Cross links between feed efficiency parameters and gut microbiota in pigs. Effect of productive type and diet protein levels

The effects of two dietary CP concentrations (Normal or Low) and two productive types (castrated Duroc (C-Du) or entire Pietrain (E-Pi)) on productivity (ADFI, ADG and FCR), digestibility of nutrients and GHG emissions were assessed in a 98 d, three-phase feeding program. Thirty two castrated male Duroc and 32 entire male Pietrain piglets were used. At the last day of each feeding phase and after 12 hours of fasting period, animals were submitted to rectal spot feces and blood sampling. Feed and feces samples at each phase were analyzed for their DM, CP, NDF contents. Genomic DNA was extracted from stool samples with a Qiagen stool mini kit, and the libraries were prepared using V3-V4 amplicons from the 16s rRNA gene. Sequencing was performed with Illumina Miseq, generating 902131 paired-end reads. Sequence data was analyzed following the UPARSE protocol. OTUs were classified taxonomically using RDPII database and Multivariate analysis was conducted using package “vegan” from R. Biodiversity indexes (Shannon Wiener, Simpson and Richness) and Spearman correlations between biodiversity and performance traits were also calculated. Firmicutes was the most abundant phyla in both productive types (72.4±6.13 % in C-Du; 73.5±4.81 % in E-Pi), followed by Bacteroides and Proteobacteria. Among the main phyla, differences were observed between productive types in the relative titers of phyla Bacteroidetes (C-Du > E-Pi, P<0.05), Proteobacteria (E-Pi> C-Du, P<0.01), and Actinobacteria (C-Du>E-Pi, P<0.1). The effect of CP supply was phyla distribution was negligible. Thirteen genera presented changes in their relative abundance between productive types and six among diets. Richness index of diversity showed significant differences between genotypes and diets, being Normal CP diets more diverse than Low CP ones, and E-Pi more diverse than C-Du (P<0.05 in both cases). Microbial community structure showed to be highly affected by productive types (P<0.001), and productive typesXdiet interaction (P=0.01). Canonical Correspondence Analysis indicated that CP and Starch digestibility, as well as Ammonia and CO2 levels were related with microbial community structure(P<0.014). Diversity correlated with ADG in C-Du and nutrients digestibility in E-Pi.