{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T04:16:31Z","timestamp":1787112991758,"version":"build-2736575974"},"reference-count":107,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2024,11,13]],"date-time":"2024-11-13T00:00:00Z","timestamp":1731456000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>\n                    Feed efficiency and growth performance are economically important traits in pigs. Precious studies have been revealed that both genetics and gut microbes could influence host phenotypes, however, the mechanisms by which they affect pig growth and feed efficiency remain poorly understood. In this study, 361 crossbred Duroc \u00d7 (Landrace \u00d7 Yorkshire) commercial pigs were genotyped using GeneSeek Porcine SNP50K BeadChip, and the microbiotas from fecal samples were acquired using microbial 16S rRNA gene sequencing technology to investigate the impact of host genetics and gut microorganisms on growth and feed efficiency. The results showed that the heritability and enterobacterial force ranged from 0.27 to 0.46 and 0 to 0.03, respectively. Genome-wide association studies (GWAS) identified seven significant SNPs to be associated with growth and feed efficiency, and several genes, including\n                    <jats:italic>AIF1L<\/jats:italic>\n                    ,\n                    <jats:italic>ASS1<\/jats:italic>\n                    , and\n                    <jats:italic>QRFP<\/jats:italic>\n                    were highlighted as candidates for the analyzed traits. Additionally, microbiome-genome-wide association studies GWAS revealed potential links between\n                    <jats:italic>CCAR2<\/jats:italic>\n                    ,\n                    <jats:italic>EGR3<\/jats:italic>\n                    ,\n                    <jats:italic>GSTM3<\/jats:italic>\n                    , and\n                    <jats:italic>GPR61<\/jats:italic>\n                    genes and the abundance of microorganisms, such as\n                    <jats:italic>Trueperella<\/jats:italic>\n                    ,\n                    <jats:italic>Victivallis<\/jats:italic>\n                    , and\n                    <jats:italic>Erysipelatoclostridium<\/jats:italic>\n                    . In addition, six microbial genera linked to growth and feed efficiency were identified as follows\n                    <jats:italic>Lachnospiraceae_UCG-005<\/jats:italic>\n                    ,\n                    <jats:italic>Prevotellaceae_UCG-003<\/jats:italic>\n                    ,\n                    <jats:italic>Prevotellaceae_NK3B31_group<\/jats:italic>\n                    ,\n                    <jats:italic>Prevotella_1<\/jats:italic>\n                    ,\n                    <jats:italic>Prevotella_9<\/jats:italic>\n                    , and\n                    <jats:italic>Veillonella<\/jats:italic>\n                    . Our findings provide novel insights into the factors influencing host phenotypic complexity and identify potential microbial targets for enhancing pig feed efficiency through selective breeding. This could aid in the development of strategies to manipulate the gut microbiota to optimize growth rates and feed efficiency in pig breeding.\n                  <\/jats:p>","DOI":"10.3389\/fmicb.2024.1459773","type":"journal-article","created":{"date-parts":[[2024,11,13]],"date-time":"2024-11-13T01:21:26Z","timestamp":1731460886000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":14,"title":["The influence of host genotype and gut microbial interactions on feed efficiency traits in pigs"],"prefix":"10.3389","volume":"15","author":[{"given":"Zhuoda","family":"Lu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tao","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yunxiang","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanqin","family":"Pang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meng","family":"Guo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoping","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ying","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhili","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2024,11,13]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1111\/jbg.12539","article-title":"Genetic relationships between feed efficiency and gut microbiome in pig lines selected for residual feed intake","volume":"138","author":"Aliakbari","year":"2021","journal-title":"J. Anim. Breed. Genet."