{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,21]],"date-time":"2026-05-21T09:13:37Z","timestamp":1779354817165,"version":"3.51.4"},"reference-count":61,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,4,9]],"date-time":"2026-04-09T00:00:00Z","timestamp":1775692800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2026,5,21]],"date-time":"2026-05-21T00:00:00Z","timestamp":1779321600000},"content-version":"vor","delay-in-days":42,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"name":"Talent Program of China Agricultural University"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Microbiol"],"DOI":"10.1186\/s12866-026-04955-3","type":"journal-article","created":{"date-parts":[[2026,4,9]],"date-time":"2026-04-09T02:58:25Z","timestamp":1775703505000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Exploring the predominant factors associated with shaping the cultivable swine gut microbiota of Wuzhishan piglets under in vitro cultivation conditions"],"prefix":"10.1186","volume":"26","author":[{"given":"Yinfeng","family":"Chen","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xin","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaozhe","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhenlong","family":"Wu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2026,4,9]]},"reference":[{"key":"4955_CR1","doi-asserted-by":"crossref","unstructured":"Quan J, Wu Z, Ye Y, Peng L, Wu J, Ruan D, Qiu Y, Ding R, Wang X, Zheng E et al. Metagenomic Characterization of Intestinal Regions in Pigs With Contrasting Feed Efficiency. FRONT MICROBIOL 2020, 11.","DOI":"10.3389\/fmicb.2020.00032"},{"issue":"12","key":"4955_CR2","doi-asserted-by":"publisher","first-page":"2973","DOI":"10.1038\/ismej.2016.77","volume":"10","author":"Y Ramayo-Caldas","year":"2016","unstructured":"Ramayo-Caldas Y, Mach N, Lepage P, Levenez F, Denis C, Lemonnier G, Leplat J, Billon Y, Berri M, Dor\u00e9 J, et al. Phylogenetic network analysis applied to pig gut microbiota identifies an ecosystem structure linked with growth traits. ISME J. 2016;10(12):2973\u20137.","journal-title":"ISME J"},{"key":"4955_CR3","doi-asserted-by":"publisher","first-page":"2663","DOI":"10.3389\/fmicb.2017.02663","volume":"8","author":"L Hu","year":"2017","unstructured":"Hu L, Geng S, Li Y, Cheng S, Fu X, Yue X, Han X. Exogenous Fecal Microbiota Transplantation from Local Adult Pigs to Crossbred Newborn Piglets. FRONT MICROBIOL. 2017;8:2663.","journal-title":"FRONT MICROBIOL"},{"issue":"6","key":"4955_CR4","doi-asserted-by":"publisher","first-page":"817","DOI":"10.1016\/j.chom.2018.11.006","volume":"24","author":"J Hu","year":"2018","unstructured":"Hu J, Ma L, Nie Y, Chen J, Zheng W, Wang X, Xie C, Zheng Z, Wang Z, Yang T, et al. A Microbiota-Derived Bacteriocin Targets the Host to Confer Diarrhea Resistance in Early-Weaned Piglets. CELL HOST MICROBE. 2018;24(6):817\u201332.","journal-title":"CELL HOST MICROBE"},{"key":"4955_CR5","doi-asserted-by":"crossref","unstructured":"Cheng S, Ma X, Geng S, Jiang X, Li Y, Hu L, Li J, Wang Y, Han X. Fecal Microbiota Transplantation Beneficially Regulates Intestinal Mucosal Autophagy and Alleviates Gut Barrier Injury. MSYSTEMS 2018, 3(5).","DOI":"10.1128\/msystems.00137-18"},{"key":"4955_CR6","doi-asserted-by":"crossref","unstructured":"Chen C, Fang S, Wei H, He M, Fu H, Xiong X, Zhou Y, Wu J, Gao J, Yang H et al. Prevotella copri increases fat accumulation in pigs fed with formula diets. MICROBIOME 2021, 9(1).","DOI":"10.1186\/s40168-021-01110-0"},{"key":"4955_CR7","doi-asserted-by":"crossref","unstructured":"Wang X, Tsai T, Deng F, Wei X, Chai J, Knapp