{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T03:16:16Z","timestamp":1789010176425,"version":"build-2803163510"},"reference-count":61,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2023,2,17]],"date-time":"2023-02-17T00:00:00Z","timestamp":1676592000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2023,2,17]],"date-time":"2023-02-17T00:00:00Z","timestamp":1676592000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"Guangxi Science and Technology Project","award":["GuiKeAA18242040"],"award-info":[{"award-number":["GuiKeAA18242040"]}]},{"name":"Start-up fund of Nanjing Agricultural University","award":["804131"],"award-info":[{"award-number":["804131"]}]},{"name":"Start-up Fund for Distinguished Scholars of Nanjing Agricultural Universitry","award":["80900219"],"award-info":[{"award-number":["80900219"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Microb Cell Fact"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>Given the crucial role of gut microbiota in animal and human health, studies on modulating the intestinal microbiome for therapeutic purposes have grasped a significant attention, of which the role of fecal microbiota transplantation (FMT) has been emphasized.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Methods<\/jats:title>\n                <jats:p>In the current study, we evaluated the effect of FMT on gut functions in <jats:italic>Escherichia coli<\/jats:italic> (<jats:italic>E. coli<\/jats:italic>) infection\u00a0by using mice model. Moreover, we\u00a0also investigated the subsequently dependent variables of infection, i.e., body weight, mortality, intestinal histopathology, and the expression\u00a0changes in tight junction proteins (TJPs).<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>The FMT effectively decreased weight loss and mortality to a certain extent\u00a0with the restoration of\u00a0intestinal villi that resulted in high histological scores for jejunum tissue damage (<jats:italic>p<\/jats:italic>\u2009&lt;\u20090.05). The effect of FMT on alleviating the reduction of intestinal TJPs was also proved by immunohistochemistry analysis and mRNA expression levels.\u00a0Moreover, the abundance of health-threatening bacteria, belonging to phylum Proteobacteria, family Enterobacteriaceae\u00a0and Tannerellaceae, genus <jats:italic>Escherichia-Shigella<\/jats:italic>, <jats:italic>Sphingomonas<\/jats:italic>, <jats:italic>Collinsella,<\/jats:italic> etc., were significantly increased, whereas beneficial bacteria, belonging to\u00a0phylum Firmicutes, family Lactobacillaceae, genus <jats:italic>Lactobacillus<\/jats:italic>\u00a0were decreased in the gut of infected mice. Furthermore, we sought to investigate the association of clinical symptoms with FMT treatment with modulation in gut microbiota. According to beta diversity, the microbial community\u00a0of gut microbiota results reflected the similarities between non-infected and FMT groups. The improvement of the intestinal microbiota in FMT\u00a0group was characterized by the significant high level of beneficial microorganisms with the\u00a0synergistic decrease of <jats:italic>Escherichia-Shigella<\/jats:italic>, <jats:italic>Acinetobacter,<\/jats:italic> and other taxa.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>The findings suggest a beneficial host-microbiome correlation following fecal microbiota transplanatation\u00a0for controlling gut infections and pathogens-associated diseases.