{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T20:15:59Z","timestamp":1790799359529,"version":"4.1.0"},"reference-count":99,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2019,12,1]],"date-time":"2019-12-01T00:00:00Z","timestamp":1575158400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2019,12,18]],"date-time":"2019-12-18T00:00:00Z","timestamp":1576627200000},"content-version":"vor","delay-in-days":17,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31420103908"],"award-info":[{"award-number":["31420103908"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010663","name":"H2020 European Research Council","doi-asserted-by":"publisher","award":["633531"],"award-info":[{"award-number":["633531"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Biol"],"published-print":{"date-parts":[[2019,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>The early-life microbiota exerts a profound and lifelong impact on host health. Longitudinal studies in humans have been informative but are mostly based on the analysis of fecal samples and cannot shed direct light on the early development of mucosa-associated intestinal microbiota and its impact on GI function. Using piglets as a model for human infants, we assess here the succession of mucosa-associated microbiota across the intestinal tract in the first 35\u2009days after birth.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Although sharing a similar composition and predicted functional profile at birth, the mucosa-associated microbiome in the small intestine (jejunum and ileum) remained relatively stable, while that of the large intestine (cecum and colon) quickly expanded and diversified by day 35. Among detected microbial sources (milk, vagina, areolar skin, and feces of sows, farrowing crate, and incubator), maternal milk microbes were primarily responsible for the colonization of the small intestine, contributing approximately 90% bacteria throughout the first 35\u2009days of the neonatal life. Although maternal milk microbes contributed greater than 90% bacteria to the large intestinal microbiota of neonates upon birth, their presence gradually diminished, and they were replaced by maternal fecal microbes by day 35. We found strong correlations between the relative abundance of specific mucosa-associated microbes, particularly those vertically transmitted from the mother, and the expression levels of multiple intestinal immune and barrier function genes in different segments of the intestinal tract.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>We revealed spatially specific trajectories of microbial colonization of the intestinal mucosa in the small and large intestines, which can be primarily attributed to the colonization by vertically transmitted maternal milk and intestinal microbes. Additionally, these maternal microbes may be involved in the establishment of intestinal immune and barrier functions in neonates. Our findings strengthen the notion that studying fecal samples alone is insufficient to fully understand the co-development of the intestinal microbiota and immune system and suggest the possibility of improving neonatal health through the manipulation of maternal microbiota.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12915-019-0729-2","type":"journal-article","created":{"date-parts":[[2019,12,18]],"date-time":"2019-12-18T10:02:50Z","timestamp":1576663370000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":82,"title":["Maternal milk and fecal microbes guide the spatiotemporal development of mucosa-associated microbiota and barrier function in the porcine neonatal