J, Apple J, Maxwell CV, Lee JA, Li Y et al. Longitudinal investigation of the swine gut microbiome from birth to market reveals stage and growth performance associated bacteria. MICROBIOME 2019, 7(1).","DOI":"10.1186\/s40168-019-0721-7"},{"issue":"1","key":"4955_CR8","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1186\/s40168-024-02013-6","volume":"13","author":"M Yang","year":"2025","unstructured":"Yang M, Xie Q, Wang J, Zha A, Chen J, Jiang Q, Kang M, Deng Q, Yin Y, Tan B. Ningxiang pig-derived lactobacillus reuteri modulates host intramuscular fat deposition via branched-chain amino acid metabolism. MICROBIOME. 2025;13(1):32.","journal-title":"MICROBIOME"},{"issue":"6","key":"4955_CR9","doi-asserted-by":"publisher","first-page":"e261","DOI":"10.1002\/imt2.261","volume":"3","author":"A Zha","year":"2024","unstructured":"Zha A, Qi M, Deng Y, Li H, Wang N, Wang C, Liao S, Wan D, Xiong X, Liao P, et al. Gut Bifidobacterium pseudocatenulatum protects against fat deposition by enhancing secondary bile acid biosynthesis. Imeta. 2024;3(6):e261.","journal-title":"Imeta"},{"issue":"12","key":"4955_CR10","doi-asserted-by":"publisher","first-page":"1185","DOI":"10.1111\/1469-0691.12023","volume":"18","author":"JC Lagier","year":"2012","unstructured":"Lagier JC, Armougom F, Million M, Hugon P, Pagnier I, Robert C, Bittar F, Fournous G, Gimenez G, Maraninchi M, et al. Microbial culturomics: paradigm shift in the human gut microbiome study. CLIN MICROBIOL INFEC. 2012;18(12):1185\u201393.","journal-title":"CLIN MICROBIOL INFEC"},{"issue":"9","key":"4955_CR11","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1038\/s41579-018-0041-0","volume":"16","author":"J Lagier","year":"2018","unstructured":"Lagier J, Dubourg G, Million M, Cadoret F, Bilen M, Fenollar F, Levasseur A, Rolain J, Fournier P, Raoult D. Culturing the human microbiota and culturomics. Nat Rev Microbiol. 2018;16(9):540\u201350.","journal-title":"Nat Rev Microbiol"},{"issue":"2","key":"4955_CR12","doi-asserted-by":"publisher","first-page":"448","DOI":"10.1007\/s00248-013-0185-4","volume":"66","author":"CJ Ziemer","year":"2013","unstructured":"Ziemer CJ. Broad Diversity and Newly Cultured Bacterial Isolates from Enrichment of Pig Feces on Complex Polysaccharides. MICROB ECOL. 2013;66(2):448\u201361.","journal-title":"MICROB ECOL"},{"issue":"12","key":"4955_CR13","doi-asserted-by":"publisher","first-page":"3879","DOI":"10.1128\/AEM.00589-13","volume":"79","author":"UY Levine","year":"2013","unstructured":"Levine UY, Looft T, Allen HK, Stanton TB. Butyrate-Producing Bacteria, Including Mucin Degraders, from the Swine Intestinal Tract. APPL ENVIRON MICROB. 2013;79(12):3879\u201381.","journal-title":"APPL ENVIRON MICROB"},{"key":"4955_CR14","doi-asserted-by":"publisher","first-page":"377","DOI":"10.2527\/jas.2015-9868","volume":"94","author":"X Li","year":"2016","unstructured":"Li X, Hojberg O, Canibe N, Jensen BB. Phylogenetic diversity of cultivable butyrate-producing bacteria from pig gut content and feces. J ANIM SCI. 2016;94:377\u201381.","journal-title":"J ANIM SCI"},{"issue":"1","key":"4955_CR15","doi-asserted-by":"publisher","first-page":"6389","DOI":"10.1038\/s41467-020-19929-w","volume":"11","author":"D Wylensek","year":"2020","unstructured":"Wylensek D, Hitch TCA, Riedel T, Afrizal A, Kumar N, Wortmann E, Liu T, Devendran S, Lesker TR, Hern\u00e1ndez SB, et al. A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity. NAT COMMUN. 