Cattle with high feed efficiencies (designated “efficient”) produce less methane gas than those with low feed efficiencies (designated “inefficient”); however, the role of the methane producers in such difference is unknown. This study investigated whether the structures and populations of methanogens in the rumen were associated with differences in cattle feed efficiencies by using culture-independent methods. Two 16S rRNA libraries were constructed using ∼800-bp amplicons generated from pooled total DNA isolated from efficient ( n = 29) and inefficient ( n = 29) animals. Sequence analysis of up to 490 randomly selected clones from each library showed that the methanogenic composition was variable: less species variation (22 operational taxonomic units [OTUs]) was detected in the rumens of efficient animals, compared to 27 OTUs in inefficient animals. The methanogenic communities in inefficient animals were more diverse than those in efficient ones, as revealed by the diversity indices of 0.84 and 0.42, respectively. Differences at the strain and genotype levels were also observed and found to be associated with feed efficiency in the host. No difference was detected in the total population of methanogens, but the prevalences of Methanosphaera stadtmanae and Methanobrevibacter sp. strain AbM4 were 1.92 ( P < 0.05) and 2.26 ( P < 0.05) times higher in inefficient animals, while Methanobrevibacter sp. strain AbM4 was reported for the first time to occur in the bovine rumen. Our data indicate that the methanogenic ecology at the species, strain, and/or genotype level in the rumen may play important roles in contributing to the difference in methane gas production between cattle with different feed efficiencies.

Understanding ruminal methanogens is essential for greenhouse gas mitigation, as well as for improving animal performance in the livestock industry. It has been speculated that ruminal methanogenic diversity affects host feed efficiency and results in differences in methane production. This study examined methanogenic profiles in the rumen using culture-independent PCR-denaturing gradient gel electrophoresis (PCR-DGGE) analysis for 56 beef cattle which differed in feed efficiency, as well as diet (the cattle were fed a low-energy diet or a high-energy diet). The methanogenic PCR-DGGE profiles detected were greatly affected by diet, and the major pattern changed from a community containing predominantlyMethanobrevibacter ruminantiumNT7 with the low-energy diet to a community containing predominantlyMethanobrevibacter smithii,Methanobrevibactersp. AbM4, and/orM.ruminantiumNT7 with the high-energy diet. For each diet, the methanogenic PCR-DGGE pattern was strongly associated with the feed efficiency of the host. Diet-associated bands forMethanobrevibactersp. AbM4 andM.smithiiSM9 and a feed efficiency-related band forM.smithiiPS were identified. The abundance of total methanogens was estimated by determining the numbers of copies of the 16S rRNA genes of methanogens. However, the size of the methanogen population did not correlate with differences in feed efficiency, diet, or metabolic measurements. Thus, the structure of the methanogenic community at the species or strain level may be more important for determining host feed efficiency under different dietary conditions.

Aims: To investigate the relationship between ruminal methanogen community and host enteric methane (CH₄) production in lactating dairy cows fed diets supplemented with an exogenous fibrolytic enzyme additive. Methods and Results: Ecology of ruminal methanogens from dairy cows fed with or without exogenous fibrolytic enzymes was examined using PCR–denaturing gradient gel electrophoresis (PCR–DGGE) analyses and quantitative real‐time PCR (qRT‐PCR). The density of methanogens was not affected by the enzyme additive or sampling times, and no relationship was observed between the total methanogen population and CH₄ yield (as g per head per day or g kg⁻¹ DMI). The PCR–DGGE profiles consisted of 26 distinctive bands, with two bands similar to Methanogenic archaeon CH1270 negatively correlated, and one band similar to Methanobrevibacter gottschalkii strain HO positively correlated, with CH₄ yield. Three bands similar to Methanogenic archaeon CH1270 or Methanobrevibacter smithii ATCC 35061 appeared after enzyme was added. Conclusions: Supplementing a dairy cow diet with an exogenous fibrolytic enzyme additive increased CH₄ yield and altered the composition of the rumen methanogen community, but not the overall density of methanogens. Significance and Impact of the Study: This is the first study to identify the correlation between methanogen ecology and host CH₄ yield from lactating dairy cows.