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1186\/s12711-022-00717-7","article-title":"Microbiability and microbiome-wide association analyses of feed efficiency and performance traits in pigs","volume":"54","author":"Aliakbari","year":"2022","journal-title":"Genet. Sel. Evol."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"18933","DOI":"10.1073\/pnas.1007028107","article-title":"Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors","volume":"107","author":"Benson","year":"2010","journal-title":"Proc. Natl. Acad. Sci."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"10134","DOI":"10.1038\/s41598-020-66791-3","article-title":"Heritability and genome-wide association of swine gut microbiome features with growth and fatness parameters","volume":"10","author":"Bergamaschi","year":"","journal-title":"Sci. Rep."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"110","DOI":"10.1186\/s40168-020-00888-9","article-title":"Gut microbiome composition differences among breeds impact feed efficiency in swine","volume":"8","author":"Bergamaschi","year":"","journal-title":"Microbiome"},{"key":"ref6","doi-asserted-by":"publisher","first-page":"819011","DOI":"10.3389\/fmicb.2022.819011","article-title":"Socializing models during lactation Alter colonic mucosal gene expression and fecal microbiota of growing piglets","volume":"13","author":"Bi","year":"2022","journal-title":"Front. Microbiol."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"E11874","DOI":"10.1073\/pnas.1807305115","article-title":"Metabolic network-based stratification of hepatocellular carcinoma reveals three distinct tumor subtypes","volume":"115","author":"Bidkhori","year":"2018","journal-title":"Proc. Natl. Acad. Sci."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1017\/s1466252318000026","article-title":"Gut immunity: its development and reasons and opportunities for modulation in monogastric production animals","volume":"19","author":"Broom","year":"2018","journal-title":"Anim. Health Res. Rev."},{"key":"ref9","doi-asserted-by":"publisher","first-page":"1880","DOI":"10.1016\/j.ajhg.2021.08.005","article-title":"Fast two-stage phasing of large-scale sequence data","volume":"108","author":"Browning","year":"2021","journal-title":"Am. J. Hum. Genet."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"1112","DOI":"10.1186\/1471-2164-15-1112","article-title":"Genome-wide association and biological pathway analysis for milk-fat composition in Danish Holstein and Danish Jersey cattle","volume":"15","author":"Buitenhuis","year":"2014","journal-title":"BMC Genomics"},{"key":"ref11","doi-asserted-by":"publisher","first-page":"1637","DOI":"10.1534\/genetics.117.200782","article-title":"Host genome influence on gut microbial composition and microbial prediction of complex traits in pigs","volume":"206","author":"Camarinha-Silva","year":"2017","journal-title":"Genetics"},{"key":"ref12","doi-asserted-by":"publisher","first-page":"969","DOI":"10.2527\/2005.835969x","article-title":"Identification of errors and factors associated with errors in data from electronic swine feeders1","volume":"83","author":"Casey","year":"2005","journal-title":"J. Anim. Sci."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"s13742-13015-10047-13748","DOI":"10.1186\/s13742-015-0047-8","article-title":"Second-generation PLINK: rising to the challenge of larger and richer datasets. Giga","volume":"4","author":"Chang","year":"2015","journal-title":"Science"},{"key":"ref14","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1186\/s40168-021-01110-0","article-title":"Prevotella copri increases fat accumulation in pigs fed with formula diets","volume":"9","author":"Chen","year":"2021","journal-title":"Microbiome"},{"key":"ref15","doi-asserted-by":"publisher","first-page":"e5","DOI":"10.1002\/imt2.5","article-title":"ImageGP: an easy-to-use data visualization web server for scientific researchers","volume":"1","author":"Chen","year":"2022","journal-title":"iMeta"},{"key":"ref16","doi-asserted-by":"publisher","first-page":"e0275604","DOI":"10.1371\/journal.pone.0275604","article-title":"The hypothalamic RFamide, QRFP, increases feeding and locomotor activity: the role of Gpr103 and orexin receptors","volume":"17","author":"Cook","year":"2022","journal-title":"PLoS One"},{"key":"ref17","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1186\/1471-2164-13-213","article-title":"Identification of differentially expressed genes and pathways for intramuscular fat deposition in pectoralis major tissues of fast-and slow-growing chickens","volume":"13","author":"Cui","year":"2012","journal-title":"BMC Genomics"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"75","DOI":"10.19103\/AS.2021.0089.04","article-title":"Microbiological services delivered by the pig gut microbiome","volume-title":"Understanding gut microbiomes as targets for improving pig gut health","author":"Cullen","year":"2022"},{"key":"ref19","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1186\/s12916-017-0792-x","article-title":"Abnormal epigenetic changes during differentiation of human skeletal muscle stem cells from obese subjects","volume":"15","author":"Daveg\u00e5rdh","year":"2017","journal-title":"BMC Med."