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12934-023-02027-z","type":"journal-article","created":{"date-parts":[[2023,2,17]],"date-time":"2023-02-17T12:03:51Z","timestamp":1676635431000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":18,"title":["Fecal microbiota transplantation attenuates Escherichia coli infected outgrowth by modulating the intestinal microbiome"],"prefix":"10.1186","volume":"22","author":[{"given":"Yaping","family":"Wang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuanyuan","family":"He","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ying","family":"Liang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Han","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiushuang","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muhammad Fakhar-e-Alam","family":"Kulyar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Asim","family":"Shahzad","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kunhua","family":"Wei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kun","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2023,2,17]]},"reference":[{"key":"2027_CR1","doi-asserted-by":"publisher","first-page":"756","DOI":"10.1093\/icb\/icx104","volume":"57","author":"TA Suzuki","year":"2017","unstructured":"Suzuki TA. Links between natural variation in the microbiome and host fitness in wild mammals. Integr Comp Biol. 2017;57:756\u201369.","journal-title":"Integr Comp Biol"},{"key":"2027_CR2","doi-asserted-by":"publisher","first-page":"3229","DOI":"10.1073\/pnas.1218525110","volume":"110","author":"M McFall-Ngai","year":"2013","unstructured":"McFall-Ngai M, Hadfield MG, Bosch TC, Carey HV, Domazet-Loso T, Douglas AE, Dubilier N, Eberl G, Fukami T, Gilbert SF, Hentschel U, King N, Kjelleberg S, Knoll AH, Kremer N, Mazmanian SK, Metcalf JL, Nealson K, Pierce NE, Rawls JF, Reid A, Ruby EG, Rumpho M, Sanders JG, Tautz D, Wernegreen JJ. Animals in a bacterial world, a new imperative for the life sciences. Proc Natl Acad Sci USA. 2013;110:3229\u201336.","journal-title":"Proc Natl Acad Sci USA"},{"key":"2027_CR3","doi-asserted-by":"publisher","first-page":"417","DOI":"10.3389\/fmicb.2012.00417","volume":"3","author":"A Shade","year":"2012","unstructured":"Shade A, Peter H, Allison SD, Baho DL, Berga M, Burgmann H, Huber DH, Langenheder S, Lennon JT, Martiny JB, Matulich KL, Schmidt TM, Handelsman J. Fundamentals of microbial community resistance and resilience. Front Microbiol. 2012;3:417.","journal-title":"Front Microbiol"},{"key":"2027_CR4","doi-asserted-by":"publisher","first-page":"480","DOI":"10.1038\/nature07540","volume":"457","author":"PJ Turnbaugh","year":"2009","unstructured":"Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, Egholm M, Henrissat B, Heath AC, Knight R, Gordon JI. A core gut microbiome in obese and lean twins. Nature. 2009;457:480\u20134.","journal-title":"Nature"},{"key":"2027_CR5","doi-asserted-by":"publisher","first-page":"242","DOI":"10.1038\/nature11552","volume":"489","author":"V Tremaroli","year":"2012","unstructured":"Tremaroli V, Backhed F. Functional interactions between the gut microbiota and host metabolism. Nature. 2012;489:242\u20139.","journal-title":"Nature"},{"key":"2027_CR6","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1038\/nri3430","volume":"13","author":"N Kamada","year":"2013","unstructured":"Kamada N, Seo SU, Chen GY, Nunez G. Role of the gut microbiota in immunity and inflammatory disease. Nat Rev Immunol. 2013;13:321\u201335.","journal-title":"Nat Rev Immunol"},{"key":"2027_CR7","doi-asserted-by":"publisher","first-page":"2394","DOI":"10.1097\/MIB.0000000000000204","volume":"20","author":"DMF Sanchez","year":"2014","unstructured":"Sanchez DMF, Romero-Calvo I, Mascaraque C, Martinez-Augustin O. Intestinal inflammation and mucosal barrier function. Inflamm Bowel Dis. 2014;20:2394\u2013404.","journal-title":"Inflamm Bowel Dis"},{"issue":"3\u201320","key":"2027_CR8","first-page":"21","volume":"124","author":"KR Groschwitz","year":"2009","unstructured":"Groschwitz KR, Hogan SP. Intestinal barrier function: molecular regulation and disease pathogenesis. J Allergy Clin Immunol. 