Roe Deer Produce Less Methane and Harbor Distinct Gut Microbiota

Enteric methane (CH₄) is an important greenhouse gas emitted by ruminants. Cervidae produces less CH₄ than other ruminants, but the underlying mechanism remains unclear. Here, we measured and compared the gas production, nutrient digestibility, gut microbiota composition, and fermentation characteristics of roe deer (<i>n</i> = 4) and goats (<i>n</i> = 4). After the animals had adapted to the same total mixed ration for 21 days, the gas yield was measured using respiration chambers, and fecal samples were collected. The CH₄ yield (g/kg DMI) was significantly lower in roe deer than in goats (<i>p</i> < 0.001), while the difference in carbon dioxide yield was not significant (<i>p</i> > 0.05). Roe deer showed lower digestibility of dry matter (<i>p</i> = 0.005), crude protein (<i>p</i> < 0.001), and neutral detergent fiber (<i>p</i> = 0.02) than goats. Principal coordinate analysis revealed that the bacterial and methanogen communities were significantly different between roe deer and goats, indicating a potential role of host genetics. Roe deer and goats showed enrichment of specific key bacterial and methanogen taxa. The relative abundances of <i>Bifidobacterium</i>, <i>Ruminococcus</i>, <i>Succinivibrio</i>, <i>Treponema</i>, <i>Prevotella</i>, <i>Lachnoclostridium</i>, Christensenellaceae R7, and members of the family Lachnospiraceae were higher in roe deer than in goats (<i>p</i> < 0.05). <i>Methanocorpusculum</i> and <i>Methanobrevibacter</i> were dominant methanogens in the guts of roe deer and goats, respectively, but their species compositions differed significantly between the host species. The predicted metabolic pathways, including those for butyrate and propionate, were significantly more abundant in roe deer than in goats (<i>p</i> < 0.05). The molar proportions of propionate and branched volatile fatty acids were significantly higher in roe deer and goats (<i>p</i> < 0.01), respectively. The variation in CH₄ yield was characterized by correlations between digestibility, bacteria and methanogens between roe deer and goats, particularly for members within the taxa Lachnospiraceae and <i>Methanosphaera</i>. In summary, our results revealed that gut bacteria and methanogens differ significantly between high- and low-CH₄ emitters and identified microbial taxa potentially involved in the mitigation of CH₄ production in ruminants.