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"903733","DOI":"10.3389\/fgene.2022.903733","article-title":"Application of genetic, genomic and biological pathways in improvement of swine feed efficiency","volume":"13","author":"Davoudi","year":"2022","journal-title":"Front. Genet."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"2875","DOI":"10.1038\/s41598-020-60003-8","article-title":"Author correction: whole rumen metagenome sequencing allows classifying and predicting feed efficiency and intake levels in cattle","volume":"10","author":"Delgado","year":"2020","journal-title":"Sci. Rep."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1186\/s12711-022-00742-6","article-title":"Gut microbiota and host genetics contribute to the phenotypic variation of digestive and feed efficiency traits in growing pigs fed a conventional and a high fiber diet","volume":"54","author":"D\u00e9ru","year":"2022","journal-title":"Genet. Sel. Evol."},{"key":"ref23","doi-asserted-by":"publisher","first-page":"5069","DOI":"10.1128\/AEM.03006-05","article-title":"Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB","volume":"72","author":"DeSantis","year":"2006","journal-title":"Appl. Environ. Microbiol."},{"key":"ref24","article-title":"Genes and microbes: the next step in dairy cattle breeding. In Book of Abstracts of the 67th Annual Meeting of the European Association for Animal Production, Wageningen Academic Publishers, Book of Abstracts of the Annual EAAP Meeting, vol. 22, 67th Annual Meeting of the European Federation of Animal Science","author":"Difford","year":"2016"},{"key":"ref25","doi-asserted-by":"publisher","first-page":"e1007580","DOI":"10.1371\/journal.pgen.1007580","article-title":"Host genetics and the rumen microbiome jointly associate with methane emissions in dairy cows","volume":"14","author":"Difford","year":"2018","journal-title":"PLoS Genet."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"220","DOI":"10.3389\/fgene.2018.00220","article-title":"Genetic architecture of feeding behavior and feed efficiency in a Duroc pig population","volume":"9","author":"Ding","year":"2018","journal-title":"Front. Genet."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1186\/1471-2156-15-27","article-title":"Genome-wide association and systems genetic analyses of residual feed intake, daily feed consumption, backfat and weight gain in pigs","volume":"15","author":"Do","year":"2014","journal-title":"BMC Genet."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"4069","DOI":"10.2527\/jas.2012-6197","article-title":"Genetic parameters for different measures of feed efficiency and related traits in boars of three pig breeds1","volume":"91","author":"Do","year":"2013","journal-title":"J. Anim. Sci."},{"key":"ref29","doi-asserted-by":"publisher","first-page":"2460","DOI":"10.1093\/bioinformatics\/btq461","article-title":"Search and clustering orders of magnitude faster than BLAST","volume":"26","author":"Edgar","year":"2010","journal-title":"Bioinformatics"},{"key":"ref30","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1016\/j.smallrumres.2017.08.009","article-title":"Diet and feed efficiency status affect rumen microbial profiles of sheep","volume":"156","author":"Ellison","year":"2017","journal-title":"Small Rumin. Res."},{"key":"ref31","doi-asserted-by":"publisher","first-page":"162","DOI":"10.1186\/s12866-017-1055-x","article-title":"16S rRNA gene-based association study identified microbial taxa associated with pork intramuscular fat content in feces and cecum lumen","volume":"17","author":"Fang","year":"2017","journal-title":"BMC Microbiol."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"30","DOI":"10.2527\/af.2016-0031","article-title":"The role of gut microbiota in the health and disease of pigs","volume":"6","author":"Fouhse","year":"2016","journal-title":"Anim. Front."},{"key":"ref33","doi-asserted-by":"publisher","first-page":"817","DOI":"10.1161\/circresaha.115.306807","article-title":"The gut microbiome contributes to a substantial proportion of the variation in blood lipids","volume":"117","author":"Fu","year":"2015","journal-title":"Circ. Res."