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Both host genetics and gut microbiota influence feed efficiency. However, the associations between gut microbiota and host genetics, as well as their combined contributions to feed efficiency in laying hens during the late laying period, remain largely unclear.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Methods<\/jats:title>\n                <jats:p>In total, 686 laying hens were used for whole-genome resequencing and liver transcriptome sequencing. 16S rRNA gene sequencing was conducted on gut chyme (duodenum, jejunum, ileum, and cecum) and fecal samples from 705 individuals. Bioinformatic analysis was performed by integrating the genome, transcriptome, and microbiome to screen for key genetic variations, genes, and gut microbiota associated with feed efficiency.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>The heritability of feed conversion ratio (FCR) and residual feed intake (RFI) was determined to be 0.28 and 0.48, respectively. The ileal and fecal microbiota accounted for 15% and 10% of the FCR variance, while the jejunal, cecal, and fecal microbiota accounted for 20%, 11%, and 10% of the RFI variance. Through SMR analysis based on summary data from liver eQTL mapping and GWAS, we further identified four protein-coding genes, <jats:italic>SUCLA2<\/jats:italic>, <jats:italic>TNFSF13B<\/jats:italic>, <jats:italic>SERTM1<\/jats:italic>, and <jats:italic>MARVELD3<\/jats:italic>, that influence feed efficiency in laying hens. The <jats:italic>SUCLA2<\/jats:italic> and <jats:italic>TNFSF13B<\/jats:italic> genes were significantly associated with SNP 1:25664581 and SNP rs312433097, respectively. <jats:italic>SERTM1<\/jats:italic> showed significant associations with rs730958360 and 1:33542680 and is a potential causal gene associated with the abundance of Corynebacteriaceae in feces. <jats:italic>MARVELD3<\/jats:italic> was significantly associated with the 1:135348198 and was significantly correlated with the abundance of <jats:italic>Enterococcus<\/jats:italic> in ileum. Specifically, a lower abundance of <jats:italic>Enterococcus<\/jats:italic> in ileum and a higher abundance of Corynebacteriaceae in feces were associated with better feed efficiency.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>This study confirms that both host genetics and gut microbiota can drive variations in feed efficiency. A small portion of the gut microbiota often interacts with host genes, collectively enhancing feed efficiency. Therefore, targeting both the gut microbiota and host genetic variation by supporting more efficient taxa and selective breeding could improve feed efficiency in laying hens during the late laying period.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s40104-024-01076-7","type":"journal-article","created":{"date-parts":[[2024,9,9]],"date-time":"2024-09-09T00:01:45Z","timestamp":1725840105000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":19,"title":["Host genetics and gut microbiota synergistically regulate feed utilization in egg-type chickens"],"prefix":"10.1186","volume":"15","author":[{"given":"Wenxin","family":"Zhang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fangren","family":"Lan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qianqian","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuang","family":"Gu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaochang","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chaoliang","family":"Wen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ning","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0520-4355","authenticated-orcid":false,"given":"Congjiao","family":"Sun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,9,9]]},"reference":[{"issue":"3","key":"1076_CR1","doi-asserted-by":"publisher","first-page":"328","DOI":"10.1079\/WPS20030020","volume":"59","author":"W Zhang","year":"2003","unstructured":"Zhang W, Aggrey S. 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