Comparative study of fermentation and methanogen community structure in the digestive tract of goats and rabbits

Abstract

SummaryMethane is the most important anthropogenic contribution to climate change after carbon dioxide and represents a loss of feed energy for the animal, mainly for herbivorous species. However, our knowledge about the ecology of Archaea, the microbial group responsible for methane synthesis in the gut, is very poor. Moreover, it is well known that hindgut fermentation differs from rumen fermentation. The composition of archaeal communities in fermentation compartments of goats and rabbits were investigated using DGGE to generate fingerprints of archaeal 16S rRNA gene. Ruminal contents and faeces from five Murciano-Granadina goats and caecal contents of five commercial White New Zealand rabbits were compared. Diversity profile of methanogenic archaea was carried out by PCR-DGGE. Quantification of methanogenic archaea and the abundance relative to bacteria was determined by real-time PCR. Methanogenic archaeal species were relatively constant across species. Dendrogram from DGGE of the methanogen community showed one cluster for goat samples with two sub-clusters by type of sample (ruminal and faeces). In a second cluster, samples from rabbit were grouped. No differences were found either in richness or Shannon index as diversity indexes. Although the primer sets used was developed to investigate rumen methanogenic archaeal community, primers specificity did not affect the assessment of rabbit methanogen community structure. Rumen content showed the highest number or methanogenic archaea (log 10 9.36), followed by faeces (log 10 8.52) and showing rabbit caecum the lower values (log 10 5.52). DGGE profile showed that pre-gastric and hindgut fermenters hold a very different methanogen community. Rabbits hold a microbial community of similar complexity than that in ruminants but less abundant, which agrees with the type of fermentation profile.

Acetogen Communities in the Gut of Herbivores and Their Potential Role in Syngas Fermentation

“…The rumens of cows harbor a significantly higher abundance of methanogens than the ceca of rabbits and the feces of horses, which is consistent with previous studies showing that methanogens are the dominant hydrogen disposal organism in rumen. A higher abundance of methanogens in the rumen when compared to the cecum of rabbits and horses was also observed in the study of Abecia et al [29] and Morvan et al [51], respectively. No significant difference in acetogen abundance was observed among all the host animals studied, suggesting an important role for reductive acetogenesis in their gut.…”

Fundamental Issues Related to the Origin of Melatonin and Melatonin Isomers during Evolution: Relation to Their Biological Functions

“…Some archaea can survive in extreme environmental conditions such as elevated temperature, high pH and high salinity [ 144 , 145 ]. Many archaea also inhabit the gastrointestinal tract of animals including that of the human [ 146 , 147 ]. The importance of archaea in ecological systems [ 148 ] and also to human health and disease [ 149 , 150 ], particularly their relation to obesity [ 151 , 152 ], has drawn much attention recently.…”

Investigation into Host Selection of the Cecal Acetogen Population in Rabbits after Weaning

“…Rabbits, as herbivores, have less methane production [ 14 ] and lower energy loss from methane production per unit of body mass than ruminants [ 15 ]. The estimated hydrogen recoveries for methane are 24.7% and 85.4% in the rabbit cecum [ 16 ] and goat rumen [ 17 ], respectively, and the ratio of acetate to propionate production is much higher in the rabbit cecum compared to rumens (17.8 vs. 2.81) [ 18 ]. The reason for this may be because reductive acetogenesis is the dominant hydrogen disposal pathway in the cecum of rabbits [ 19 , 20 ].…”