gut"],"prefix":"10.1186","volume":"17","author":[{"given":"Hongbin","family":"Liu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiangfang","family":"Zeng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guolong","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chengli","family":"Hou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ning","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haitao","family":"Yu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lijun","family":"Shang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoya","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paolo","family":"Trevisi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Feiyun","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zuohua","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1133-1393","authenticated-orcid":false,"given":"Shiyan","family":"Qiao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2019,12,18]]},"reference":[{"key":"729_CR1","doi-asserted-by":"publisher","first-page":"609","DOI":"10.1002\/wnan.1333","volume":"7","author":"S Bellmann","year":"2015","unstructured":"Bellmann S, Carlander D, Fasano A, Momcilovic D, Scimeca JA, Waldman WJ, et al. Mammalian gastrointestinal tract parameters modulating the integrity, surface properties, and absorption of food-relevant nanomaterials. Wiley Interdiscip Rev Nanomed Nanobiotechnol. 2015;7:609\u201322.","journal-title":"Wiley Interdiscip Rev Nanomed Nanobiotechnol."},{"key":"729_CR2","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1038\/nrgastro.2014.200","volume":"12","author":"L Ohman","year":"2015","unstructured":"Ohman L, Tornblom H, Simren M. Crosstalk at the mucosal border: importance of the gut microenvironment in IBS. Nat Rev Gastroenterol Hepatol. 2015;12:36\u201349.","journal-title":"Nat Rev Gastroenterol Hepatol."},{"key":"729_CR3","doi-asserted-by":"publisher","first-page":"2369","DOI":"10.1056\/NEJMra1600266","volume":"375","author":"SV Lynch","year":"2016","unstructured":"Lynch SV, Pedersen O. The human intestinal microbiome in health and disease. New Engl J Med. 2016;375:2369\u201379.","journal-title":"New Engl J Med."},{"issue":"5","key":"729_CR4","doi-asserted-by":"publisher","first-page":"567","DOI":"10.1038\/mi.2012.32","volume":"5","author":"Sahar El Aidy","year":"2012","unstructured":"El Aidy S, van Baarlen P, Derrien M, Lindenbergh-Kortleve DJ, Hooiveld G, Levenez F, et al. Temporal and spatial interplay of microbiota and intestinal mucosa drive establishment of immune homeostasis in conventionalized mice. Mucosal Immunol. 2012. https:\/\/doi.org\/10.1038\/mi.2012.32.","journal-title":"Mucosal Immunology"},{"issue":"6285","key":"729_CR5","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1126\/science.aad9378","volume":"352","author":"Thomas Gensollen","year":"2016","unstructured":"Gensollen T, Iyer SS, Kasper DL, Blumberg RS. How colonization by microbiota in early life shapes the immune system. Science. 2016. https:\/\/doi.org\/10.1126\/science.aad9378.","journal-title":"Science"},{"key":"729_CR6","doi-asserted-by":"publisher","first-page":"713","DOI":"10.1038\/nm.4142","volume":"22","author":"S Tamburini","year":"2016","unstructured":"Tamburini S, Shen N, Wu HC, Clemente JC. The microbiome in early life: implications for health outcomes. Nat Med. 2016;22:713\u201322.","journal-title":"Nat Med."},{"key":"729_CR7","doi-asserted-by":"publisher","first-page":"489","DOI":"10.1126\/science.1219328","volume":"336","author":"T Olszak","year":"2012","unstructured":"Olszak T, An D, Zeissig S, Vera MP, Richter J, Franke A, et al. Microbial exposure during early life has persistent effects on natural killer T cell function. Science. 2012;336:489\u201393.","journal-title":"Science."},{"issue":"7505","key":"729_CR8","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1038\/nature13421","volume":"510","author":"Sathish Subramanian","year":"2014","unstructured":"Subramanian S, Huq S, Yatsunenko T, Haque R, Mahfuz M, Alam MA, et al. Persistent gut microbiota immaturity in malnourished Bangladeshi children. Nature. 2014. https:\/\/doi.org\/10.1038\/nature13421.","journal-title":"Nature"},{"key":"729_CR9","doi-asserted-by":"publisher","first-page":"260","DOI":"10.1016\/j.chom.2015.01.001","volume":"17","author":"AD Kostic","year":"2015","unstructured":"Kostic AD, Gevers D, Siljander H, Vatanen T, Hy\u00f6tyl\u00e4inen T, H\u00e4m\u00e4l\u00e4inen A, et al. The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes. Cell Host Microbe. 2015;17:260\u201373.","journal-title":"Cell Host Microbe."