Correlated Responses to Selection for Intramuscular Fat on the Gut Microbiome in Rabbits

Intramuscular fat (IMF) content is important for meat production and human health, where the host genetics and its microbiome greatly contribute to its variation. The aim of this study is to describe the consequences of the genetic modification of IMF by selecting the taxonomic composition of the microbiome, using rabbits from the 10th generation of a divergent selection experiment for IMF (high (H) and low (L) lines differ by 3.8 standard deviations). The selection altered the composition of the gut microbiota. Correlated responses were better distinguished at the genus level (51 genera) than at the phylum level (10 phyla). The H-line was enriched in Hungateiclostridium, Limosilactobacillus, Legionella, Lysinibacillus, Phorphyromonas, Methanosphaera, Desulfovibrio, and Akkermansia, while the L-line was enriched in Escherichia, Methanobrevibacter, Fonticella, Candidatus Amulumruptor, Methanobrevibacter, Exiguobacterium, Flintibacter, and Coprococcus, among other genera with smaller line differences. A microbial biomarker generated from the abundance of four of these genera classified the lines with 78% accuracy in a logit regression. Our results demonstrate different gut microbiome compositions in hosts with divergent IMF genotypes. Furthermore, we provide a microbial biomarker to be used as an indicator of hosts genetically predisposed to accumulate muscle lipids, which opens up the opportunity for research to develop probiotics or microbiome-based breeding strategies targeting IMF.