},{"key":"ref34","doi-asserted-by":"publisher","first-page":"1886","DOI":"10.3390\/microorganisms8121886","article-title":"Impact of intestinal microbiota on growth and feed efficiency in pigs: a review","volume":"8","author":"Gardiner","year":"2020","journal-title":"Microorganisms"},{"key":"ref35","doi-asserted-by":"publisher","first-page":"32263","DOI":"10.1074\/jbc.m112.375840","article-title":"Phosphatidylinositol transfer protein, cytoplasmic 1 (PITPNC1) binds and transfers phosphatidic acid","volume":"287","author":"Garner","year":"2012","journal-title":"J. Biol. Chem."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"skad185","DOI":"10.1093\/jas\/skad185","article-title":"Appropriate cold stimulation changes energy distribution to improve stress resistance in broilers","volume":"101","author":"Gong","year":"2023","journal-title":"J. Anim. Sci."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"136492","DOI":"10.1016\/j.foodchem.2023.136492","article-title":"The multi-faceted food odorant 4-methylphenol selectively activates evolutionary conserved receptor OR9Q2","volume":"426","author":"Haag","year":"2023","journal-title":"Food Chem."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"2108","DOI":"10.3389\/fmicb.2016.02108","article-title":"Evaluating the contribution of gut microbiota to the variation of porcine fatness with the cecum and fecal samples","volume":"7","author":"He","year":"2016","journal-title":"Front. Microbiol."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"198","DOI":"10.1186\/s40168-023-01627-6","article-title":"Combined effect of microbially derived cecal SCFA and host genetics on feed efficiency in broiler chickens","volume":"11","author":"He","year":"2023","journal-title":"Microbiome"},{"key":"ref40","doi-asserted-by":"publisher","first-page":"skac231","DOI":"10.1093\/jas\/skac231","article-title":"Exploring methods to summarize gut microbiota composition for microbiability estimation and phenotypic prediction in swine","volume":"100","author":"He","year":"2022","journal-title":"J. Anim. Sci."},{"key":"ref41","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1017\/S1751731119002179","article-title":"Indirect genetic effects on the relationships between production and feeding behaviour traits in growing Duroc pigs","volume":"14","author":"Herrera-C\u00e1ceres","year":"2020","journal-title":"Animal"},{"key":"ref42","doi-asserted-by":"publisher","first-page":"e00004","DOI":"10.1128\/msystems.00004-17","article-title":"Meta-analysis to define a Core microbiota in the swine gut","volume":"2","author":"Holman","year":"2017","journal-title":"mSystems"},{"key":"ref43","doi-asserted-by":"publisher","first-page":"e0173482","DOI":"10.1371\/journal.pone.0173482","article-title":"Genome-wide association analysis and functional annotation of positional candidate genes for feed conversion efficiency and growth rate in pigs","volume":"12","author":"Horodyska","year":"2017","journal-title":"PLoS One"},{"key":"ref44","doi-asserted-by":"publisher","first-page":"2663","DOI":"10.3389\/fmicb.2017.02663","article-title":"Exogenous fecal microbiota transplantation from local adult pigs to crossbred newborn piglets","volume":"8","author":"Hu","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref45","doi-asserted-by":"publisher","first-page":"e665","DOI":"10.1002\/ctm2.665","article-title":"ACSS3 in brown fat drives propionate catabolism and its deficiency leads to autophagy and systemic metabolic dysfunction","volume":"12","author":"Jia","year":"2022","journal-title":"Clin. Transl. Med."},{"key":"ref46","doi-asserted-by":"publisher","first-page":"2377","DOI":"10.2527\/jas.2013-7338","article-title":"Feed intake, average daily gain, feed efficiency, and real-time ultrasound traits in Duroc pigs: I. Genetic parameter estimation and accuracy of genomic prediction","volume":"92","author":"Jiao","year":"2014","journal-title":"J. Anim. Sci."},{"key":"ref47","doi-asserted-by":"publisher","first-page":"1146","DOI":"10.1096\/fj.04-3144fje","article-title":"Effects of \u03b1-AMPK knockout on exercise-induced gene activation in mouse skeletal muscle","volume":"19","author":"J\u00f8rgensen","year":"2005","journal-title":"FASEB J."},{"key":"ref48","doi-asserted-by":"publisher","first-page":"497","DOI":"10.1038\/nrmicro3050","article-title":"The abundance and variety of carbohydrate-active enzymes in the human gut microbiota","volume":"11","author":"Kaoutari","year":"2013","journal-title":"Nat. Rev. Microbiol."