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 ϳ800-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.Microbial fermentation and ruminal nutrient absorption are key steps in the energy metabolism of cattle. The microbiota in the rumen is highly associated with the diet, age, antibiotic use, and health of host animals (32). Different types of symbiotic anaerobic microorganisms, including bacteria, archaea, ciliated protozoa, and fungi, inhabit the rumen (15), interact with each other, and play important roles in affecting the host's performance. The microbial-host relationships are highly complex and varied, ranging from mutually beneficial cooperation to competition (10). Among ruminal microbes, bacteria decompose the feed into short-chain (C 1 to C 5 ) fatty acids, amino acids, H 2 , and CO 2 , etc. (20). To maintain the low hydrogen level in this habitat, hydrogen-utilizing microbes, such as methanogens, utilize H 2 and carbon substrates, mainly CO 2 , acetate, or methanol, to generate methane gas and hence to reduce hydrogen pressure in the rumen (8). However, this process causes a significant (6%) loss of dietary energy in the form of methane emission (14), which contributes to 13 to 19% of global greenhouse gas (16), and is one of the significant agricultural "causative sectors" contributing to global warming (13). Therefore, the energy loss and the consequent methane emission arouse both nutritional an...