Abstract
BackgroundFeed contributes most to livestock production costs. Improving feed efficiency is crucial to increase profitability and sustainability for animal production. Host genetics and the gut microbiota can both influence the host phenotype. However, the association between the gut microbiota and host genetics and their joint contribution to feed efficiency in chickens is largely unclear.ResultsHere, we examined microbial data from the duodenum, jejunum, ileum, cecum, and feces in 206 chickens and their host genotypes and confirmed that the microbial phenotypes and co-occurrence networks exhibited dramatic spatial heterogeneity along the digestive tract. The correlations between host genetic kinship and gut microbial similarities within different sampling sites were weak, with coefficients ranging from − 0.07 to 0.08. However, microbial genome-wide analysis revealed that genetic markers near or inside the genes MTHFD1L and LARGE1 were associated with the abundances of cecal Megasphaera and Parabacteroides, respectively. The effect of host genetics on residual feed intake (RFI) was 39%. We further identified three independent genetic variations that were related to feed efficiency and had a modest effect on the gut microbiota. The contributions of the gut microbiota from the different parts of the intestinal tract on RFI were distinct. The cecal microbiota accounted for 28% of the RFI variance, a value higher than that explained by the duodenal, jejunal, ileal, and fecal microbiota. Additionally, six bacteria exhibited significant associations with RFI. Specifically, lower abundances of duodenal Akkermansia muciniphila and cecal Parabacteroides and higher abundances of cecal Lactobacillus, Corynebacterium, Coprobacillus, and Slackia were related to better feed efficiency.ConclusionsOur findings solidified the notion that both host genetics and the gut microbiota, especially the cecal microbiota, can drive the variation in feed efficiency. Although host genetics has a limited effect on the entire microbial community, a small fraction of gut microorganisms tends to interact with host genes, jointly contributing to feed efficiency. Therefore, the gut microbiota and host genetic variations can be simultaneously targeted by favoring more-efficient taxa and selective breeding to improve feed efficiency in chickens.EooUS9Np68nMFAp4xE4K1kVideo abstract
Highlights
Feed contributes most to livestock production costs
After detecting single-nucleotide polymorphisms (SNPs) that are associated with residual feed intake (RFI), we further investigated the effects of host genotypes on the gut microbiota
Feed efficiency-related microorganisms and their spatial distribution host genetics could influence a small number of gut microorganisms, our results revealed that host genetics and the gut microbiota contributed concurrently to feed efficiency in chickens
Summary
Feed contributes most to livestock production costs. Improving feed efficiency is crucial to increase profitability and sustainability for animal production. The association between the gut microbiota and host genetics and their joint contribution to feed efficiency in chickens is largely unclear. More than 72 billion broiler chickens were produced and chicken had become the largest meat producer worldwide in 2019 (FAOSTAT) This production level has mainly been achieved using high-quality feed ingredients, such as maize, soybean, and wheat [3]. Feed accounts for nearly 70% of the total variable costs in modern chicken production. In recent years, these ingredients have generally become more expensive because of a combination of increased demand from human nutrition [4], biofuel production [5], and shortages due to crop failures in parts of the world [6]. To meet the increasing demand for chicken meat, the efficiency of converting feed into edible products should be improved
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