Research Article: Two Different Bacterial Community Types Are Linked with the Low-Methane Emission Trait in Sheep

Date Published: July 31, 2014

Publisher: Public Library of Science

Author(s): Sandra Kittelmann, Cesar S. Pinares-Patiño, Henning Seedorf, Michelle R. Kirk, Siva Ganesh, John C. McEwan, Peter H. Janssen, Hauke Smidt.


The potent greenhouse gas methane (CH4) is produced in the rumens of ruminant animals from hydrogen produced during microbial degradation of ingested feed. The natural animal-to-animal variation in the amount of CH4 emitted and the heritability of this trait offer a means for reducing CH4 emissions by selecting low-CH4 emitting animals for breeding. We demonstrate that differences in rumen microbial community structure are linked to high and low CH4 emissions in sheep. Bacterial community structures in 236 rumen samples from 118 high- and low-CH4 emitting sheep formed gradual transitions between three ruminotypes. Two of these (Q and S) were linked to significantly lower CH4 yields (14.4 and 13.6 g CH4/kg dry matter intake [DMI], respectively) than the third type (H; 15.9 g CH4/kg DMI; p<0.001). Low-CH4 ruminotype Q was associated with a significantly lower ruminal acetate to propionate ratio (3.7±0.4) than S (4.4±0.7; p<0.001) and H (4.3±0.5; p<0.001), and harbored high relative abundances of the propionate-producing Quinella ovalis. Low-CH4 ruminotype S was characterized by lactate- and succinate-producing Fibrobacter spp., Kandleria vitulina, Olsenella spp., Prevotella bryantii, and Sharpea azabuensis. High-CH4 ruminotype H had higher relative abundances of species belonging to Ruminococcus, other Ruminococcaceae, Lachnospiraceae, Catabacteriaceae, Coprococcus, other Clostridiales, Prevotella, other Bacteroidales, and Alphaproteobacteria, many of which are known to form significant amounts of hydrogen. We hypothesize that lower CH4 yields are the result of bacterial communities that ferment ingested feed to relatively less hydrogen, which results in less CH4 being formed.

Partial Text

The forestomachs of ruminant animals contain a great diversity of prokaryotic and eukaryotic microorganisms that together break down and ferment the feed ingested by the host animal. Volatile fatty acids (VFAs), such as acetate, propionate and butyrate, are formed, together with varying amounts of hydrogen (H2). Methanogenic archaea in the rumen use H2 to gain energy, producing methane (CH4) in the process. CH4 is of no nutritional value to the animal, and is eructed and exhaled into the atmosphere, where it acts as a potent greenhouse gas. This CH4 also represents a major loss of energy to the animal [1], [2]. To reduce CH4 emissions from enteric fermentation, and increase animal productivity, a number of different mitigation strategies have been tested, e.g., feed supplementation with lipids [3], [4], [5], inhibition of enzymes involved in CH4 formation [6], [7], depletion of ciliate protozoa [8], or vaccination against methanogens (for a recent review see Wedlock et al.[9]). Another potentially very effective way to reduce CH4 emissions from ruminant animals is to specifically select naturally low-CH4 emitting animals for breeding and to avoid proliferation of high-CH4 emitting animals. Measurements of CH4 emissions from individual sheep in highly-sensitive open-circuit respiration chambers showed that animals in the same flock, even though feeding on the same diet, varied significantly and consistently in their CH4 yields, measured in g CH4 per kg of dry matter intake (DMI; [10]). Some individuals have a naturally lower CH4 yield (low emitters) than others (high emitters). The genetics of the low CH4 trait, including estimates of heritability, repeatability and genetic correlations with productive traits, are starting to be better understood [11]. Of increasing interest are the underlying factors, both genetic and non-genetic, that explain the observed natural differences in CH4 yields between individual animals. It is assumed that certain host-related characteristics, such as genotype, physiological state, or development of the animal, influence CH4 yields by controlling the presence and/or abundance of certain microbial populations in the rumen. Studies that analyze the microbiota of ruminants that naturally vary in the amount of CH4 produced have so far been missing from the literature, and detailed microbial analyses of hundreds of samples have only become possible with the development of next generation sequencing technologies. Understanding the differences in rumen microbial community structure between low- and high-emitting animals will point to those microbial groups that play key roles in the expression of the host trait or that have adapted to it. Isolation and cultivation efforts can then be made to study these particular taxa in greater detail in the future. Knowledge on the physiology of these groups may be useful for targeted modification of rumen microbial communities and promotion of the low-CH4 trait, or help understand the circumstances that lead to a low-CH4 trait and any production benefits or tradeoffs. Here, we applied high-throughput barcoded 454 Titanium amplicon sequencing of bacterial, archaeal, and eukaryotic marker genes to determine correlations between rumen microbial community structure and CH4 yields of 60 high- and 58 low-emitting sheep.

This work demonstrates that the natural variation in the CH4 emission trait is reflected in the composition of the microbial community in the rumen of the host animal. We analyzed bacterial, archaeal, and eukaryotic communities in rumen samples obtained from sheep identified as naturally high or low emitting animals using the most accurate method of CH4 yield measurement to date (respiration chambers). We reasoned that, if there were differences in the microbial communities of sheep emitting different amounts of CH4, these differences should be most apparent in comparisons of the highest and lowest emitting animals, and that they should be consistently found in different groups of animals. Our data on the rumen microbial communities from the 60 highest and 58 lowest CH4 emitters from four different cohorts of sheep suggest that differences in bacterial and archaeal community structures are associated with a naturally lower CH4 yield and are consistent with consequent differences in rumen fermentation.