},{"key":"ref49","doi-asserted-by":"publisher","first-page":"5988","DOI":"10.3168\/jds.2023-24084","article-title":"Association of clinical respiratory disease signs and lower respiratory tract bacterial pathogens with systemic inflammatory response in pre-weaned dairy calves","volume":"107","author":"Kaura","year":"2024","journal-title":"J. Dairy Sci."},{"key":"ref50","doi-asserted-by":"publisher","first-page":"172","DOI":"10.1186\/s12917-019-1918-5","article-title":"Age-based dynamic changes of phylogenetic composition and interaction networks of health pig gut microbiome feeding in a uniformed condition","volume":"15","author":"Ke","year":"2019","journal-title":"BMC Vet. Res."},{"key":"ref51","doi-asserted-by":"publisher","first-page":"814","DOI":"10.1038\/nbt.2676","article-title":"Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences","volume":"31","author":"Langille","year":"2013","journal-title":"Nat. Biotechnol."},{"key":"ref52","doi-asserted-by":"publisher","first-page":"lxad197","DOI":"10.1093\/jambio\/lxad197","article-title":"Metagenomic insights into the microbiota involved in lactate and butyrate production and manipulating their synthesis in alfalfa silage","volume":"134","author":"Li","year":"2023","journal-title":"J. Appl. Microbiol."},{"key":"ref53","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1186\/s40168-019-0699-1","article-title":"Host genetics influence the rumen microbiota and heritable rumen microbial features associate with feed efficiency in cattle","volume":"7","author":"Li","year":"2019","journal-title":"Microbiome"},{"key":"ref54","doi-asserted-by":"publisher","first-page":"683","DOI":"10.1016\/j.jes.2022.05.005","article-title":"Ammonia-induced oxidative stress triggered proinflammatory response and apoptosis in pig lungs","volume":"126","author":"Li","year":"2023","journal-title":"J. Environ. Sci."},{"key":"ref55","doi-asserted-by":"publisher","first-page":"1902","DOI":"10.3390\/ani12151902","article-title":"Genome-wide association analysis and genetic parameters for feed efficiency and related traits in Yorkshire and Duroc pigs","volume":"12","author":"Li","year":"2022","journal-title":"Animals"},{"key":"ref56","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1007\/s13238-020-00724-8","article-title":"A practical guide to amplicon and metagenomic analysis of microbiome data. Protein & amp","volume":"12","author":"Liu","year":"2021","journal-title":"Cell"},{"key":"ref57","doi-asserted-by":"publisher","first-page":"3974","DOI":"10.3390\/ijms25073974","article-title":"Phenotypic characteristics, antimicrobial susceptibility and virulence genotype features of Trueperella pyogenes associated with Endometritis of dairy cows","volume":"25","author":"Liu","year":"2024","journal-title":"Int. J. Mol. Sci."},{"key":"ref58","doi-asserted-by":"publisher","first-page":"232","DOI":"10.1186\/s12864-021-07459-8","article-title":"Identification of the molecular regulation of differences in lipid deposition in dedifferentiated preadipocytes from different chicken tissues","volume":"22","author":"Ma","year":"2021","journal-title":"BMC Genomics"},{"key":"ref59","doi-asserted-by":"publisher","first-page":"e0190184","DOI":"10.1371\/journal.pone.0190184","article-title":"Using genome wide association studies to identify common QTL regions in three different genetic backgrounds based on Iberian pig breed","volume":"13","author":"Mart\u00ednez-Montes","year":"2018","journal-title":"PLoS One"},{"key":"ref60","doi-asserted-by":"publisher","first-page":"e00380","DOI":"10.1128\/AEM.00380-17","article-title":"Exploring a possible link between the intestinal microbiota and feed efficiency in pigs","volume":"83","author":"McCormack Ursula","year":"2017","journal-title":"Appl. Environ. Microbiol."},{"key":"ref61","doi-asserted-by":"publisher","first-page":"e110105","DOI":"10.1371\/journal.pone.0110105","article-title":"Genetic and phenotypic correlations between performance traits with meat quality and carcass characteristics in commercial crossbred pigs","volume":"9","author":"Miar","year":"2014","journal-title":"PLoS One"},{"key":"ref62","doi-asserted-by":"publisher","first-page":"523","DOI":"10.1007\/s11367-019-01686-8","article-title":"A method to estimate the environmental impacts from genetic change in pig production systems","volume":"25","author":"Ottosen","year":"2020","journal-title":"Int. J. Life Cycle Assess."