2020;11(1):6389.","journal-title":"NAT COMMUN"},{"issue":"1","key":"4955_CR16","doi-asserted-by":"publisher","first-page":"86","DOI":"10.1186\/s40168-025-02064-3","volume":"13","author":"IMF de Oliveira","year":"2025","unstructured":"de Oliveira IMF, Fredriksen S, Guti\u00e9rrez MF, Harmsen HJM, Boekhorst J, van Baarlen P, Wells JM. Culturomics of the pig tonsil microbiome identifies new species and an untapped source of novel antimicrobials. MICROBIOME. 2025;13(1):86.","journal-title":"MICROBIOME"},{"issue":"1","key":"4955_CR17","doi-asserted-by":"publisher","first-page":"e0241721","DOI":"10.1128\/spectrum.02417-21","volume":"10","author":"B Dong","year":"2022","unstructured":"Dong B, Lin X, Jing X, Hu T, Zhou J, Chen J, Xiao L, Wang B, Chen Z, Liu J, et al. A Bacterial Genome and Culture Collection of Gut Microbial in Weanling Piglet. MICROBIOL SPECTR. 2022;10(1):e0241721.","journal-title":"MICROBIOL SPECTR"},{"issue":"9","key":"4955_CR18","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1128\/AEM.00088-21","volume":"87","author":"PE Moote","year":"2021","unstructured":"Moote PE, Bescucci DM, Ortega Polo R, Uwiera RRE, Inglis GD, Rudi K. Comparison of Strategies for Isolating Anaerobic Bacteria from the Porcine Intestine. APPL ENVIRON MICROB. 2021;87(9):1.","journal-title":"APPL ENVIRON MICROB"},{"key":"4955_CR19","doi-asserted-by":"crossref","unstructured":"Wang X, Howe S, Wei X, Deng F, Tsai T, Chai J, Xiao Y, Yang H, Maxwell CV, Li Y et al. Comprehensive Cultivation of the Swine Gut Microbiome Reveals High Bacterial Diversity and Guides Bacterial Isolation in Pigs. MSYSTEMS 2021, 6(4):e0047721.","DOI":"10.1128\/msystems.00477-21"},{"issue":"1","key":"4955_CR20","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1038\/nrmicro3552","volume":"14","author":"GP Donaldson","year":"2016","unstructured":"Donaldson GP, Lee SM, Mazmanian SK. Gut biogeography of the bacterial microbiota. NAT REV MICROBIOL. 2016;14(1):20\u201332.","journal-title":"NAT REV MICROBIOL"},{"issue":"4","key":"4955_CR21","doi-asserted-by":"publisher","first-page":"514","DOI":"10.1038\/s41564-018-0123-9","volume":"3","author":"M Tramontano","year":"2018","unstructured":"Tramontano M, Andrejev S, Pruteanu M, Kl\u00fcnemann M, Kuhn M, Galardini M, Jouhten P, Zelezniak A, Zeller G, Bork P, et al. Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies. NAT MICROBIOL. 2018;3(4):514\u201322.","journal-title":"NAT MICROBIOL"},{"key":"4955_CR22","doi-asserted-by":"crossref","unstructured":"Knudsen KEB, L\u00e6rke HN, J\u00f8rgensen H. Carbohydrates and Carbohydrate Utilization in Swine. In; 2022: 151\u201387.","DOI":"10.1002\/9781119583998.ch6"},{"key":"4955_CR23","doi-asserted-by":"publisher","first-page":"1095740","DOI":"10.3389\/fimmu.2023.1095740","volume":"14","author":"R Hu","year":"2023","unstructured":"Hu R, Li S, Diao H, Huang C, Yan J, Wei X, Zhou M, He P, Wang T, Fu H, et al. The interaction between dietary fiber and gut microbiota, and its effect on pig intestinal health. FRONT IMMUNOL. 2023;14:1095740.","journal-title":"FRONT IMMUNOL"},{"key":"4955_CR24","doi-asserted-by":"publisher","first-page":"719935","DOI":"10.3389\/fnut.2021.719935","volume":"8","author":"Y Bai","year":"2021","unstructured":"Bai Y, Zhou X, Zhao J, Wang Z, Ye H, Pi Y, Che D, Han D, Zhang S, Wang J. Sources of Dietary Fiber Affect the SCFA Production and Absorption in the Hindgut of Growing Pigs. FRONT NUTR. 2021;8:719935.","journal-title":"FRONT NUTR"},{"issue":"11","key":"4955_CR25","doi-asserted-by":"publisher","first-page":"100625","DOI":"10.1016\/j.animal.2022.100625","volume":"16","author":"AF Bekebrede","year":"2022","unstructured":"Bekebrede AF, Noorman L, Keijer J, de Boer VCJ, Gerrits WJJ. Functional metabolic capacity of pig colonocytes is differentially modulated by fermentable fibre and poorly digestible protein. Animal: Int J Anim bioscience. 