It has been assumed that the feeding habits of vertebrates predispose
the variety of intestinal differentiations and the composition of the
microbial biota living in their intestinal tracts. Consequently, the p
resence of methanogenic bacteria in the various differentiations of th
e large intestine and the foregut of herbivorous vertebrates had been
attributed primarily to the existence of anaerobic habitats and the av
ailability of carbon dioxide and hydrogen originating from the ferment
ative microbial digestion of plant-based diets. However, Australian ra
tites, many murids, and several New World primates lack methanogens, d
espite their intestinal differentiations and their vegetarian feeding
habits. Crocodiles, giant snakes, aardvarks, and ant-eaters on the oth
er hand release significant amounts of methane. A determination of met
hane emissions by 253 vertebrate species confirmed that competence for
intestinal methanogenic bacteria is shared by related species and hig
her taxa, irrespective of different feeding habits. In ''methaogenic''
branches of the evolutionary tree, a variety of differentiations of t
he large intestine evolved and, in some cases, differentiations of the
foregut. In contrast, the lack of competence for methanogens in chiro
pterans/insectivores and carnivores apparently has precluded the evolu
tion of specialized fermenting differentiations of the digestive tract
. Our observations reveal that the presence of intestinal methanogenic
bacteria is under phylogenetic rather than dietary control: competenc
e for intestinal methanogenic bacteria is a plesiomorphic (primitive-s
hared) character among reptiles, birds, and mammals. This competence f
or methanogenic bacteria has been crucial for the evolution of the amn
iotes.