Caecal microbiota composition in chickens of different genotypes fed low-input diets

Due to the key role of gut microbiota on chicken health, its management can contribute to the improvement in the resiliency of poultry production based on alternative genotypes and low-input diets. Thus, the current study assessed the changes in the caecal microbiota composition in chickens belonging to a standard fast-growing genotype (Ross 308), two local breeds (Bionda Piemontese, BP; Robusta Maculata, RM), and their crosses (BP×S and RM×S) with a moderate-growth genotype (Sasso, S) fed standard and low-input diets. A total of 441 chickens were housed in 40 pens, half of the pens were fed a low-input diet (diet LI: ME 2,921 kcal/kg; CP 17.5%; lysine: 0.95%) and half a standard diet (diet S: ME 3,050 kcal/kg; CP 18.5%; lysine: 1.07%) from 20 days of age until slaughtering (47 days for Ross and 105 days for the other genotypes), when caecal contents were sampled from 60 chickens (12 for each genotype), and analysed using a 16S rDNA multi-amplicon sequencing approach. Within Ross chickens, sequencing results did not evidence any differences in the microbiota composition between chickens fed the two diets (False Discovery Rate, FDR, P > 0.05). As for the other genotypes, differences in the beta diversity were found between chickens fed the standard and low-input diets in BP, BP×S, and RM×S chickens (PERMANOVA, FDR P ≤ 0.05) without significant differences as for the Shannon index for the alpha diversity measure and the Wilcoxon test for the differential abundance analysis. Then, as for the effect of the genotype, the beta diversity of caecal microbiota significantly changed between BP vs. RM and BP×S vs. RM (PERMANOVA, FDR P ≤ 0.05). In conclusion, under the conditions of the present study, moving from a standard to a low-input diet had no main effects on gut microbiota composition, whereas differences in gut microbiota composition according to genotype were not so relevant to be expected to modify poultry health, and welfare.