Over the last decade, pre-treatment and even anaerobic co-digestion strategies have emerged in order to make organic matter more accessible. However, these technologies have been reached less than 60% degradation/conversion of organic matter to methane. In comparison, over millions of years, living organisms have explored and optimized the digestion of a wide variety of substrates with high yields (> 70%). The aim of the study is the analysis of natural innovation in animal digestive tracts in order to improve anaerobic digestion processes. The approach consists of a large descriptive inventory of animal digestive tracts. Animals (vertebrates, arthropods, molluscs, etc.) use all types of organic matter as food. Moreover over evolutionary time, organisms become more and more specialized and use only specific type of food (leaves, seed, meat, bones, faeces, etc.). In parallel, the digestive systems evolve to optimize the nutrient recovery. Each animal species domesticates its own microbe consortium and develops its own digestive tract structure. The digestive systems can be seen as a microbial reactor with abiotic pre- and/or post-treatments. When considering their functions, physiological compartments can be imagined as reactors. Thus, continuous stirred-tank reactors, continuous stirred-tank reactors in series, plug-flow reactors, and batch reactors can be used to model the function of these compartments. In this paper, we relate animal size, animal phylogeny and the feeding habit (carnivorous, omnivorous, granivorous, herbivorous) to the type and the position of microbial compartment with respect to the abiotic compartments within the digestive tract. We also relate the role of these parameters on the microbial diversity within the microbial compartment. The results show that (i) the feeding habit determines the type of microbial reactor and its position within the digestive tract; (ii) the phylogeny of the animal determines the type of abiotic pre- and/or post-treatment; (iii) finally, the size of the animal determines the level of diversity of the microbial communities.