},{"key":"729_CR10","doi-asserted-by":"publisher","first-page":"152r","DOI":"10.1126\/scitranslmed.aab2271","volume":"7","author":"MC Arrieta","year":"2015","unstructured":"Arrieta MC, Stiemsma LT, Dimitriu PA, Thorson L, Russell S, Yurist-Doutsch S, et al. Early infancy microbial and metabolic alterations affect risk of childhood asthma. Sci Transl Med. 2015;7:152r\u2013307r.","journal-title":"Sci Transl Med"},{"key":"729_CR11","doi-asserted-by":"publisher","first-page":"522","DOI":"10.1038\/ijo.2011.27","volume":"35","author":"TA Ajslev","year":"2011","unstructured":"Ajslev TA, Andersen CS, Gamborg M, Sorensen TI, Jess T. Childhood overweight after establishment of the gut microbiota: the role of delivery mode, pre-pregnancy weight and early administration of antibiotics. Int J Obes (Lond). 2011;35:522\u20139.","journal-title":"Int J Obes (Lond)."},{"key":"729_CR12","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1038\/nature11582","volume":"491","author":"L Jostins","year":"2012","unstructured":"Jostins L, Ripke S, Weersma RK, Duerr RH, McGovern DP, Hui KY, et al. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature. 2012;491:119\u201324.","journal-title":"Nature."},{"key":"729_CR13","doi-asserted-by":"publisher","first-page":"496","DOI":"10.1056\/NEJMra0804595","volume":"361","author":"FO Nestle","year":"2009","unstructured":"Nestle FO, Kaplan DH, Barker J. Psoriasis. N Engl J Med. 2009;361:496\u2013509.","journal-title":"N Engl J Med."},{"key":"729_CR14","doi-asserted-by":"publisher","first-page":"1228","DOI":"10.1038\/nm.3950","volume":"21","author":"ES Lim","year":"2015","unstructured":"Lim ES, Zhou Y, Zhao G, Bauer IK, Droit L, Ndao IM, et al. Early life dynamics of the human gut virome and bacterial microbiome in infants. Nat Med. 2015;21:1228\u201334.","journal-title":"Nat Med."},{"key":"729_CR15","doi-asserted-by":"publisher","first-page":"250","DOI":"10.1038\/nm.4039","volume":"22","author":"MG Dominguez-Bello","year":"2016","unstructured":"Dominguez-Bello MG, De Jesus-Laboy KM, Shen N, Cox LM, Amir A, Gonzalez A, et al. Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. Nat Med. 2016;22:250\u20133.","journal-title":"Nat Med."},{"issue":"1","key":"729_CR16","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1038\/nri3112","volume":"12","author":"Harald Renz","year":"2011","unstructured":"Renz H, Brandtzaeg P, Hornef M. The impact of perinatal immune development on mucosal homeostasis and chronic inflammation. Nat Rev Immunol. 2011. https:\/\/doi.org\/10.1038\/nri3112.","journal-title":"Nature Reviews Immunology"},{"key":"729_CR17","doi-asserted-by":"publisher","first-page":"485","DOI":"10.1016\/j.cell.2009.09.033","volume":"139","author":"II Ivanov","year":"2009","unstructured":"Ivanov II, Atarashi K, Manel N, Brodie EL, Shima T, Karaoz U, et al. Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell. 2009;139:485\u201398.","journal-title":"Cell."},{"key":"729_CR18","doi-asserted-by":"publisher","first-page":"594","DOI":"10.1016\/j.immuni.2014.03.005","volume":"40","author":"Y Goto","year":"2014","unstructured":"Goto Y, Panea C, Nakato G, Cebula A, Lee C, Diez MG, et al. Segmented filamentous bacteria antigens presented by intestinal dendritic cells drive mucosal Th17 cell differentiation. Immunity. 2014;40:594\u2013607.","journal-title":"Immunity."},{"key":"729_CR19","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1016\/j.cell.2015.08.058","volume":"163","author":"K Atarashi","year":"2015","unstructured":"Atarashi K, Tanoue T, Ando M, Kamada N, Nagano Y, Narushima S, et al. Th17 cell induction by adhesion of microbes to intestinal epithelial cells. Cell. 2015;163:367\u201380.","journal-title":"Cell."},{"key":"729_CR20","doi-asserted-by":"publisher","first-page":"3401","DOI":"10.1128\/AEM.68.7.3401-3407.2002","volume":"68","author":"EG Zoetendal","year":"2002","unstructured":"Zoetendal EG, von Wright A, Vilpponen-Salmela T, Ben-Amor K, Akkermans AD, de Vos WM. Mucosa-associated bacteria in the human gastrointestinal tract are uniformly distributed along the colon and differ from the community recovered from feces. Appl Environ Microbiol. 2002;68:3401\u20137.","journal-title":"Appl Environ Microbiol."