2009;124(3\u201320):21\u20132.","journal-title":"J Allergy Clin Immunol"},{"key":"2027_CR9","doi-asserted-by":"publisher","first-page":"769","DOI":"10.3945\/jn.110.135657","volume":"141","author":"D Ulluwishewa","year":"2011","unstructured":"Ulluwishewa D, Anderson RC, McNabb WC, Moughan PJ, Wells JM, Roy NC. Regulation of tight junction permeability by intestinal bacteria and dietary components. J Nutr. 2011;141:769\u201376.","journal-title":"J Nutr"},{"key":"2027_CR10","doi-asserted-by":"publisher","first-page":"586392","DOI":"10.3389\/fcimb.2021.586392","volume":"11","author":"Y Jian","year":"2021","unstructured":"Jian Y, Zhang D, Liu M, Wang Y, Xu ZX. The impact of gut microbiota on radiation-induced enteritis. Front Cell Infect Microbiol. 2021;11:586392.","journal-title":"Front Cell Infect Microbiol"},{"key":"2027_CR11","doi-asserted-by":"publisher","first-page":"1403","DOI":"10.1001\/jama.2019.3849","volume":"323","author":"K Rao","year":"2020","unstructured":"Rao K, Malani PN. Diagnosis and treatment of Clostridioides (Clostridium) difficile infection in adults in 2020. JAMA J Am Med Assoc. 2020;323:1403\u20134.","journal-title":"JAMA J Am Med Assoc"},{"key":"2027_CR12","doi-asserted-by":"publisher","first-page":"500","DOI":"10.1038\/ajg.2013.59","volume":"108","author":"Z Kassam","year":"2013","unstructured":"Kassam Z, Lee CH, Yuan Y, Hunt RH. Fecal microbiota transplantation for clostridium difficile infection: systematic review and meta-analysis. Am J Gastroenterol. 2013;108:500\u20138.","journal-title":"Am J Gastroenterol"},{"key":"2027_CR13","doi-asserted-by":"publisher","first-page":"1772","DOI":"10.1001\/jama.2014.13875","volume":"312","author":"I Youngster","year":"2014","unstructured":"Youngster I, Russell GH, Pindar C, Ziv-Baran T, Sauk J, Hohmann EL. Oral, capsulized, frozen fecal microbiota transplantation for relapsing Clostridium difficile infection. Jama J Am Med Assoc. 2014;312:1772\u20138.","journal-title":"Jama J Am Med Assoc"},{"key":"2027_CR14","doi-asserted-by":"publisher","first-page":"2043","DOI":"10.1056\/NEJMoa1910437","volume":"381","author":"Z DeFilipp","year":"2019","unstructured":"DeFilipp Z, Bloom PP, Torres SM, Mansour MK, Sater M, Huntley MH, Turbett S, Chung RT, Chen YB, Hohmann E-R, E. Coli bacteremia transmitted by fecal microbiota transplant. N Engl J Med. 2019;381:2043\u201350.","journal-title":"N Engl J Med"},{"key":"2027_CR15","doi-asserted-by":"publisher","first-page":"407","DOI":"10.1056\/NEJMoa1205037","volume":"368","author":"E van Nood","year":"2013","unstructured":"van Nood E, Vrieze A, Nieuwdorp M, Fuentes S, Zoetendal EG, de Vos WM, Visser CE, Kuijper EJ, Bartelsman JF, Tijssen JG, Speelman P, Dijkgraaf MG, Keller JJ. Duodenal infusion of donor feces for recurrent Clostridium difficile. N Engl J Med. 2013;368:407\u201315.","journal-title":"N Engl J Med"},{"key":"2027_CR16","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1186\/s40168-016-0225-7","volume":"5","author":"DW Kang","year":"2017","unstructured":"Kang DW, Adams JB, Gregory AC, Borody T, Chittick L, Fasano A, Khoruts A, Geis E, Maldonado J, McDonough-Means S, Pollard EL, Roux S, Sadowsky MJ, Lipson KS, Sullivan MB, Caporaso JG, Krajmalnik-Brown R. Microbiota transfer therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study. Microbiome. 