Kim KA, Gu W, Lee IA, Joh EH, Kim DH. High fat diet-induced gut microbiota exacerbates inflammation and obesity in mice via the TLR4 signaling pathway. PLoS One. 2012;7:e47713.
Bäckhed F, Ding H, Wang T, Hooper LV, Koh GY, Nagy A, et al. The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci. 2004;101:15718–23.
Bäckhed F, Manchester JK, Semenkovich CF, Gordon JI. Mechanisms underlying the resistance to diet-induced obesity in germ-free mice. Proc Natl Acad Sci. 2007;104:979–84.
Deshmukh AS, Murgia M, Nagaraj N, Treebak JT, Cox J, Mann M. Deep proteomics of mouse skeletal muscle enables quantitation of protein isoforms, metabolic pathways, and transcription factors. Mol Cell Proteomics. 2015;14:841–53.
Lahiri S, Kim H, Garcia-Perez I, Reza MM, Martin KA, Kundu P, et al. The gut microbiota influences skeletal muscle mass and function in mice. Sci Transl Med. 2019;11:eaan5662.
Grosicki GJ, Fielding RA, Lustgarten MS. Gut microbiota contribute to age-related changes in skeletal muscle size, composition, and function: biological basis for a gut-muscle axis. Calcified Tissue Int. 2018;102:433–42.
Yan H, Diao H, Xiao Y, Li W, Yu B, He J, et al. Gut microbiota can transfer fiber characteristics and lipid metabolic profiles of skeletal muscle from pigs to germ-free mice. Sci Rep-UK. 2016;6:31786.
Dibner J, Richards J. Antibiotic growth promoters in agriculture: history and mode of action. Poult Sci. 2005;84:634–43.
Mahana D, Trent CM, Kurtz ZD, Bokulich NA, Battaglia T, Chung J, et al. Antibiotic perturbation of the murine gut microbiome enhances the adiposity, insulin resistance, and liver disease associated with high-fat diet. Genome Med. 2016;8:48.
Cho I, Yamanishi S, Cox L, Methé BA, Zavadil J, Li K, et al. Antibiotics in early life alter the murine colonic microbiome and adiposity. Nature. 2012;488:621–6.
Livanos AE, Greiner TU, Vangay P, Pathmasiri W, Stewart D, McRitchie S, et al. Antibiotic-mediated gut microbiome perturbation accelerates development of type 1 diabetes in mice. Nat Microbiol. 2016;1:16140.
Cox LM, Yamanishi S, Sohn J, Alekseyenko AV, Leung JM, Cho I, et al. Altering the intestinal microbiota during a critical developmental window has lasting metabolic consequences. Cell. 2014;158:705–21.
Coates ME, Fuller R, Harrison G, Lev M, Suffolk S. A comparison of the growth of chicks in the Gustafsson germ-free apparatus and in a conventional environment, with and without dietary supplements of penicillin. Brit J Nutr. 1963;17:141–50.
Gaskins H, Collier C, Anderson D. Antibiotics as growth promotants: mode of action. Anim Biotechnol. 2002;13:29–42.
Moeser AJ, Vander Klok C, Ryan KA, Wooten JG, Little D, Cook VL, et al. Stress signaling pathways activated by weaning mediate intestinal dysfunction in the pig. Am J Physiol-Gastr L. 2007;292:G173–81.
Kim HB, Borewicz K, White BA, Singer RS, Sreevatsan S, Tu ZJ, et al. Microbial shifts in the swine distal gut in response to the treatment with antimicrobial growth promoter, tylosin. P Natl Acad Sci. 2012;109:15485–90.
Nobel YR, Cox LM, Kirigin FF, Bokulich NA, Yamanishi S, Teitler I, et al. Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment. Nat Commun. 2015;6.
Lim KS, Lee SH, Lee EA, Kim JM, Hong KC. Effects of intergenic single nucleotide polymorphisms in the fast myosin heavy chain cluster on muscle fiber characteristics and meat quality in Berkshire pigs. Meat Sci. 2015;110:224–9.
Friedewald WT, Levy RI, Fredrickson DS. Estimation of the concentration of low-density lipoprotein cholesterol in plasma, without use of the preparative ultracentrifuge. Clin Chem. 1972;18:499–502.
Erkens T, Van Poucke M, Vandesompele J, Goossens K, Van Zeveren A, Peelman LJ. Development of a new set of reference genes for normalization of real-time RT-PCR data of porcine backfat and longissimus dorsi muscle, and evaluation with PPARGC1A. BMC Biotechnol. 2006;6:41.
Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, et al. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 2002;3:research0034.1.
Vilchez-Vargas R, Geffers R, Suárez-Diez M, Conte I, Waliczek A, Kaser VS, et al. Analysis of the microbial gene landscape and transcriptome for aromatic pollutants and alkane degradation using a novel internally calibrated microarray system. Environ Microbiol. 2013;15:1016–39.
Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 2012;41:e1.
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microb. 2009;75:7537–41.
Ihaka R, Gentleman R. R: a language for data analysis and graphics. J Comput Graph Stat. 1996;5:299–314.
Dixon P. VEGAN, a package of R functions for community ecology. J Veg Sci. 2003;14:927–30.
McMurdie PJ, Holmes S. Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PloS One. 2013;8:e61217.
Ju T, Shoblak Y, Gao Y, Yang K, Fouhse J, Finlay BB, et al. Initial gut microbial composition as a key factor driving host response to antibiotic treatment, as exemplified by the presence or absence of commensal Escherichia coli. Appl Environ Microb. 2017. https://doi.org/10.1128/AEM.01107-17.
Han GG, Lee J-Y, Jin G-D, Park J, Choi YH, Chae BJ, et al. Evaluating the association between body weight and the intestinal microbiota of weaned piglets via 16S rRNA sequencing. Appl Environ Microb. 2017;101:5903–11.
Bian G, Ma S, Zhu Z, Su Y, Zoetendal EG, Mackie R, et al. Age, introduction of solid feed and weaning are more important determinants of gut bacterial succession in piglets than breed and nursing mother as revealed by a reciprocal cross-fostering model. Environ Microbiol. 2016;18:1566–77.
Van Lunen T. Growth performance of pigs fed diets with and without tylosin phosphate supplementation and reared in a biosecure all-in all-out housing system. Can Vet J. 2003;44:571.
Kim J, Guevarra RB, Nguyen SG, Lee JH, Jeong DK, Unno T. Effects of the antibiotics growth promoter tylosin on swine gut microbiota. J Microbiol Biotechnol. 2016;26:876–82.
Yu M, Zhang C, Yang Y, Mu C, Su Y, Yu K, et al. Long-term effects of early antibiotic intervention on blood parameters, apparent nutrient digestibility, and fecal microbial fermentation profile in pigs with different dietary protein levels. J Anim Sci Biotechnol. 2017;8:60.
Skinner L, Levesque C, Wey D, Rudar M, Zhu J, Hooda S, et al. Impact of nursery feeding program on subsequent growth performance, carcass quality, meat quality, and physical and chemical body composition of growing-finishing pigs. J Anim Sci. 2014;92:1044–54.
Larzul C, Lefaucheur L, Ecolan P, Gogue J, Talmant A, Sellier P, et al. Phenotypic and genetic parameters for longissimus muscle fiber characteristics in relation to growth, carcass, and meat quality traits in large white pigs. J Anim Sci. 1997;75:3126–37.
Lefaucheur L, Lebret B, Ecolan P, Louveau I, Damon M, Prunier A, et al. Muscle characteristics and meat quality traits are affected by divergent selection on residual feed intake in pigs. J Anim Sci. 2011;89:996–1010.
Kim GD, Kim BW, Jeong JY, Hur SJ, Cho IC, Lim HT, et al. Relationship of carcass weight to muscle fiber characteristics and pork quality of crossbred (Korean native black pig× landrace) F2 pigs. Food Bioprocess Tech. 2013;6:522–9.
Handschin C, Chin S, Li P, Liu F, Maratos-Flier E, LeBrasseur NK, et al. Skeletal muscle fiber-type switching, exercise intolerance, and myopathy in PGC-1α muscle-specific knock-out animals. J Biol Chem. 2007;282:30014–21.
Chikuni K, Nakajima I, Oe M, Muroya S. Peroxisome proliferator-activated receptor-γ coactivator 1 α (PGC-1 α) expression and the formation of slow-twitch muscle fibers in porcine and bovine skeletal muscles. Anim Sci J. 2005;76:375–80.
Zhang C, Luo J, Zheng P, Yu B, Huang Z, Mao X, et al. Differential expression of lipid metabolism-related genes and myosin heavy chain isoform genes in pig muscle tissue leading to different meat quality. Animal. 2015;9:1073–80.
Shulman GI. Cellular mechanisms of insulin resistance. J Clin Invest. 2000;106:171.