2022;16(11):100625.","journal-title":"Animal: Int J Anim bioscience"},{"issue":"1","key":"4955_CR26","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1186\/s40104-021-00581-3","volume":"12","author":"H Zhou","year":"2021","unstructured":"Zhou H, Yu B, Sun J, Liu Z, Chen H, Ge L, Chen D. Short-chain fatty acids can improve lipid and glucose metabolism independently of the pig gut microbiota. J ANIM SCI BIOTECHNO. 2021;12(1):61.","journal-title":"J ANIM SCI BIOTECHNO"},{"key":"4955_CR27","doi-asserted-by":"publisher","first-page":"1449030","DOI":"10.3389\/fcimb.2024.1449030","volume":"14","author":"H Liu","year":"2024","unstructured":"Liu H, Lu H, Wang Y, Yu C, He Z, Dong H. Unlocking the power of short-chain fatty acids in ameliorating intestinal mucosal immunity: a new porcine nutritional approach. FRONT CELL INFECT MI. 2024;14:1449030.","journal-title":"FRONT CELL INFECT MI"},{"issue":"1","key":"4955_CR28","doi-asserted-by":"publisher","first-page":"88","DOI":"10.1186\/s13568-021-01249-x","volume":"11","author":"M Shao","year":"2021","unstructured":"Shao M, Wang Z, He Y, Tan Z, Zhang J. Fecal microbial composition and functional diversity of Wuzhishan pigs at different growth stages. AMB EXPRESS. 2021;11(1):88.","journal-title":"AMB EXPRESS"},{"issue":"7604","key":"4955_CR29","doi-asserted-by":"publisher","first-page":"543","DOI":"10.1038\/nature17645","volume":"533","author":"HP Browne","year":"2016","unstructured":"Browne HP, Forster SC, Anonye BO, Kumar N, Neville BA, Stares MD, Goulding D, Lawley TD. Culturing of \u2018unculturable\u2019 human microbiota reveals novel taxa and extensive sporulation. Nature. 2016;533(7604):543\u20136.","journal-title":"Nature"},{"key":"4955_CR30","doi-asserted-by":"crossref","unstructured":"Chen J, Li Z, Wang X, Fan B, Deng F, Yu D, Ze H, Zhu X, Yin L, Chen Y. Y : Isomaltooligosaccharides Sustain the Growth of Prevotella BothIn Vitro and in Animal Models. MICROBIOL SPECTR 2022, 10(6).","DOI":"10.1128\/spectrum.02621-21"},{"key":"4955_CR31","doi-asserted-by":"crossref","unstructured":"Amir A, McDonald D, Navas-Molina JA, Kopylova E, Morton JT, Zech XZ, Kightley EP, Thompson LR, Hyde ER, Gonzalez A et al. Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns. MSYSTEMS 2017, 2(2):10-1128.","DOI":"10.1128\/mSystems.00191-16"},{"issue":"1","key":"4955_CR32","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1186\/s13073-016-0327-7","volume":"8","author":"JT Lau","year":"2016","unstructured":"Lau JT, Whelan FJ, Herath I, Lee CH, Collins SM, Bercik P, Surette MG. Capturing the diversity of the human gut microbiota through culture-enriched molecular profiling. GENOME MED. 2016;8(1):72.","journal-title":"GENOME MED"},{"issue":"1","key":"4955_CR33","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1186\/s40168-018-0470-z","volume":"6","author":"NA Bokulich","year":"2018","unstructured":"Bokulich NA, Kaehler BD, Rideout JR, Dillon M, Bolyen E, Knight R, Huttley GA, Gregory CJ. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2\u2019s q2-feature-classifier plugin. MICROBIOME. 2018;6(1):90.","journal-title":"MICROBIOME"},{"key":"4955_CR34","unstructured":"Oksanen J, Simpson GL, Blanchet FG, Kindt R, Legendre P, Minchin PR, O\u2019Hara RB, Solymos P, Stevens MHH, Szoecs E et al. vegan: Community Ecology Package. In.; 2024."},{"key":"4955_CR35","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-319-24277-4","volume-title":"ggplot2: Elegant Graphics for Data Analysis","author":"H Wickham","year":"2016","unstructured":"Wickham H. ggplot2: Elegant Graphics for Data Analysis. New York: Springer-; 2016."