Effect of Phenotypic Residual Feed Intake and Dietary Forage Content on the Rumen Microbial Community of Beef Cattle

Carberry, Crea; Kenny, David A.; Han, Sukkyan; McCabe, Matthew S.; Waters, Sinéad M.

doi:10.1128/aem.07759-11

Cited by 256 publications

(252 citation statements)

References 53 publications

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“…Low-RFI animals (Nkrumah et al 2006;Hegarty et al 2007). Comparisons of ruminal microbiomes between low-and high-RFI animals using a variety of methods have shown differences in bacterial and archaeal community profiles correlated with RFI, although these associations are often influenced by the energy content of the diet (Guan et al 2008;Zhou et al 2010;Carberry et al 2012;Hernandez-Sanabria et al 2012). Methanogen-related differences observed in these studies included a specific high-RFI-related PCR-DGGE band associated with Methanobrevibacter smithii PS (Zhou et al 2010), an elevated abundance of Methanosphaera stadtmanae, and Methanobrevibacter sp.…”

Section: Discussionmentioning

confidence: 99%

Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome

et al. 2014

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Ruminant livestock represent the single largest anthropogenic source of the potent greenhouse gas methane, which is generated by methanogenic archaea residing in ruminant digestive tracts. While differences between individual animals of the same breed in the amount of methane produced have been observed, the basis for this variation remains to be elucidated. To explore the mechanistic basis of this methane production, we measured methane yields from 22 sheep, which revealed that methane yields are a reproducible, quantitative trait. Deep metagenomic and metatranscriptomic sequencing demonstrated a similar abundance of methanogens and methanogenesis pathway genes in high and low methane emitters. However, transcription of methanogenesis pathway genes was substantially increased in sheep with high methane yields. These results identify a discrete set of rumen methanogens whose methanogenesis pathway transcription profiles correlate with methane yields and provide new targets for CH 4 mitigation at the levels of microbiota composition and transcriptional regulation.

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Section: Discussionmentioning

confidence: 99%

Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome

et al. 2014

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“…The diet and feeding pattern are recognized as the key factors affecting rumen efficiency and the rumen microbial community composition [88]. Consequently, according to previous studies [9,33,35], it was speculated that differences in rumen microbial communities in yaks and Tibetan sheep under different feeding paradigms could cause variations in CH 4 formation and the conversion of feed to animal products. Consequently, a deep understanding of rumen microbial composition and variation is essential not only for developing appropriate feeding and management strategies for enhancing health and productivity of yaks and Tibetan sheep, but also for reducing CH 4 emission from ruminants on the QTP.…”

Section: Introductionmentioning

confidence: 99%

Rumen prokaryotic communities of ruminants under different feeding paradigms on the Qinghai-Tibetan Plateau

Xue

Chen

Zhao

et al. 2017

Systematic and Applied Microbiology

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“…The animal model The animal model on which this work is based has been described previously (Carberry et al, 2012) and was part of a larger study designed to examine the physiological control of energetic efficiency in growing beef heifers (Kelly et al, 2010). Our analysis centred on samples taken during this study from 14 Limousin x Friesian heifers following a 44-day period of ad libitum access to a high-forage diet of grass silage.…”

Section: Methodsmentioning

confidence: 99%

“…Samples of rumen fluid were collected using a transesophageal sampling device (FLORA rumen scoop; Guelph, ON, Canada). Subsequently, a 20-ml aliquot was transferred using a pipette and sterilised tip into a separate labelled sterilised container, immediately frozen in liquid nitrogen, and stored at 80°C until processing (Carberry et al, 2012).…”

Section: Methodsmentioning

confidence: 99%

Erratum: Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome

Rubino¹,

Carberry²,

Waters³

et al. 2017

The ISME Journal

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Many microbes in complex competitive environments share genes for acquiring and utilising nutrients, questioning whether niche specialisation exists and if so, how it is maintained. We investigated the genomic signatures of niche specialisation in the rumen microbiome, a highly competitive, anaerobic environment, with limited nutrient availability determined by the biomass consumed by the host. We generated individual metagenomic libraries from 14 cows fed an ad libitum diet of grass silage and calculated functional isoform diversity for each microbial gene identified. The animal replicates were used to calculate confidence intervals to test for differences in diversity of functional isoforms between microbes that may drive niche specialisation. We identified 153 genes with significant differences in functional isoform diversity between the two most abundant bacterial genera in the rumen (Prevotella and Clostridium). We found Prevotella possesses a more diverse range of isoforms capable of degrading hemicellulose, whereas Clostridium for cellulose. Furthermore, significant differences were observed in key metabolic processes indicating that isoform diversity plays an important role in maintaining their niche specialisation. The methods presented represent a novel approach for untangling complex interactions between microorganisms in natural environments and have resulted in an expanded catalogue of gene targets central to rumen cellulosic biomass degradation.

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Effect of Phenotypic Residual Feed Intake and Dietary Forage Content on the Rumen Microbial Community of Beef Cattle

Cited by 256 publications

References 53 publications

Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome

Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome

Rumen prokaryotic communities of ruminants under different feeding paradigms on the Qinghai-Tibetan Plateau

Erratum: Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome

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