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Nutrigenomics in Animal Health and Production

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Front. Genet. | doi: 10.3389/fgene.2018.00062

Genetic Markers are Associated with the Ruminal Microbiome and Metabolome in Grain and Sugar Challenged Dairy Heifers

  • 1Scibus, Australia
  • 2School of Life and Environmental Sciences, University of Sydney, Australia
  • 3Department of Animal and Range Sciences, Montana State University, United States
  • 4CSIRO Animal, Food and Health Services, Australia

Dairy heifers were subjected to a non-life-threatening challenge designed to induce ruminal acidosis by feeding grain and sugar. Large among animal variation in clinical signs of acidosis, rumen metabolite concentrations, and the rumen microbiome occurred. This exploratory study investigates sources of the variation by examining associations between the genome, metabolome, and microbiome, albeit with a limited population. The broader objective is to provide a rationale for a larger field study to identify markers for susceptibility to ruminal acidosis. Initially, heifers (n = 40) allocated to five feed additive groups were fed 20-days pre-challenge with a total mixed ration and additives. Fructose (0.1% of bodyweight/day) was added for the last 10 days pre-challenge. On day-21 heifers were challenged with 1.0% of bodyweight dry matter wheat + 0.2% of bodyweight fructose + additives. Rumen samples were collected via stomach tube weekly (day-0, 7, and 14) and at five times over 3.6 hours after challenge and analyzed for pH and volatile fatty acid, ammonia, D- and L-lactate concentrations. Relative abundance of bacteria and archaea were determined using Illumina MiSeq. Genotyping was undertaken using a 150K Illumina SNPchip. Genome-wide association was performed for metabolite and microbiome measures (n = 33). Few genome associations occurred with rumen pH, concentration of acetate, propionate, total volatile fatty acids, or ammonia, or the relative abundance of the Firmicutes, Bacteroidetes, and Spirochaetes phyla. Metabolites and microbial phyla that had markers associated and quantitative trait loci were: acetate to propionate ratio (A:P), D-, L-, and total lactate, butyrate, acidosis eigenvalue, Actinobacteria, Chloroflexi, Euryarchaeota, Fibrobacteres, Planctomycetes, Proteobacteria, and Tenericutes. A putative genomic region overlapped for Actinobacteria, Euryarchaeota, and Fibrobacteres and covered the region that codes for matrix extracellular phosphoglycoprotein. Other overlapping regions were: (1) Chloroflexi, Tenericutes, and A:P, (2) L- and total lactate and Actinobacteria, and (3) Actinobacteria, Euryarchaeota, Fibrobacteres, and A:P. Genome-wide associations with the metabolome and microbiome occurred despite the small population, suggesting that markers for ruminal acidosis susceptibility exist. The findings may explain some of the variation in metabolomic and microbial data and provide a rationale for a larger study with a population that has variation in acidosis.

Keywords: Fructose, genome-wide association, Lactic Acid, Matrix extracellular phosphoglycoprotein, pleiotropy, Ruminal microbiome, Ruminal acidosis

Received: 21 Aug 2017; Accepted: 12 Feb 2018.

Edited by:

Stephen B. Smith, Texas A&M University College Station, United States

Reviewed by:

Caren Smith, Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, United States
Delisha A. Stewart, University of North Carolina at Chapel Hill, United States  

Copyright: © 2018 Golder, Thomson, Denman, McSweeney and Lean. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Helen M. Golder, Scibus, Camden, Australia,