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

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.

A restriction enzyme reduced representation sequencing approach for low-cost, high-throughput metagenome profiling

“…In an agricultural setting, rumen microbial community (RMC) profiles have been associated with environmentally and economically important traits, such as methane emissions (3, 4) and feed efficiency (5, 6). The RMC breaks down ingested feed to produce volatile or short chain fatty acids, which are a source of energy for the host.…”

Can the microbiome influence host evolutionary trajectories?

“…Indeed, in hosts dominated by environmentally acquired microbes, the contribution of host genetic variation to the relative abundance of particular microbes is as high as 42% in humans 31,32 , 39% in Drosophila 33 , and 25% in maize 34 . Interestingly, these and other studies show that not all components of the microbiome are heritable with only a portion of the microbiome faithfully transmitted, with estimates ranging from 8-56% of microbes 32,[34][35][36] .…”

“…Similarly, though another study in humans found little influence of host genetics on microbiome composition, microbial variation still explained 22-36% of metabolic traits 39 . Microbial variation explained 33% of weight gain in pigs 35 and 13% of methane emissions in cows 36 but also occurred largely independently of host genetic control of the microbiome. In other words, we still do not know whether the most heritable microbes explain the most significant variation in host traits.…”

Microbiability of meat quality and carcass composition traits in swine

“…The authors also suggested that inclusion of genetic diversity of individual microbiome will most likely increase the accuracy of heritability of various traits. The heritability and microbiability estimation of daily gain, feed intake and feed conversion ratio in swine by Camarinha-Silva et al (2017) and methane emission in cattle by Difford et al (2018) strongly suggested the significant contribution of microbiome in the total variation in the complex phenotypes of livestock. In human, Richards et al (2018) reported that host genes are affected by the microbiome and are involved in the complex traits.…”

“…In livestock, Difford et al (2016) termed “microbiability” the proportion of total variance explained by microbiome for performance traits of dairy cattle. Difford et al (2018) reported the effect of microbiota variation in methane production in dairy cows while, Mach et al (2015) reported the impact of gut microbiome at early life on phenotypes of pig. Gut microbiome also has a significant impact on porcine fatness (He et al, 2016).…”