Determining the hierarchical order by which intestinal tract, administered diet, and individual relay can shape the gut microbiome of fattening quails

A bacterial metabarcoding approach was used to compare the microbiome composition of caecal and faecal samples from fattening Japanese quails (Coturnix coturnix japonica) fed three different diet regimes. The tested feedstuffs included (1) a commercial diet for fattening quails, (2) a commercial diet containing 12% full-fat silkworm (Bombyx mori) pupae meal, and (3) a commercial diet containing 12% defatted silkworm pupae meal. The aim of the experiment was to verify the relative effect of three variables (diet type, gut tract comparing caecum to rectum, and individual animal) in determining the level of bacterial community dissimilarity to rank the relevance of each of the three factors in affecting and shaping community composition. To infer such ranking, the communities resulting from the high-throughput sequencing from each sample were used to calculate the Bray-Curtis distances in all the pairwise combinations, whereby identical communities would score 0 and totally different ones would yield the maximum distance, equal to 1. The results indicated that the main driver of divergence was the gut tract, as distances between caecal and faecal samples were higher on average, irrespective of diet composition, which scored second in rank, and of whether they had been sampled from the same individual, which was the least effective factor. Simpson's species diversity indexes was not significantly different when comparing tracts or diets, while community evenness was reduced in full-fat silkworm diet-fed animals. The identities of the differentially displayed taxa that were statistically significant as a function of gut tract and diet regimen are discussed in light of their known physiological and functional traits.