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Open AccessArticle

Rumen and Fecal Microbial Community Structure of Holstein and Jersey Dairy Cows as Affected by Breed, Diet, and Residual Feed Intake

1
Department of Animal Science, AU-Foulum, Aarhus University, DK-8830 Tjele, Denmark
2
Department of Molecular Biology and Genetics, AU-Foulum, Aarhus University, DK-8830 Tjele, Denmark
*
Author to whom correspondence should be addressed.
Animals 2019, 9(8), 498; https://doi.org/10.3390/ani9080498
Received: 28 May 2019 / Revised: 24 July 2019 / Accepted: 25 July 2019 / Published: 29 July 2019
(This article belongs to the Special Issue Reducing Enteric Methane Emissions from Ruminants)
Dietary interventions aimed at reducing methane production may be influenced by other factors such as animal breed and feed efficiency (indicated by residual feed intake (RFI) status). We examined the rumen and fecal microbiota of Holstein and Jersey dairy cows with diverging RFI status fed diets differing in concentrate-to-forage ratio. Community differences seen in the rumen were reduced or absent in feces, except in the case of animal-to-animal variation, where differences were more pronounced. Understanding factors that influence methane production will be key to determining effective methane reduction strategies in the future.
Identifying factors that influence the composition of the microbial population in the digestive system of dairy cattle will be key in regulating these populations to reduce greenhouse gas emissions. In this study, we analyzed rumen and fecal samples from five high residual feed intake (RFI) Holstein cows, five low RFI Holstein cows, five high RFI Jersey cows and five low RFI Jersey cows, fed either a high-concentrate diet (expected to reduce methane emission) or a high-forage diet. Bacterial communities from both the rumen and feces were profiled using Illumina sequencing on the 16S rRNA gene. Rumen archaeal communities were profiled using Terminal-Restriction Fragment Length Polymorphism (T-RFLP) targeting the mcrA gene. The rumen methanogen community was influenced by breed but not by diet or RFI. The rumen bacterial community was influenced by breed and diet but not by RFI. The fecal bacterial community was influenced by individual animal variation and, to a lesser extent, by breed and diet but not by RFI. Only the bacterial community correlated with methane production. Community differences seen in the rumen were reduced or absent in feces, except in the case of animal-to-animal variation, where differences were more pronounced. The two cattle breeds had different levels of response to the dietary intervention; therefore, it may be appropriate to individually tailor methane reduction strategies to each cattle breed. View Full-Text
Keywords: next-generation sequencing; microbiome; cattle breed; residual feed intake; methane next-generation sequencing; microbiome; cattle breed; residual feed intake; methane
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Noel, S.J.; Olijhoek, D.W.; Mclean, F.; Løvendahl, P.; Lund, P.; Højberg, O. Rumen and Fecal Microbial Community Structure of Holstein and Jersey Dairy Cows as Affected by Breed, Diet, and Residual Feed Intake. Animals 2019, 9, 498.

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