A major factor that may explain part of the unexplained 69.2% of biological variation is microbial interactions. Following niche construction theory, microbiota play a role in modifying physicochemical conditions of the digestive gland and apply selection pressure to themselves, their descendants, and immigrating cells . Here, the selection of the holobiont microbiota may result in the cooperation between degraders of algal polysaccharides and fermenters of the resulting products in microaerophilic and acidic conditions. Indeed, aerobic bacteria ingested with the diet have been shown to rapidly consume all the available oxygen in the gastrointestinal tract, providing ideal conditions for fermentation of pyruvate from algal polysaccharide degradation [36, 76]. Genomes closely related to Psychrilyobacter, Mycoplasma, and Vibrio possess enzymes for the acetate pathway, allowing pyruvate fermentation to short chain fatty acids (SCFA) for further assimilation by the host (Additional file 5: Table S4, Additional file 8, Fig. 6). As hypothesized for gut colonization of the sea squirt Ciona intestinalis , these dominant fermenters, may be part of a resident anaerobic biofilm within the outer mucus layer at the epithelial cell surface and benefit from the host digestive properties such as the secretion of mucin-like glycoproteins .Fig. 6Proposed processes of algal polysaccharide degradation in the abalone digestive gland. For information, localization of the abalone digestive gland on an abalone without the shell (a). The schematic illustration recapitulates hypothetical processes of algal polysaccharide degradation in the case of a brown algal cell wall (b). The algal diet comes along with epiphytic bacteria, including (1) strictly aerobic bacteria which may die due to specific physiochemical conditions (low O2, low pH) and (2) facultative aerobic bacteria, which may act as primary degraders of complex algal polysaccharides. Primary degraders may (3) directly ferment polysaccharides to short-chain fatty acids (SCFA, e.g. Vibrio) or (4) transform polysaccharides into pyruvate or solubilized mono- and oligosaccharides (members of Flavobacteriia, Alpha-, and Gammaproteobacteria). These may then be (5) fermented by strictly or facultative anaerobic bacteria (e.g. Psychrilyobacter, Mycoplasma), which are probably localized in an anaerobic or microaerophilic part of the gland, such as the epithelial mucus. Resulting SCFA are then (6) assimilated by the host. Parts of the illustration are inspired from [6, 96]. Abalone picture: courtesy of Monique Ras