},{"key":"ref63","doi-asserted-by":"publisher","first-page":"1839","DOI":"10.3390\/ani12141839","article-title":"Identification of body size determination related candidate genes in domestic pig using genome-wide selection signal analysis","volume":"12","author":"Pan","year":"2022","journal-title":"Animals"},{"key":"ref64","doi-asserted-by":"publisher","first-page":"1240","DOI":"10.3390\/ani12101240","article-title":"Transcriptome analysis of breast muscle reveals pathways related to protein deposition in high feed efficiency of native turkeys","volume":"12","author":"Pezeshkian","year":"2022","journal-title":"Animals"},{"key":"ref65","doi-asserted-by":"publisher","first-page":"4536","DOI":"10.1038\/s41598-018-22692-0","article-title":"A global comparison of the microbiome compositions of three gut locations in commercial pigs with extreme feed conversion ratios","volume":"8","author":"Quan","year":"2018","journal-title":"Sci. Rep."},{"key":"ref66","doi-asserted-by":"publisher","first-page":"32","DOI":"10.3389\/fmicb.2020.00032","article-title":"Metagenomic characterization of intestinal regions in pigs with contrasting feed efficiency","volume":"11","author":"Quan","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref67","doi-asserted-by":"publisher","first-page":"D590","DOI":"10.1093\/nar\/gks1219","article-title":"The SILVA ribosomal RNA gene database project: improved data processing and web-based tools","volume":"41","author":"Quast","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"ref68","doi-asserted-by":"publisher","first-page":"2973","DOI":"10.1038\/ismej.2016.77","article-title":"Phylogenetic network analysis applied to pig gut microbiota identifies an ecosystem structure linked with growth traits","volume":"10","author":"Ramayo-Caldas","year":"2016","journal-title":"ISME J."},{"key":"ref69","doi-asserted-by":"publisher","first-page":"1975","DOI":"10.1136\/gutjnl-2019-319726","article-title":"Discovery of the gut microbial signature driving the efficacy of prebiotic intervention in obese patients","volume":"69","author":"Rodriguez","year":"2020","journal-title":"Gut"},{"key":"ref70","doi-asserted-by":"publisher","first-page":"e2584","DOI":"10.7717\/peerj.2584","article-title":"VSEARCH: a versatile open source tool for metagenomics","volume":"4","author":"Rognes","year":"2016","journal-title":"Peer J"},{"key":"ref71","doi-asserted-by":"publisher","first-page":"161","DOI":"10.1016\/j.cbi.2015.07.001","article-title":"Prophylaxis with human serum butyrylcholinesterase protects G\u00f6ttingen minipigs exposed to a lethal high-dose of sarin vapor","volume":"238","author":"Saxena","year":"2015","journal-title":"Chem. Biol. Interact."},{"key":"ref72","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1186\/s13568-020-01050-2","article-title":"Evaluating the association between feed efficiency and the fecal microbiota of early-life Duroc pigs using 16S rRNA sequencing","volume":"10","author":"Si","year":"2020","journal-title":"AMB Express"},{"key":"ref73","doi-asserted-by":"publisher","first-page":"2447","DOI":"10.1017\/s1751731119000910","article-title":"A genome-wide association study for feed efficiency-related traits in a crossbred pig population","volume":"13","author":"Silva","year":"2019","journal-title":"Animal"},{"key":"ref74","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1007\/s11367-020-01860-3","article-title":"An approach to achieve overall farm feed efficiency in pig production: environmental evaluation through individual life cycle assessment","volume":"26","author":"Soleimani","year":"2021","journal-title":"Int. J. Life Cycle Assess."},{"key":"ref75","doi-asserted-by":"publisher","first-page":"e0408422","DOI":"10.1128\/spectrum.04084-22","article-title":"Fermented bamboo Fiber improves productive performance by regulating gut microbiota and inhibiting chronic inflammation of sows and piglets during late gestation and lactation. Microbiology","volume":"11","author":"Sun","year":"2023","journal-title":"Spectrum"},{"key":"ref76","doi-asserted-by":"publisher","first-page":"1546","DOI":"10.3389\/fmicb.2017.01546","article-title":"Metagenomic analysis of Cecal microbiome identified microbiota and functional capacities associated with feed efficiency in landrace finishing pigs","volume":"8","author":"Tan","year":"2017","journal-title":"Front. Microbiol."},{"key":"ref77","doi-asserted-by":"publisher","first-page":"586776","DOI":"10.3389\/fmicb.2020.586776","article-title":"Screening of microbes associated with swine growth and fat deposition traits across the intestinal tract","volume":"11","author":"Tang","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref78","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1111\/jbg.12433","article-title":"Prediction of nutrient digestibility in grower-finisher pigs based on faecal microbiota composition","volume":"137","author":"Verschuren","year":"2020","journal-title":"J. Anim. Breed. Genet."