SR = Solid Restricted (n = 14), LA = Liquid Ad lib (n = 13), SA = Solid Ad lib (n = 13). Line plot (top panel) shows an increase in group R relative to the other groups, in the average number of OTUs for which the relative abundance <0.1%. Box and whisker plot shows median, quartiles and maximum and minimum values of the sums of the number of OTUs identified within in each sample. P-values are BH-corrected and derived from Wilcoxon pairwise comparisons of number of OTUs between different treatment groups.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0133234.g003: Difference between diversity of OTUs in rumens of restricted and ad libitum treatment groupsLR = Liquid Restricted (n = 14), SR = Solid Restricted (n = 14), LA = Liquid Ad lib (n = 13), SA = Solid Ad lib (n = 13). Line plot (top panel) shows an increase in group R relative to the other groups, in the average number of OTUs for which the relative abundance <0.1%. Box and whisker plot shows median, quartiles and maximum and minimum values of the sums of the number of OTUs identified within in each sample. P-values are BH-corrected and derived from Wilcoxon pairwise comparisons of number of OTUs between different treatment groups.
Mentions: The diversity of prokaryotic OTUs was also greatly increased in group R compared to groups A, RA and AA (Fig 3). This increased diversity was probably due to the slower passage rate in group R which would have allowed the slower growing microbes to become established. There have been numerous studies spanning several decades on the effects of feed restriction on rumen fermentation activity and these generally show that as long as maintenance requirements are met, as was the case in group R, there is a negative relationship between level of feed intake and digestability. This is mostly attributed to slower passage rate of feed and increased particle retention time in the rumen when intake decreases [28, 29] but could also be due to increased microbial diversity. If the increased microbial diversity in the rumen persisted for the early part of the post-restriction period, this may have contributed to improved fermentation of the ad libitum diet in the group RA (compensating) animals compared to the group AA animals. Unfortunately we only took samples for DNA extraction and VFA analysis at 55 days post-restriction so it was not possible to determine how many days post-restriction that it took for the rumen microbiota to revert to the ad libitum state in group RA animals.

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