2017;5:10.","journal-title":"Microbiome"},{"key":"2027_CR17","doi-asserted-by":"publisher","first-page":"226","DOI":"10.1186\/s40168-021-01107-9","volume":"9","author":"Z Zhao","year":"2021","unstructured":"Zhao Z, Ning J, Bao XQ, Shang M, Ma J, Li G, Zhang D. Fecal microbiota transplantation protects rotenone-induced Parkinson\u2019s disease mice via suppressing inflammation mediated by the lipopolysaccharide-TLR4 signaling pathway through the microbiota-gut-brain axis. Microbiome. 2021;9:226.","journal-title":"Microbiome"},{"key":"2027_CR18","doi-asserted-by":"publisher","first-page":"1132","DOI":"10.4014\/jmb.2002.02044","volume":"30","author":"W Zhang","year":"2020","unstructured":"Zhang W, Zou G, Li B, Du X, Sun Z, Sun Y, Jiang X. Fecal microbiota transplantation (FMT) alleviates experimental colitis in mice by gut microbiota regulation. J Microbiol Biotechnol. 2020;30:1132\u201341.","journal-title":"J Microbiol Biotechnol"},{"key":"2027_CR19","doi-asserted-by":"publisher","first-page":"465054","DOI":"10.1155\/2014\/465054","volume":"2014","author":"VL Koga","year":"2014","unstructured":"Koga VL, Tomazetto G, Cyoia PS, Neves MS, Vidotto MC, Nakazato G, Kobayashi RK. Molecular screening of virulence genes in extraintestinal pathogenic Escherichia coli isolated from human blood culture in Brazil. Biomed Res Int. 2014;2014:465054.","journal-title":"Biomed Res Int"},{"key":"2027_CR20","doi-asserted-by":"publisher","first-page":"i1585","DOI":"10.1136\/bmj.i1585","volume":"353","author":"JE Gotts","year":"2016","unstructured":"Gotts JE, Matthay MA. Sepsis: pathophysiology and clinical management. BMJ British Med J. 2016;353:i1585.","journal-title":"BMJ British Med J"},{"key":"2027_CR21","doi-asserted-by":"publisher","first-page":"103760","DOI":"10.1016\/j.micpath.2019.103760","volume":"137","author":"Y Wang","year":"2019","unstructured":"Wang Y, Li A, Zhang L, Waqas M, Mehmood K, Iqbal M, Muyou C, Li Z, Lian Y, Sizhu S, Li J. Probiotic potential of Lactobacillus on the intestinal microflora against Escherichia coli induced mice model through high-throughput sequencing. Microb Pathog. 2019;137:103760.","journal-title":"Microb Pathog"},{"key":"2027_CR22","doi-asserted-by":"publisher","first-page":"e2101119","DOI":"10.1002\/mnfr.202101119","volume":"66","author":"R Ishibashi","year":"2022","unstructured":"Ishibashi R, Furusawa Y, Honda H, Watanabe Y, Fujisaka S, Nishikawa M, Ikushiro S, Kurihara S, Tabuchi Y, Tobe K, Takatsu K, Nagai Y. Isoliquiritigenin attenuates adipose tissue inflammation and metabolic syndrome by modifying gut bacteria composition in mice. Mol Nutr Food Res. 2022;66:e2101119.","journal-title":"Mol Nutr Food Res"},{"key":"2027_CR23","doi-asserted-by":"publisher","first-page":"935","DOI":"10.1136\/gutjnl-2014-308323","volume":"65","author":"K Vlantis","year":"2016","unstructured":"Vlantis K, Polykratis A, Welz PS, van Loo G, Pasparakis M, Wullaert A. TLR-independent anti-inflammatory function of intestinal epithelial TRAF6 signalling prevents DSS-induced colitis in mice. Gut. 2016;65:935\u201343.","journal-title":"Gut"},{"key":"2027_CR24","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00137-18","author":"S Cheng","year":"2018","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. https:\/\/doi.org\/10.1128\/mSystems.00137-18.","journal-title":"Msystems"},{"key":"2027_CR25","doi-asserted-by":"publisher","first-page":"723","DOI":"10.1016\/j.chom.2013.05.004","volume":"13","author":"JL Benjamin","year":"2013","unstructured":"Benjamin JL, Sumpter RJ, Levine B, Hooper LV. Intestinal epithelial autophagy is essential for host defense against invasive bacteria. Cell Host Microbe. 