},{"key":"ref79","doi-asserted-by":"publisher","first-page":"2472","DOI":"10.1017\/s1751731120001500","article-title":"Colonic microbiome profiles for improved feed efficiency can be identified despite major effects of farm of origin and contemporary group in pigs","volume":"14","author":"Vigors","year":"2020","journal-title":"Animal"},{"key":"ref80","doi-asserted-by":"publisher","first-page":"2795","DOI":"10.1096\/fj.09-148551","article-title":"Identification of glycine N-acyltransferase-like 2 (GLYATL2) as a transferase that produces N-acyl glycines in humans","volume":"24","author":"Waluk","year":"2010","journal-title":"FASEB J."},{"key":"ref81","doi-asserted-by":"publisher","first-page":"151","DOI":"10.1038\/s41586-022-05067-4","article-title":"Post-translational control of beige fat biogenesis by PRDM16 stabilization","volume":"609","author":"Wang","year":"2022","journal-title":"Nature"},{"key":"ref82","doi-asserted-by":"publisher","first-page":"405","DOI":"10.1139\/gen-2021-0105","article-title":"Genome-wide association studies identified loci associated with both feed conversion ratio and residual feed intake in Yorkshire pigs","volume":"65","author":"Wang","year":"2022","journal-title":"Genome"},{"key":"ref83","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1186\/s40168-023-01642-7","article-title":"Heritability and recursive influence of host genetics on the rumen microbiota drive body weight variance in male Hu sheep lambs","volume":"11","author":"Wang","year":"2023","journal-title":"Microbiome"},{"key":"ref84","doi-asserted-by":"publisher","first-page":"925200","DOI":"10.3389\/fmicb.2022.925200","article-title":"Effect of host genetics and gut microbiome on fat deposition traits in pigs","volume":"13","author":"Wang","year":"2022","journal-title":"Front. Microbiol."},{"key":"ref85","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1111\/jbg.12447","article-title":"Selecting the hologenome to breed for an improved feed efficiency in pigs\u2014a novel selection index","volume":"137","author":"Weishaar","year":"2020","journal-title":"J. Anim. Breed. Genet."},{"key":"ref86","doi-asserted-by":"publisher","first-page":"126","DOI":"10.1186\/s40168-021-01040-x","article-title":"Joint contributions of the gut microbiota and host genetics to feed efficiency in chickens","volume":"9","author":"Wen","year":"2021","journal-title":"Microbiome"},{"key":"ref87","doi-asserted-by":"publisher","first-page":"1422","DOI":"10.1038\/s41396-019-0367-2","article-title":"The gut microbiota is largely independent of host genetics in regulating fat deposition in chickens","volume":"13","author":"Wen","year":"2019","journal-title":"ISME J."},{"key":"ref88","first-page":"464","article-title":"Novel technique for retroperitoneal implantation of telemetry transmitters for physiologic monitoring in G\u00f6ttingen Minipigs (Sus scrofa domesticus)","volume":"60","author":"Willens","year":"2014","journal-title":"Comp. Med."},{"key":"ref89","doi-asserted-by":"publisher","first-page":"779","DOI":"10.3390\/ani10050779","article-title":"Estimation of genetic parameters for pork quality, novel carcass, primal-cut and growth traits in Duroc pigs","volume":"10","author":"Willson","year":"2020","journal-title":"Animals"},{"key":"ref90","doi-asserted-by":"publisher","first-page":"891","DOI":"10.1038\/s42003-021-02416-3","article-title":"A combined GWAS approach reveals key loci for socially-affected traits in Yorkshire pigs","volume":"4","author":"Wu","year":"2021","journal-title":"Commun. Biol."},{"key":"ref91","doi-asserted-by":"publisher","first-page":"980","DOI":"10.3390\/genes15080980","article-title":"Integrating multi-omics data to identify key functional variants affecting feed efficiency in large white boars","volume":"15","author":"Xiang","year":"2024","journal-title":"Genes [Online]"},{"key":"ref92","doi-asserted-by":"publisher","first-page":"16161","DOI":"10.1038\/nmicrobiol.2016.161","article-title":"A reference gene catalogue of the pig gut microbiome","volume":"1","author":"Xiao","year":"2016","journal-title":"Nat. Microbiol."},{"key":"ref93","doi-asserted-by":"publisher","first-page":"e0071722","DOI":"10.1128\/spectrum.00717-22","article-title":"Changes in the mucosa-associated microbiome and transcriptome across gut segments are associated with obesity in a metabolic syndrome porcine model","volume":"10","author":"Xu","year":"2022","journal-title":"Microbiol. Spectr."