Goldberg IJ, Eckel RH, Abumrad NA. Regulation of fatty acid uptake into tissues: lipoprotein lipase-and CD36-mediated pathways. J Lipid Res. 2009;50:S86–90.
Yoshida K, Shimizugawa T, Ono M, Furukawa H. Angiopoietin-like protein 4 is a potent hyperlipidemia-inducing factor in mice and inhibitor of lipoprotein lipase. J Lipid Res. 2002;43:1770–2.
Looft T, Allen HK, Cantarel BL, Levine UY, Bayles DO, Alt DP, et al. Bacteria, phages and pigs: the effects of in-feed antibiotics on the microbiome at different gut locations. Isme J. 2014;8:1566.
Schwiertz A, Taras D, Schäfer K, Beijer S, Bos NA, Donus C, et al. Microbiota and SCFA in lean and overweight healthy subjects. Obesity. 2010;18:190–5.
Ley RE, Bäckhed F, Turnbaugh P, Lozupone CA, Knight RD, Gordon JI. Obesity alters gut microbial ecology. Proc Natl Acad Sci. 2005;102:11070–5.
Niu Q, Li P, Hao S, Zhang Y, Kim SW, Li H, et al. Dynamic distribution of the gut microbiota and the relationship with apparent crude fiber digestibility and growth stages in pigs. Sci Rep-UK. 2015;5:9938.
Fevrier C, Bourdon D, Aumaitre A. Effects of level of dietary fibre from wheat bran on digestibility of nutrients, digestive enzymes and performance in the European large White and Chinese Mei Shan pig. J Anim Physiol An N. 1992;68:60–72.
Duca FA, Sakar Y, Lepage P, Devime F, Langelier B, Doré J, et al. Replication of obesity and associated signaling pathways through transfer of microbiota from obese prone rat. Diabetes. 2014;63(5):1624–36.
McCormack UM, Curião T, Buzoianu SG, Prieto ML, Ryan T, Varley P, et al. Exploring a possible link between the intestinal microbiota and feed efficiency in pigs. Appl Environ Microb. 2017. https://doi.org/10.1128/AEM.00380-17.
Ramayo-Caldas Y, Mach N, Lepage P, Levenez F, Denis C, Lemonnier G, et al. Phylogenetic network analysis applied to pig gut microbiota identifies an ecosystem structure linked with growth traits. Isme J. 2016;10:2973–7.
Brown K, Godovannyi A, Ma C, Zhang Y, Ahmadi-Vand Z, Dai C, et al. Prolonged antibiotic treatment induces a diabetogenic intestinal microbiome that accelerates diabetes in NOD mice. Isme J. 2016;10:321.
Jiang W, Wu N, Wang X, Chi Y, Zhang Y, Qiu X, et al. Dysbiosis gut microbiota associated with inflammation and impaired mucosal immune function in intestine of humans with non-alcoholic fatty liver disease. Sci Rep-UK. 2015;5:8096.
Collins KH, Paul HA, Hart DA, Reimer RA, Smith IC, Rios JL, et al. A high-fat high-sucrose diet rapidly alters muscle integrity, inflammation and gut microbiota in male rats. Sci Rep-UK. 2016;6:37278.
Holman D: Impact of subtherapeutic administration of tylosin and chlortetracycline on antibiotic resistance and the gut microbiota in farrow-to-finish swine. McGill University; 2014.
Li TT, Liu YY, Wan XZ, Huang ZR, Liu B, Zhao C. Regulatory efficacy of the polyunsaturated fatty acids from microalgae spirulina platensis on lipid metabolism and gut microbiota in high-fat diet rats. Int J Mol Sci. 2018;19:3075.
Hua P, Yu Z, Xiong Y, Liu B, Zhao L. Regulatory efficacy of Spirulina platensis protease hydrolyzate on lipid metabolism and gut microbiota in high-fat diet-fed rats. Int J Mol Sci. 2018;19:4023.
Nagao-Kitamoto H, Leslie JL, Kitamoto S, Jin C, Thomsson KA, Gillilland MG, et al. Interleukin-22-mediated host glycosylation prevents Clostridioides difficile infection by modulating the metabolic activity of the gut microbiota. Nat Med. 2020;26:608–17.
Ferreyra JA, Wu KJ, Hryckowian AJ, Bouley DM, Weimer BC, Sonnenburg JL. Gut microbiota-produced succinate promotes C. difficile infection after antibiotic treatment or motility disturbance. Cell Host Microbe. 2014;16:770–7.