},{"key":"4955_CR36","doi-asserted-by":"crossref","unstructured":"Yu M, Zhang C, Yang Y, Mu C, Su Y, Yu K, Zhu W. 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 BIOTECHNO 2017, 8(1).","DOI":"10.1186\/s40104-017-0192-2"},{"key":"4955_CR37","unstructured":"Wickham H, Fran\u00e7ois R, Henry L, M\u00fcller K. Vaughan D: dplyr: A Grammar of Data Manipulation. In.; 2023."},{"key":"4955_CR38","unstructured":"Kassambara A. ggpubr: \u2018ggplot2\u2019 Based Publication Ready Plots. In.; 2023."},{"issue":"12","key":"4955_CR39","doi-asserted-by":"publisher","first-page":"1","DOI":"10.18637\/jss.v021.i12","volume":"21","author":"H Wickham","year":"2007","unstructured":"Wickham H. Reshaping Data with the {reshape} Package. J STAT SOFTW. 2007;21(12):1\u201320.","journal-title":"J STAT SOFTW"},{"issue":"3","key":"4955_CR40","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1016\/j.aninu.2019.04.003","volume":"5","author":"UP Tiwari","year":"2019","unstructured":"Tiwari UP, Singh AK, Jha R. Fermentation characteristics of resistant starch, arabinoxylan, and \u03b2-glucan and their effects on the gut microbial ecology of pigs: A review. Anim Nutr. 2019;5(3):217\u201326.","journal-title":"Anim Nutr"},{"key":"4955_CR41","doi-asserted-by":"crossref","unstructured":"Mora-Flores LP, Moreno-Terrazas Casildo R, Fuentes-Cabrera J, P\u00e9rez-Vicente HA, de Anda-J\u00e1uregui G, Neri-Torres EE. The Role of Carbohydrate Intake on the Gut Microbiome: A Weight of Evidence Systematic Review. MICROORGANISMS. 2023;11(7):1728.","DOI":"10.3390\/microorganisms11071728"},{"key":"4955_CR42","doi-asserted-by":"publisher","first-page":"951840","DOI":"10.3389\/fanim.2022.951840","volume":"3","author":"J Sun","year":"2022","unstructured":"Sun J, Li M, Zhou H, Chong J, Zhang J, Yu B, Chen D, Ge L. Importance of gut microbiota for bile acid composition and concentration in pigs. Front Anim Sci. 2022;3:951840.","journal-title":"Front Anim Sci"},{"issue":"1","key":"4955_CR43","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1211\/0022357011775163","volume":"53","author":"SS Davis","year":"2001","unstructured":"Davis SS, Illum L, Hinchcliffe M. Gastrointestinal transit of dosage forms in the pig. J PHARM PHARMACOL. 2001;53(1):33\u20139.","journal-title":"J PHARM PHARMACOL"},{"issue":"4","key":"4955_CR44","doi-asserted-by":"publisher","first-page":"e0017021","DOI":"10.1128\/mmbr.00170-21","volume":"86","author":"M Schopping","year":"2022","unstructured":"Schopping M, Zeidan AA, Franzen CJ. Stress Response in Bifidobacteria. MICROBIOL MOL BIOL R. 2022;86(4):e0017021.","journal-title":"MICROBIOL MOL BIOL R"},{"key":"4955_CR45","doi-asserted-by":"crossref","unstructured":"Li DH, Abuduaini R, Du MX, Wang YJ, Chen HH, Zhou N, Zhu HZ, Lu Y, Yu PJ, Yang YP et al. Alkaliphilus flagellatus sp. nov., Butyricicoccus intestinisimiae sp. nov., Clostridium mobile sp. nov., Clostridium simiarum sp. nov., Dysosmobacter acutus sp. nov., Paenibacillus brevis sp. nov., Peptoniphilus ovalis sp. nov. and Tissierella simiarum sp. nov., isolated from monkey faeces. INT J SYST EVOL MICR 2022, 72(3).","DOI":"10.1099\/ijsem.0.005276"},{"issue":"3","key":"4955_CR46","doi-asserted-by":"publisher","first-page":"285","DOI":"10.1007\/s12263-010-0206-6","volume":"6","author":"K Pokusaeva","year":"2011","unstructured":"Pokusaeva K, Fitzgerald GF, van Sinderen D. Carbohydrate metabolism in Bifidobacteria. Genes Nutr. 2011;6(3):285\u2013306.","journal-title":"Genes Nutr"},{"issue":"1","key":"4955_CR47","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1186\/s13068-024-02539-9","volume":"17","author":"C Doring","year":"2024","unstructured":"Doring C, Basen M. Propionate production by Bacteroidia gut bacteria and its dependence on substrate concentrations differs among species. Biotechnol Biofuels Bioprod. 