The objective was to determine if supplementing a dairy cow diet with an exogenous fibrolytic enzyme additive (Econase RDE; AB Vista, Marlborough, Wiltshire, UK) altered fermentation, pH, and microbial populations in the rumen or enteric methane (CH(4)) emissions. In a companion study, this enzyme additive improved efficiency of fat-corrected milk production in a dose-dependent manner by up to 11% for early lactation dairy cows. Nine ruminally cannulated, lactating Holstein cows were used in a replicated 3 × 3 Latin square design with 21-d periods. Dietary treatments were 0 (control), 0.5 (low), and 1.0 (high) mL of enzyme/kg of total mixed ration dry matter. Rumen contents were collected on 2 d (d 15 and 19), ruminal pH was measured continuously for 6 d (d 13 to 18) by using an indwelling system, and enteric CH(4) production was measured for 3 d (d 16 to 18) using the sulfur hexafluoride tracer gas technique. The enzyme additive did not alter volatile fatty acids, NH(3), pH, or population densities of total protozoa, bacteria, and methanogens in ruminal fluid. However, population densities of certain bacteria, calculated as copy number of species-specific 16S-rRNA, were affected by enzyme treatment. Population density of Ruminobacter amylophilus was increased and that of Fibrobacter succinogenes tended to be increased by the high enzyme treatment. Selenomonas ruminantium tended to increase linearly with increasing levels of enzyme in the diet, although its population density was only numerically increased by the high enzyme treatment. Streptococcus bovis, however, tended to be decreased by the low enzyme treatment. Increasing the level of enzyme supplement in the diet also linearly increased enteric CH(4) production, even when adjusted for feed intake or milk production (19.3, 20.8, and 21.7 g of CH(4)/kg of dry matter intake or 12.9, 13.6, and 15.1g of CH(4)/kg of milk for the control, low, and high enzyme treatments, respectively). This shift in ruminal bacterial communities and higher CH(4) emissions could imply increased ruminal digestion of feed, which needs to be substantiated in longer term studies.

This study aimed to evaluate whether the host genetic background impact the ruminal microbial communities of the progeny of sires from three different breeds under different diets. Eighty five bacterial and twenty eight methanogen phylotypes from 49 individuals of diverging sire breed (Angus, ANG; Charolais, CHA; and Hybrid, HYB), fed high energy density (HE) and low energy density (LE) diets were determined and correlated with breed, rumen fermentation and phenotypic variables, using multivariate statistical approaches. When bacterial phylotypes were compared between diets, ANG offspring showed the lowest number of diet-associated phylotypes, whereas CHA and HYB progenies had seventeen and twenty-three diet-associated phylotypes, respectively. For the methanogen phylotypes, there were no sire breed-associated phylotypes; however, seven phylotypes were significantly different among breeds on either diet (P<0.05). Sire breed did not influence the metabolic variables measured when high energy diet was fed. A correlation matrix of all pairwise comparisons among frequencies of bacterial and methanogen phylotypes uncovered their relationships with sire breed. A cluster containing methanogen phylotypes M16 (Methanobrevibacter gottschalkii) and M20 (Methanobrevibacter smithii), and bacterial phylotype B62 (Robinsoniella sp.) in Angus offspring fed low energy diet reflected the metabolic interactions among microbial consortia. The clustering of the phylotype frequencies from the three breeds indicated that phylotypes detected in CHA and HYB progenies are more similar among them, compared to ANG animals. Our results revealed that the frequency of particular microbial phylotypes in the progeny of cattle may be influenced by the sire breed when different diets are fed and ultimately further impact host metabolic functions, such as feed efficiency.