},{"key":"ref94","doi-asserted-by":"publisher","first-page":"525","DOI":"10.21037\/tcr-23-1640","article-title":"A novel gene signature related to fatty acid metabolism predicts prognosis, immune landscape, and drug sensitivity in early-stage lung squamous cell carcinoma","volume":"13","author":"Xu","year":"2024","journal-title":"Transl. Cancer Res."},{"key":"ref95","doi-asserted-by":"publisher","first-page":"64","DOI":"10.1186\/s40168-020-00819-8","article-title":"Multi-omics reveals that the rumen microbiome and its metabolome together with the host metabolome contribute to individualized dairy cow performance","volume":"8","author":"Xue","year":"2020","journal-title":"Microbiome"},{"key":"ref96","doi-asserted-by":"publisher","first-page":"1555","DOI":"10.3389\/fmicb.2017.01555","article-title":"Unraveling the fecal microbiota and metagenomic functional capacity associated with feed efficiency in pigs","volume":"8","author":"Yang","year":"2017","journal-title":"Front. Microbiol."},{"key":"ref97","doi-asserted-by":"publisher","first-page":"76","DOI":"10.1016\/j.ajhg.2010.11.011","article-title":"GCTA: a tool for genome-wide complex trait analysis","volume":"88","author":"Yang","year":"2011","journal-title":"Am. J. Hum. Genet."},{"key":"ref98","doi-asserted-by":"publisher","first-page":"499","DOI":"10.1038\/s41586-020-2569-1","article-title":"Structural basis of GPBAR activation and bile acid recognition","volume":"587","author":"Yang","year":"2020","journal-title":"Nature"},{"key":"ref99","doi-asserted-by":"publisher","first-page":"358","DOI":"10.1038\/s41586-022-04769-z","article-title":"ABO genotype alters the gut microbiota by regulating GalNAc levels in pigs","volume":"606","author":"Yang","year":"2022","journal-title":"Nature"},{"key":"ref100","doi-asserted-by":"publisher","first-page":"3501","DOI":"10.1093\/nar\/gkad074","article-title":"HIBLUP: an integration of statistical models on the BLUP framework for efficient genetic evaluation using big genomic data","volume":"51","author":"Yin","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref101","doi-asserted-by":"publisher","first-page":"902180","DOI":"10.3389\/fgene.2022.902180","article-title":"Fatty acid metabolism-related genes are associated with flavor-presenting aldehydes in Chinese local chicken","volume":"13","author":"Yuan","year":"2022","journal-title":"Front. Genet."},{"key":"ref102","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1016\/j.semcdb.2017.11.011","article-title":"Function of the myogenic regulatory factors Myf5, MyoD, Myogenin and MRF4 in skeletal muscle, satellite cells and regenerative myogenesis","volume":"72","author":"Zammit","year":"2017","journal-title":"Semin. Cell Dev. Biol."},{"key":"ref103","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1186\/s40104-024-01076-7","article-title":"Host genetics and gut microbiota synergistically regulate feed utilization in egg-type chickens","volume":"15","author":"Zhang","year":"2024","journal-title":"J. Anim. Sci. Biotechnol."},{"key":"ref104","doi-asserted-by":"publisher","first-page":"813","DOI":"10.1038\/s41586-023-06893-w","article-title":"Host genetic regulation of human gut microbial structural variation","volume":"625","author":"Zhernakova","year":"2024","journal-title":"Nature"},{"key":"ref105","doi-asserted-by":"publisher","first-page":"841","DOI":"10.7150\/thno.49384","article-title":"ACSS3 represses prostate cancer progression through downregulating lipid droplet-associated protein PLIN3","volume":"11","author":"Zhou","year":"2021","journal-title":"Theranostics"},{"key":"ref106","doi-asserted-by":"publisher","first-page":"821","DOI":"10.1038\/ng.2310","article-title":"Genome-wide efficient mixed-model analysis for association studies","volume":"44","author":"Zhou","year":"2012","journal-title":"Nat. Genet."},{"key":"ref107","doi-asserted-by":"publisher","first-page":"790","DOI":"10.1038\/s41588-018-0135-7","article-title":"The fecal metabolome as a functional readout of the gut microbiome","volume":"50","author":"Zierer","year":"2018","journal-title":"Nat. Genet."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2024.1459773\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,11,13]],"date-time":"2024-11-13T01:21:31Z","timestamp":1731460891000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2024.1459773\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,11,13]]},"references-count":107,"alternative-id":["10.3389\/fmicb.2024.1459773"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2024.1459773","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,11,13]]},"article-number":"1459773"}}