2013;13:723\u201334.","journal-title":"Cell Host Microbe"},{"key":"2027_CR26","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"},{"key":"2027_CR27","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1016\/B978-0-12-381300-8.00008-3","volume":"107","author":"J Chow","year":"2010","unstructured":"Chow J, Lee SM, Shen Y, Khosravi A, Mazmanian SK. Host-bacterial symbiosis in health and disease. Adv Immunol. 2010;107:243\u201374.","journal-title":"Adv Immunol"},{"key":"2027_CR28","doi-asserted-by":"publisher","first-page":"389","DOI":"10.1016\/j.tem.2011.06.001","volume":"22","author":"BA White","year":"2011","unstructured":"White BA, Creedon DJ, Nelson KE, Wilson BA. The vaginal microbiome in health and disease. Trends Endocrinol Metab. 2011;22:389\u201393.","journal-title":"Trends Endocrinol Metab"},{"key":"2027_CR29","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1111\/j.1601-0825.2011.01851.x","volume":"18","author":"MF Zarco","year":"2012","unstructured":"Zarco MF, Vess TJ, Ginsburg GS. The oral microbiome in health and disease and the potential impact on personalized dental medicine. Oral Dis. 2012;18:109\u201320.","journal-title":"Oral Dis"},{"key":"2027_CR30","doi-asserted-by":"publisher","first-page":"954","DOI":"10.1016\/j.ccell.2018.03.004","volume":"33","author":"H Tilg","year":"2018","unstructured":"Tilg H, Adolph TE, Gerner RR, Moschen AR. The intestinal microbiota in colorectal cancer. Cancer Cell. 2018;33:954\u201364.","journal-title":"Cancer Cell"},{"key":"2027_CR31","doi-asserted-by":"publisher","first-page":"1575","DOI":"10.1056\/NEJMoa1109400","volume":"368","author":"WH Tang","year":"2013","unstructured":"Tang WH, Wang Z, Levison BS, Koeth RA, Britt EB, Fu X, Wu Y, Hazen SL. Intestinal microbial metabolism of phosphatidylcholine and cardiovascular risk. N Engl J Med. 2013;368:1575\u201384.","journal-title":"N Engl J Med"},{"key":"2027_CR32","doi-asserted-by":"publisher","first-page":"1022","DOI":"10.1038\/4441022a","volume":"444","author":"RE Ley","year":"2006","unstructured":"Ley RE, Turnbaugh PJ, Klein S, Gordon JI. Microbial ecology: human gut microbes associated with obesity. Nature. 2006;444:1022\u20133.","journal-title":"Nature"},{"key":"2027_CR33","doi-asserted-by":"publisher","first-page":"2559","DOI":"10.1017\/S0950268814000181","volume":"142","author":"M Escher","year":"2014","unstructured":"Escher M, Scavia G, Morabito S, Tozzoli R, Maugliani A, Cantoni S, Fracchia S, Bettati A, Casa R, Gesu GP, Torresani E, Caprioli A. A severe foodborne outbreak of diarrhoea linked to a canteen in Italy caused by enteroinvasive Escherichia coli, an uncommon agent. Epidemiol Infect. 2014;142:2559\u201366.","journal-title":"Epidemiol Infect"},{"key":"2027_CR34","doi-asserted-by":"publisher","first-page":"761","DOI":"10.11150\/kansenshogakuzasshi1970.66.761","volume":"66","author":"K Yamamura","year":"1992","unstructured":"Yamamura K, Sumi N, Egashira Y, Fukuoka I, Motomura S, Tsuchida R. Food poisoning caused by enteroinvasive Escherichia coli (O164:H-)\u2013a case in which the causative agent was identified. Kansenshogaku Zasshi. 1992;66:761\u20138.","journal-title":"Kansenshogaku Zasshi"},{"key":"2027_CR35","doi-asserted-by":"publisher","first-page":"607","DOI":"10.1016\/j.ijpara.2006.01.013","volume":"36","author":"KS Kim","year":"2006","unstructured":"Kim KS. Microbial translocation of the blood-brain barrier. Int J Parasit. 2006;36:607\u201314.","journal-title":"Int J Parasit"},{"key":"2027_CR36","doi-asserted-by":"publisher","first-page":"e1004383","DOI":"10.1371\/journal.ppat.1004383","volume":"10","author":"AO Brown","year":"2014","unstructured":"Brown AO, Mann B, Gao G, Hankins JS, Humann J, Giardina J, Faverio P, Restrepo MI, Halade GV, Mortensen EM, Lindsey ML, Hanes M, Happel KI, Nelson S, Bagby GJ, Lorent JA, Cardinal P, Granados R, Esteban A, LeSaux CJ, Tuomanen EI, Orihuela CJ. Streptococcus pneumoniae translocates into the myocardium and forms unique microlesions that disrupt cardiac function. Plos Pathog. 