2024;17(1):95.","journal-title":"Biotechnol Biofuels Bioprod"},{"key":"4955_CR48","doi-asserted-by":"publisher","first-page":"1324396","DOI":"10.3389\/fbioe.2023.1324396","volume":"11","author":"T Zaplana","year":"2023","unstructured":"Zaplana T, Miele S, Tolonen AC. Lachnospiraceae are emerging industrial biocatalysts and biotherapeutics. FRONT BIOENG BIOTECH. 2023;11:1324396.","journal-title":"FRONT BIOENG BIOTECH"},{"key":"4955_CR49","doi-asserted-by":"publisher","first-page":"612285","DOI":"10.3389\/fbioe.2021.612285","volume":"9","author":"Y Wang","year":"2021","unstructured":"Wang Y, Wu J, Lv M, Shao Z, Hungwe M, Wang J, Bai X, Xie J, Wang Y, Geng W. Metabolism Characteristics of Lactic Acid Bacteria and the Expanding Applications in Food Industry. FRONT BIOENG BIOTECH. 2021;9:612285.","journal-title":"FRONT BIOENG BIOTECH"},{"issue":"8","key":"4955_CR50","doi-asserted-by":"publisher","first-page":"2112","DOI":"10.1111\/j.1462-2920.2009.01931.x","volume":"11","author":"SH Duncan","year":"2009","unstructured":"Duncan SH, Louis P, Thomson JM, Flint HJ. The role of pH in determining the species composition of the human colonic microbiota. ENVIRON MICROBIOL. 2009;11(8):2112\u201322.","journal-title":"ENVIRON MICROBIOL"},{"issue":"1","key":"4955_CR51","doi-asserted-by":"publisher","first-page":"3510","DOI":"10.1038\/s41467-023-39121-0","volume":"14","author":"X Jin","year":"2023","unstructured":"Jin X, Yu FB, Yan J, Weakley AM, Dubinkina V, Meng X, Pollard KS. Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization. NAT COMMUN. 2023;14(1):3510.","journal-title":"NAT COMMUN"},{"issue":"9","key":"4955_CR52","doi-asserted-by":"publisher","first-page":"7892","DOI":"10.1039\/D0FO01103G","volume":"11","author":"G Feng","year":"2020","unstructured":"Feng G, Mikkelsen D, Hoedt EC, Williams BA, Flanagan BM, Morrison M, Gidley MJ. In vitro fermentation outcomes of arabinoxylan and galactoxyloglucan depend on fecal inoculum more than substrate chemistry. FOOD FUNCT. 2020;11(9):7892\u2013904.","journal-title":"FOOD FUNCT"},{"issue":"1","key":"4955_CR53","doi-asserted-by":"publisher","first-page":"20361","DOI":"10.1038\/s41598-024-71370-x","volume":"14","author":"H Park","year":"2024","unstructured":"Park H, Yeo S, Ryu CB, Huh CS. A streamlined culturomics case study for the human gut microbiota research. SCI REP-UK. 2024;14(1):20361.","journal-title":"SCI REP-UK"},{"key":"4955_CR54","doi-asserted-by":"crossref","unstructured":"Guevarra RB, Hong SH, Cho JH, Kim B, Shin J, Lee JH, Kang BN, Kim YH, Wattanaphansak S, Isaacson RE et al. The dynamics of the piglet gut microbiome during the weaning transition in association with health and nutrition. J ANIM SCI BIOTECHNO 2018, 9(1).","DOI":"10.1186\/s40104-018-0269-6"},{"issue":"1","key":"4955_CR55","doi-asserted-by":"publisher","first-page":"48","DOI":"10.1186\/s40168-019-0662-1","volume":"7","author":"W Wang","year":"2019","unstructured":"Wang W, Hu H, Zijlstra RT, Zheng J, G\u00e4nzle MG. Metagenomic reconstructions of gut microbial metabolism in weanling pigs. MICROBIOME. 