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. 2018 Oct 12;14(10):e1007580.
doi: 10.1371/journal.pgen.1007580. eCollection 2018 Oct.

Host genetics and the rumen microbiome jointly associate with methane emissions in dairy cows

Gareth Frank Difford  1   2 , Damian Rafal Plichta  3   4 , Peter Løvendahl  1 , Jan Lassen  1   5 , Samantha Joan Noel  6 , Ole Højberg  6 , André-Denis G Wright  7 , Zhigang Zhu  6 , Lise Kristensen  1 , Henrik Bjørn Nielsen  3   4 , Bernt Guldbrandtsen  1 , Goutam Sahana  1
Affiliations

Host genetics and the rumen microbiome jointly associate with methane emissions in dairy cows

Gareth Frank Difford et al. PLoS Genet. .

Abstract

Cattle and other ruminants produce large quantities of methane (~110 million metric tonnes per annum), which is a potent greenhouse gas affecting global climate change. Methane (CH4) is a natural by-product of gastro-enteric microbial fermentation of feedstuffs in the rumen and contributes to 6% of total CH4 emissions from anthropogenic-related sources. The extent to which the host genome and rumen microbiome influence CH4 emission is not yet well known. This study confirms individual variation in CH4 production was influenced by individual host (cow) genotype, as well as the host's rumen microbiome composition. Abundance of a small proportion of bacteria and archaea taxa were influenced to a limited extent by the host's genotype and certain taxa were associated with CH4 emissions. However, the cumulative effect of all bacteria and archaea on CH4 production was 13%, the host genetics (heritability) was 21% and the two are largely independent. This study demonstrates variation in CH4 emission is likely not modulated through cow genetic effects on the rumen microbiome. Therefore, the rumen microbiome and cow genome could be targeted independently, by breeding low methane-emitting cows and in parallel, by investigating possible strategies that target changes in the rumen microbiome to reduce CH4 emissions in the cattle industry.

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Conflict of interest statement

DRP and HBN are employed by Clinical-Microbiomics A/S. JL is employed by Viking Genetics. These organization have no financial or other interests in this manuscript or its findings; no other competing interests exist.

Figures

Fig 1
Fig 1. Phylogeny of 3,894 rumen bacterial OTU.
Branch lengths represent substitution number per site calculated by FastTree2[81]. Heritability estimates (h2) for each OTU abundance are plotted with a horizontal bar and colored by taxonomic group classification.
Fig 2
Fig 2. Phylogeny of 189 rumen archaeal OTU abundance.
Branch lengths represent substitution number per site calculated by FastTree2[81]. Heritability estimates (h2) for each OTU abundance is plotted with a horizontal bar and colored by taxonomic group classification.
Fig 3
Fig 3. Manhattan plot of rumen bacterial and archaeal genera associations with methane emissions (g/day) colored by heritability (h2) estimates.
Color gradient indicates genera h2 with light blue (h2 = 0) ranging to dark blue (h2 = 0.30). The y-axis is -log10(P) for association tests. The horizontal line represents the Benjamini-Hochberg FDR 15% for multiple testing significance thresholds. Genera above the threshold are a) Unclassified BS11 group; b) Sporobacter; c) Unclassified Victivallaceae; d) Unclassified Lentisphaeria; e) Unclassified Alphaproteobacteria; f) Unclassified Rickettsiales; and g) Sphaerochaeta.
Fig 4
Fig 4
Principal coordinate analysis (PCoA) of rumen bacterial community diversity (a) and archaeal community diversity (b) based on 16S rRNA amplicon sequencing contrasting 10% highest methane emitters (orange), 10% lowest methane emitters (blue), and 80% intermediate emitters (grey). Distribution of high and low emitters along PCo1 showed significant differences (P < 0.001) for both figures.
Fig 5
Fig 5. Proportion of variance in CH4 explained by different sources (Intra-class correlation coefficients, ICC) due to additive genetic effects (heritability) and rumen microbe content (microbiability), with respective standard errors when fit separately or jointly.
See this image and copyright information in PMC

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