2014;10:e1004383.","journal-title":"Plos Pathog"},{"key":"2027_CR37","first-page":"9","volume":"2018","author":"G Wang","year":"1977","unstructured":"Wang G, He Y, Jin X, Zhou Y, Chen X, Zhao J, Zhang H, Chen W. The effect of co-infection of food-borne pathogenic bacteria on the progression of campylobacter jejuni infection in mice. Front Microbiol. 1977;2018:9.","journal-title":"Front Microbiol"},{"key":"2027_CR38","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1016\/j.revmed.2003.10.002","volume":"25","author":"G Kaltenbach","year":"2004","unstructured":"Kaltenbach G, Heitz D. Antibiotic-associated diarrhea in the elderly. Rev Med Interne. 2004;25:46\u201353.","journal-title":"Rev Med Interne"},{"key":"2027_CR39","doi-asserted-by":"publisher","first-page":"544","DOI":"10.1126\/science.aad9358","volume":"352","author":"MJ Blaser","year":"2016","unstructured":"Blaser MJ. Antibiotic use and its consequences for the normal microbiome. Science. 2016;352:544\u20135.","journal-title":"Science"},{"key":"2027_CR40","doi-asserted-by":"publisher","first-page":"287","DOI":"10.1007\/s00005-015-0332-3","volume":"63","author":"M Muszer","year":"2015","unstructured":"Muszer M, Noszczynska M, Kasperkiewicz K, Skurnik M. Human microbiome: when a friend becomes an enemy. Arch Immunol Ther Exp. 2015;63:287\u201398.","journal-title":"Arch Immunol Ther Exp"},{"key":"2027_CR41","doi-asserted-by":"publisher","first-page":"727","DOI":"10.1016\/j.drudis.2012.02.014","volume":"17","author":"A Takahashi","year":"2012","unstructured":"Takahashi A, Kondoh M, Suzuki H, Watari A, Yagi K. Pathological changes in tight junctions and potential applications into therapies. Drug Discov Today. 2012;17:727\u201332.","journal-title":"Drug Discov Today"},{"key":"2027_CR42","doi-asserted-by":"publisher","first-page":"439","DOI":"10.1136\/gut.52.3.439","volume":"52","author":"J Berkes","year":"2003","unstructured":"Berkes J, Viswanathan VK, Savkovic SD, Hecht G. Intestinal epithelial responses to enteric pathogens: effects on the tight junction barrier, ion transport, and inflammation. Gut. 2003;52:439\u201351.","journal-title":"Gut"},{"key":"2027_CR43","doi-asserted-by":"publisher","first-page":"612","DOI":"10.1038\/nrmicro3315","volume":"12","author":"JW Collins","year":"2014","unstructured":"Collins JW, Keeney KM, Crepin VF, Rathinam VA, Fitzgerald KA, Finlay BB, Frankel G. Citrobacter rodentium: infection, inflammation and the microbiota. Nat Rev Microbiol. 2014;12:612\u201323.","journal-title":"Nat Rev Microbiol"},{"key":"2027_CR44","doi-asserted-by":"publisher","first-page":"547","DOI":"10.1136\/gutjnl-2018-316906","volume":"68","author":"MB Zeisel","year":"2019","unstructured":"Zeisel MB, Dhawan P, Baumert TF. Tight junction proteins in gastrointestinal and liver disease. Gut. 2019;68:547\u201361.","journal-title":"Gut"},{"key":"2027_CR45","doi-asserted-by":"publisher","DOI":"10.3390\/nu13103315","author":"Q Zhang","year":"2021","unstructured":"Zhang Q, Cheng L, Wang J, Hao M, Che H. Antibiotic-induced gut microbiota dysbiosis damages the intestinal barrier, increasing food allergy in adult mice. Nutrients. 