Joint contributions of the gut microbiota and host genetics to feed efficiency in chickens

Abstract

Background Feed 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. Results Here, 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. Conclusions Our 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.

Microbial Composition in the Duodenum and Ileum of Yellow Broilers With High and Low Feed Efficiency

“…In addition to the genera we identified, Acinetobacter and Arcobacter have also been reported to be predominant in broilers with high FCR, whereas microbes such as Barnesiella and Cloacibacillus were found to be abundant in broilers with low FCR ( Singh et al, 2012 ). Wen et al (2021) have demonstrated that lower abundances of duodenal Akkermansia muciniphila and cecal Parabacteroides , and higher abundances of cecal Lactobacillus , Corynebacterium , Coprobacillus , and Slackia were interrelated to better feed efficiency. Interestingly, Akkermansia muciniphila , as a member of phylum Verrucomicrobia, was also detected in the duodenum of our experimental broilers with extreme low relative abundance.…”

“…Longer digestion time of nutrients in the cecum allows enhanced microbial fermentation ( Rehman et al, 2007 ). Feces are easy to sample for subsequent analysis and are usually used as substitutes for intestinal microbiota ( Wen et al, 2021 ). However, the heterogeneity of digestive tract function leads to the regional differences within the intestinal microbial populations ( Martinez-Guryn et al, 2019 ).…”

“…Microbial density and diversity were found to be greatest in the cecum ( Rehman et al, 2007 ). Fecal samples were easy to obtain and usually used as substitutes for gut microbes ( Wen et al, 2021 ). Studies on the relationship between FE and gastrointestinal microbes in broilers have mainly focused on microbes in the cecum and feces, whereas few studies have focused on those in the duodenum and ileum.…”

Gastrointestinal Development and Microbiota Responses of Geese to Honeycomb Flavonoids Supplementation

“…In the latest years, the chicken gut metagenome and its modulatory effects on production performance, the heritability of chicken gut microbe, and the interactive regulation on feed efficiency between host genetics and gut microbiome have been well-studied ( 1 , 2 ). However, little information could be acquired about geese.…”

“…The gut microbiome is considered the host second genome, which emerged as a key determinant of many aspects including the capability of shaping developmental, physiological and reproductive phenotypes ( 5 ), the enhancement of feed digestibility and nutrient absorption throughout the digestive tract ( 2 ), and the inhibition on intestinal pathogenic bacteria ( 6 ). Further, unlike other environmental factors, the microbiomes may be transmitted between generations carrying the potentiality to alter traits beyond the limits of the host's genetics ( 7 ), and further worked on shaping the phenotypes of the progenies.…”