2019;7(1):48.","journal-title":"MICROBIOME"},{"issue":"8","key":"4955_CR56","doi-asserted-by":"publisher","first-page":"1566","DOI":"10.1038\/ismej.2014.12","volume":"8","author":"T Looft","year":"2014","unstructured":"Looft T, Allen HK, Cantarel BL, Levine UY, Bayles DO, Alt DP, Henrissat B, Stanton TB. Bacteria, phages and pigs: the effects of in-feed antibiotics on the microbiome at different gut locations. ISME J. 2014;8(8):1566\u201376.","journal-title":"ISME J"},{"issue":"1","key":"4955_CR57","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1186\/s42523-025-00465-1","volume":"7","author":"C Durif","year":"2025","unstructured":"Durif C, Denis S, Lemoine N, Deschamps C, Uriot O, Brun M, Guillou D, Blanquet-Diot S. A new in vitro model of the adult pig colon microbiome: application to the study of feed ingredients. ANIM MICROBIOME. 2025;7(1):100.","journal-title":"ANIM MICROBIOME"},{"issue":"1","key":"4955_CR58","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1186\/s40104-022-00699-y","volume":"13","author":"UP Tiwari","year":"2022","unstructured":"Tiwari UP, Mandal RK, Neupane KR, Mishra B, Jha R. Starchy and fibrous feedstuffs differ in their in vitro digestibility and fermentation characteristics and differently modulate gut microbiota of swine. J ANIM SCI BIOTECHNO. 2022;13(1):53.","journal-title":"J ANIM SCI BIOTECHNO"},{"issue":"2","key":"4955_CR59","doi-asserted-by":"publisher","first-page":"186","DOI":"10.1038\/s41587-018-0009-7","volume":"37","author":"SC Forster","year":"2019","unstructured":"Forster SC, Kumar N, Anonye BO, Almeida A, Viciani E, Stares MD, Dunn M, Mkandawire TT, Zhu A, Shao Y, et al. A human gut bacterial genome and culture collection for improved metagenomic analyses. NAT BIOTECHNOL. 2019;37(2):186\u201392.","journal-title":"NAT BIOTECHNOL"},{"issue":"1","key":"4955_CR60","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1186\/s13568-019-0790-9","volume":"9","author":"F Yousi","year":"2019","unstructured":"Yousi F, Kainan C, Junnan Z, Chuanxing X, Lina F, Bangzhou Z, Jianlin R, Baishan F. Evaluation of the effects of four media on human intestinal microbiota culture in vitro. AMB EXPRESS. 2019;9(1):69.","journal-title":"AMB EXPRESS"},{"key":"4955_CR61","doi-asserted-by":"crossref","unstructured":"Chang Y, Hou F, Pan Z, Huang Z, Han N, Bin L, Deng H, Li Z, Ding L, Gao H et al. Optimization of Culturomics Strategy in Human Fecal Samples. FRONT MICROBIOL 2019, 10.","DOI":"10.3389\/fmicb.2019.02891"}],"container-title":["BMC Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12866-026-04955-3","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12866-026-04955-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12866-026-04955-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,21]],"date-time":"2026-05-21T09:04:12Z","timestamp":1779354252000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1186\/s12866-026-04955-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,4,9]]},"references-count":61,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["4955"],"URL":"https:\/\/doi.org\/10.1186\/s12866-026-04955-3","relation":{},"ISSN":["1471-2180"],"issn-type":[{"value":"1471-2180","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,4,9]]},"assertion":[{"value":"22 December 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"10 March 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 April 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"All animal experiments were approved by the Institutional Animal Care and Use Committee of China Agricultural University under the permit number AW70210202-1-2. All experiments were performed in accordance with the approved guidelines and regulations (Guide for the Care and Use of Laboratory Animals, GB\/T 35892\u2009\u2212\u20092018). Informed consent was obtained from all owners.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"475"}}