Divergent selection for intramuscular fat shapes the gut enterotypes

Abstract

Abstract Background Intramuscular fat (IMF) content is an important trait for both meat production and human health, where the host genetics and its microbiome greatly contribute to its phenotypic variation. An appropriate experimental design allows to approach the linkage between both effects. The aim of this study is to describe the consequences of genetic modification of IMF by selection on the taxonomic composition of the microbiome, using rabbits from the 10th generation of a divergent selection experiment for IMF, in which lines with high (H) and low (L) IMF differ by 3.8 standard deviations. Results Microbiability estimate of IMF was 44.5%, with a probability of being greater than 25% of 0.86. Selection altered the composition of the gut microbiota and differentiated the microbiome of the lines into two gut enterotypes attributable to IMF genetic differences. The two enterotypes were better distinguished at the genus level than at the phylum level, with 51 microbial genera capable of classifying between the lines with 91% accuracy. The H-enterotype was mainly enriched in Hungateiclostridium, Limosilactobacillus, Legionella, Lysinibacillus, Phorphyromonas, Methanosphaera, and Desulfovibrio, while the L-enterotype was mainly enriched in Escherichia, Fonticella, Candidatus Amulumruptor, Methanobrevicater, Exiguobacterium, Flintibacter and Coprococcus, among other genera with smaller differences between enterotypes. A microbial biomarker generated from the abundance of 26 of these 51 genera classified the enterotypes with 93% accuracy in a logit regression and predicted IMF with a prediction accuracy of 0.69 in a linear regression. Conclusions Our results demonstrate divergent gut enterotype composition in hosts with divergent genotypes for IMF content. Furthermore, we provide a microbial biomarker that can be used as an indicator of host predisposition to muscle lipid accumulation based on its genes, and open the way for research to develop probiotics targeting IMF modulation.