2021. https:\/\/doi.org\/10.3390\/nu13103315.","journal-title":"Nutrients"},{"key":"2027_CR46","doi-asserted-by":"publisher","first-page":"1339","DOI":"10.1016\/j.cell.2016.10.043","volume":"167","author":"MS Desai","year":"2016","unstructured":"Desai MS, Seekatz AM, Koropatkin NM, Kamada N, Hickey CA, Wolter M, Pudlo NA, Kitamoto S, Terrapon N, Muller A, Young VB, Henrissat B, Wilmes P, Stappenbeck TS, Nunez G, Martens EC. A dietary fiber-deprived gut microbiota degrades the colonic mucus barrier and enhances pathogen susceptibility. Cell. 2016;167:1339\u201353.","journal-title":"Cell"},{"key":"2027_CR47","doi-asserted-by":"publisher","first-page":"1555","DOI":"10.1136\/gutjnl-2017-314759","volume":"67","author":"BR Stevens","year":"2018","unstructured":"Stevens BR, Goel R, Seungbum K, Richards EM, Holbert RC, Pepine CJ, Raizada MK. Increased human intestinal barrier permeability plasma biomarkers zonulin and FABP2 correlated with plasma LPS and altered gut microbiome in anxiety or depression. Gut. 2018;67:1555\u20137.","journal-title":"Gut"},{"key":"2027_CR48","doi-asserted-by":"publisher","DOI":"10.3390\/nu11123002","author":"R Moron","year":"2019","unstructured":"Moron R, Galvez J, Colmenero M, Anderson P, Cabeza J, Rodriguez-Cabezas ME. The importance of the microbiome in critically ill patients: role of nutrition. Nutrients. 2019. https:\/\/doi.org\/10.3390\/nu11123002.","journal-title":"Nutrients"},{"key":"2027_CR49","doi-asserted-by":"publisher","first-page":"1628","DOI":"10.1007\/s10620-015-4011-3","volume":"61","author":"M Ojima","year":"2016","unstructured":"Ojima M, Motooka D, Shimizu K, Gotoh K, Shintani A, Yoshiya K, Nakamura S, Ogura H, Iida T, Shimazu T. Metagenomic analysis reveals dynamic changes of whole gut microbiota in the acute phase of intensive care unit patients. Dig Dis Sci. 2016;61:1628\u201334.","journal-title":"Dig Dis Sci"},{"key":"2027_CR50","doi-asserted-by":"publisher","first-page":"1599","DOI":"10.1007\/s10096-019-03580-5","volume":"38","author":"M Fatahi-Bafghi","year":"2019","unstructured":"Fatahi-Bafghi M. Antibiotic resistance genes in the actinobacteria phylum. Eur J Clin Microbiol Infect Dis. 2019;38:1599\u2013624.","journal-title":"Eur J Clin Microbiol Infect Dis"},{"key":"2027_CR51","doi-asserted-by":"publisher","first-page":"1318034","DOI":"10.1080\/16546628.2017.1318034","volume":"61","author":"SE Evivie","year":"2017","unstructured":"Evivie SE, Huo GC, Igene JO, Bian X. Some current applications, limitations and future perspectives of lactic acid bacteria as probiotics. Food Nutr Res. 2017;61:1318034.","journal-title":"Food Nutr Res"},{"key":"2027_CR52","doi-asserted-by":"publisher","DOI":"10.1093\/femsle\/fny213","author":"R Hatti-Kaul","year":"2018","unstructured":"Hatti-Kaul R, Chen L, Dishisha T, Enshasy HE. Lactic acid bacteria: from starter cultures to producers of chemicals. Fems Microbiol Lett. 2018. https:\/\/doi.org\/10.1093\/femsle\/fny213.","journal-title":"Fems Microbiol Lett"},{"key":"2027_CR53","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000472","author":"D Davray","year":"2021","unstructured":"Davray D, Deo D, Kulkarni R. Plasmids encode niche-specific traits in lactobacillaceae. Microb Genomics. 2021. https:\/\/doi.org\/10.1099\/mgen.0.000472.","journal-title":"Microb Genomics"},{"key":"2027_CR54","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1007\/s12250-014-3543-6","volume":"30","author":"Y Xu","year":"2015","unstructured":"Xu Y, Liu Y, Liu Y, Pei J, Yao S, Cheng C. Bacteriophage therapy against enterobacteriaceae. Virol Sin. 2015;30:11\u20138.","journal-title":"Virol Sin"},{"key":"2027_CR55","doi-asserted-by":"publisher","first-page":"267","DOI":"10.1016\/S0378-1135(02)00066-4","volume":"87","author":"RL van Winsen","year":"2002","unstructured":"van Winsen RL, Keuzenkamp D, Urlings BA, Lipman LJ, Snijders JA, Verheijden JH, van Knapen F. Effect of fermented feed on shedding of Enterobacteriaceae by fattening pigs. Vet Microbiol. 