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dc.contributor.author Li, Fuyong
dc.contributor.author Hitch, Thomas
dc.contributor.author Chen, Yanhong
dc.contributor.author Creevey, Christopher
dc.contributor.author Guan, Le Luo
dc.date.accessioned 2020-02-23T01:29:44Z
dc.date.available 2020-02-23T01:29:44Z
dc.date.issued 2019-01-14
dc.identifier.citation Li , F , Hitch , T , Chen , Y , Creevey , C & Guan , L L 2019 , ' Comparative metagenomic and metatranscriptomic analyses reveal the breed effect on the rumen microbiome and its associations with feed efficiency in beef cattle ' Microbiome , vol. 7 , pp. 6 . https://doi.org/10.1186/s40168-019-0618-5 en
dc.identifier.issn 2049-2618
dc.identifier.other PURE: 28853713
dc.identifier.other PURE UUID: bd08df70-dcfc-4e1c-ad5e-420f37fdf26e
dc.identifier.other ORCID: /0000-0001-7183-1555/work/52963621
dc.identifier.other Scopus: 85060006332
dc.identifier.other handle.net: http://hdl.handle.net/2160/bd08df70-dcfc-4e1c-ad5e-420f37fdf26e
dc.identifier.uri http://hdl.handle.net/2160/47211
dc.description.abstract Background Microorganisms are responsible for fermentation within the rumen and have been reported to contribute to the variation in feed efficiency of cattle. However, to what extent the breed affects the rumen microbiome and its association with host feed efficiency is unknown. Here, rumen microbiomes of beef cattle (n = 48) from three breeds (Angus, Charolais, Kinsella composite hybrid) with high and low feed efficiency were explored using metagenomics and metatranscriptomics, aiming to identify differences between functional potentials and activities of same rumen microbiomes and to evaluate the effects of host breed and feed efficiency on the rumen microbiome. Results Rumen metagenomes were more closely clustered together and thus more conserved among individuals than metatranscriptomes, suggesting that inter-individual functional variations at the RNA level were higher than those at the DNA level. However, while mRNA enrichment significantly increased the sequencing depth of mRNA and generated similar functional profiles to total RNA-based metatranscriptomics, it led to biased abundance estimation of several transcripts. We observed divergent rumen microbial composition (metatranscriptomic level) and functional potentials (metagenomic level) among three breeds, but differences in functional activity (metatranscriptomic level) were less apparent. Differential rumen microbial features (e.g., taxa, diversity indices, functional categories, and genes) were detected between cattle with high and low feed efficiency, and most of them were breed-specific. Conclusions Metatranscriptomes represent real-time functional activities of microbiomes and have the potential to better associate rumen microorganisms with host performances compared to metagenomics. As total RNA-based metatranscriptomics seem to avoid potential biases caused by mRNA enrichment and allow simultaneous use of rRNA for generation of compositional profiles, we suggest their use for linking the rumen microbiome with host phenotypes in future studies. However, if exploration of specific lowly expressed genes is desired, mRNA enrichment is recommended as it will enhance the resolution of mRNA. Finally, the differential microbial features observed between efficient and inefficient steers tended to be specific to breeds, suggesting that interactions between host breed genotype and the rumen microbiome contribute to the variations in feed efficiency observed. These breed-associated differences represent an opportunity to engineer specific rumen microbiomes through selective breeding of the hosts en
dc.format.extent 21 en
dc.language.iso eng
dc.relation.ispartof Microbiome en
dc.rights en
dc.subject rumen en
dc.subject microbiome en
dc.subject metagenomics metatranscriptomics en
dc.subject feed efficiency en
dc.subject beef breed en
dc.title Comparative metagenomic and metatranscriptomic analyses reveal the breed effect on the rumen microbiome and its associations with feed efficiency in beef cattle en
dc.type /dk/atira/pure/researchoutput/researchoutputtypes/contributiontojournal/article en
dc.description.version publishersversion en
dc.identifier.doi https://doi.org/10.1186/s40168-019-0618-5
dc.contributor.institution Department of Biological, Environmental and Rural Sciences en
dc.description.status Peer reviewed en


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