ABSTRACTAlthough dynamics of the complex microbial ecosystem populating the gastrointestinal tract of animals has profound and multifaceted impacts on host’s metabolism and health, it remains unclear whether it is the intrinsic or extrinsic factors that play a more dominant role in mediating variations in the composition of intestinal microbiota. To address this, two strikingly different diets were studied: a high-protein, low-fiber formula feed (FF), and low-protein, high-fiber Sudan grass (SG). After a 16-week feeding trial on a herbivorous fish, grass carp, microbial profiles of midgut (M) and hindgut (H) segments of both groups were compared. Bacteroidetes were more abundant in the hindgut (T=-7.246, p<0.001), and Proteobacteria in the midgut (T=4.383, p<0.001). Fusobacteria were more abundant in the FF group (compared to the SG group, T=2.927, p<0.001). Bacterial composition was different (p<0.05) between the midguts of formula feed (M-FF) and Sudan grass (M-SG) groups, but not between the hindguts of two groups (H-FF and H-SG; p=0.269). PerMANOVA and VPA indicated that the gut segment contributed 19.8% (p<0.001) and 28% (p<0.001) of the variation of microbial communities, whereas diet contributed only 8.0% (p<0.001) and 14% (p<0.001), respectively. Overall, results suggest that intestinal compartments are a stronger determinant than diet in shaping the intestinal microbiota. Specifically, whereas diet has a strong impact on the microbiome composition in proximal gut compartments, this impact is much less pronounced distally, which is likely to be a reflection of a limited ability of some microbial taxa to thrive in the anoxic environment in distal segments.IMPORTANCEThe impact of compositional dynamics of gut microbiota on host’s metabolism and health is so profound that the traditional idea of biological individual is increasingly replaced with "holobiont", comprising both the host and its microbiome. Composition of gut microbiota is strongly influenced by extrinsic (such as diet) and intrinsic (such as gut compartment) factors. Despite ample scientific attention both of these factors have received individually, their relative contributions in mediating the dynamics of the microbiome remain unknown. Given the importance of this issue, we set out to disentangle their individual contributions in a herbivorous fish, grass carp. We found that intestinal compartments are a stronger determinant than diet in shaping the intestinal microbiota. Whereas the impact of diet is strongly pronounced in proximal gut compartments, it appears that limited ability of some microbial taxa to thrive in the anoxic environment in distal segments strongly reduces the impact of diet distally.
Gut segments outweigh the diet in shaping the intestinal microbiome composition in grass carp Ctenopharyngodon idellus