2002;87:267\u201376.","journal-title":"Vet Microbiol"},{"key":"2027_CR56","doi-asserted-by":"publisher","DOI":"10.3390\/life11020099","author":"JJ Xiao","year":"2021","unstructured":"Xiao JJ, Tseng YC, Wu JL, Lu MW. The alteration of intestinal microbiota profile and immune response in epinephelus coioides during pathogen infection. Life Basel. 2021. https:\/\/doi.org\/10.3390\/life11020099.","journal-title":"Life Basel"},{"key":"2027_CR57","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1186\/s13073-016-0299-7","volume":"8","author":"J Chen","year":"2016","unstructured":"Chen J, Wright K, Davis JM, Jeraldo P, Marietta EV, Murray J, Nelson H, Matteson EL, Taneja V. An expansion of rare lineage intestinal microbes characterizes rheumatoid arthritis. Genome Med. 2016;8:43.","journal-title":"Genome Med"},{"key":"2027_CR58","doi-asserted-by":"publisher","first-page":"1091","DOI":"10.1136\/gut.2008.165886","volume":"58","author":"PD Cani","year":"2009","unstructured":"Cani PD, Possemiers S, Van de Wiele T, Guiot Y, Everard A, Rottier O, Geurts L, Naslain D, Neyrinck A, Lambert DM, Muccioli GG, Delzenne NM. Changes in gut microbiota control inflammation in obese mice through a mechanism involving GLP-2-driven improvement of gut permeability. Gut. 2009;58:1091\u2013103.","journal-title":"Gut"},{"key":"2027_CR59","first-page":"78","volume":"23","author":"AR Prior","year":"2017","unstructured":"Prior AR, Gunaratnam C, Humphreys H. Ralstonia species\u2014do these bacteria matter in cystic fibrosis? Paediatr Respir Rev. 2017;23:78\u201383.","journal-title":"Paediatr Respir Rev"},{"key":"2027_CR60","doi-asserted-by":"publisher","first-page":"2045","DOI":"10.1007\/s10096-018-3364-x","volume":"37","author":"M Majidzadeh","year":"2018","unstructured":"Majidzadeh M, Fatahi-Bafghi M. Current taxonomy of rhodococcus species and their role in infections. Eur J Clin Microbiol Infect Dis. 2018;37:2045\u201362.","journal-title":"Eur J Clin Microbiol Infect Dis"},{"key":"2027_CR61","doi-asserted-by":"publisher","first-page":"779","DOI":"10.1007\/s10096-020-04075-4","volume":"40","author":"I Bloise","year":"2021","unstructured":"Bloise I, Guedez-Lopez GV, Tejedor-Rodriguez M, Romero-Gomez MP, Garcia-Rodriguez J, Mingorance J, Cendejas-Bueno E. Bloodstream infection due to herbaspirillum sp.: case series and review of literature. Eur J Clin Microbiol Infect Dis. 2021;40:779\u201385.","journal-title":"Eur J Clin Microbiol Infect Dis"}],"container-title":["Microbial Cell Factories"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12934-023-02027-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12934-023-02027-z\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12934-023-02027-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,17]],"date-time":"2023-02-17T13:08:23Z","timestamp":1676639303000},"score":1,"resource":{"primary":{"URL":"https:\/\/microbialcellfactories.biomedcentral.com\/articles\/10.1186\/s12934-023-02027-z"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,2,17]]},"references-count":61,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2023,12]]}},"alternative-id":["2027"],"URL":"https:\/\/doi.org\/10.1186\/s12934-023-02027-z","relation":{},"ISSN":["1475-2859"],"issn-type":[{"value":"1475-2859","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,2,17]]},"assertion":[{"value":"23 October 2022","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 January 2023","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 February 2023","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 performed under the approval of Animal Ethics and Welfare Committee of Nanjing Agricultural University.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Yes.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"30"}}