},{"key":"729_CR21","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1186\/1757-4749-2-19","volume":"2","author":"IM Carroll","year":"2010","unstructured":"Carroll IM, Chang YH, Park J, Sartor RB, Ringel Y. Luminal and mucosal-associated intestinal microbiota in patients with diarrhea-predominant irritable bowel syndrome. Gut Pathog. 2010;2:19.","journal-title":"Gut Pathog."},{"key":"729_CR22","doi-asserted-by":"publisher","first-page":"1635","DOI":"10.1126\/science.1110591","volume":"308","author":"PB Eckburg","year":"2005","unstructured":"Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, et al. Diversity of the human intestinal microbial flora. Science. 2005;308:1635\u20138.","journal-title":"Science."},{"key":"729_CR23","doi-asserted-by":"publisher","first-page":"385","DOI":"10.1016\/j.chom.2015.01.015","volume":"17","author":"K Yasuda","year":"2015","unstructured":"Yasuda K, Oh K, Ren B, Tickle TL, Franzosa EA, Wachtman LM, et al. Biogeography of the intestinal mucosal and lumenal microbiome in the rhesus macaque. Cell Host Microbe. 2015;17:385\u201391.","journal-title":"Cell Host Microbe."},{"key":"729_CR24","doi-asserted-by":"publisher","first-page":"478","DOI":"10.1016\/j.chom.2015.09.002","volume":"18","author":"KA Earle","year":"2015","unstructured":"Earle KA, Billings G, Sigal M, Lichtman JS, Hansson GC, Elias JE, et al. Quantitative imaging of gut microbiota spatial organization. Cell Host Microbe. 2015;18:478\u201388.","journal-title":"Cell Host Microbe."},{"key":"729_CR25","doi-asserted-by":"publisher","first-page":"50","DOI":"10.1016\/j.tim.2011.11.002","volume":"20","author":"F Meurens","year":"2012","unstructured":"Meurens F, Summerfield A, Nauwynck H, Saif L, Gerdts V. The pig: a model for human infectious diseases. Trends Microbiol. 2012;20:50\u20137.","journal-title":"Trends Microbiol."},{"key":"729_CR26","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1017\/S0954422410000077","volume":"23","author":"P Guilloteau","year":"2010","unstructured":"Guilloteau P, Zabielski R, Hammon HM, Metges CC. Nutritional programming of gastrointestinal tract development. Is the pig a good model for man? Nutr Res Rev. 2010;23:4\u201322.","journal-title":"Nutr Res Rev."},{"key":"729_CR27","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1017\/S0954422413000152","volume":"26","author":"SN Heinritz","year":"2013","unstructured":"Heinritz SN, Mosenthin R, Weiss E. Use of pigs as a potential model for research into dietary modulation of the human gut microbiota. Nutr Res Rev. 2013;26:191\u2013209.","journal-title":"Nutr Res Rev."},{"issue":"Suppl 4","key":"729_CR28","doi-asserted-by":"publisher","first-page":"290","DOI":"10.2527\/jas.54604","volume":"90","author":"RK Buddington","year":"2012","unstructured":"Buddington RK, Sangild PT, Hance B, Huang EY, Black DD. Prenatal gastrointestinal development in the pig and responses after preterm birth. J Anim Sci. 2012;90(Suppl 4):290\u20138.","journal-title":"J Anim Sci."},{"key":"729_CR29","doi-asserted-by":"publisher","first-page":"774","DOI":"10.1079\/BJN20061881","volume":"96","author":"PC Calder","year":"2006","unstructured":"Calder PC, Krauss-Etschmann S, de Jong EC, Dupont C, Frick JS, Frokiaer H, et al. Early nutrition and immunity - progress and perspectives. Br J Nutr. 2006;96:774\u201390.","journal-title":"Br J Nutr."},{"key":"729_CR30","doi-asserted-by":"publisher","first-page":"16161","DOI":"10.1038\/nmicrobiol.2016.161","volume":"1","author":"L Xiao","year":"2016","unstructured":"Xiao L, Estell\u00e9 J, Kiilerich P, Ramayo-Caldas Y, Xia Z, Feng Q, et al. A reference gene catalogue of the pig gut microbiome. Nat Microbiol. 2016;1:16161.","journal-title":"Nat Microbiol."},{"key":"729_CR31","doi-asserted-by":"publisher","first-page":"2577","DOI":"10.1039\/c1mb05023k","volume":"7","author":"CA Merrifield","year":"2011","unstructured":"Merrifield CA, Lewis M, Claus SP, Beckonert OP, Dumas ME, Duncker S, et al. A metabolic system-wide characterisation of the pig: a model for human physiology. Mol Biosyst. 2011;7:2577\u201388.","journal-title":"Mol Biosyst."},{"key":"729_CR32","doi-asserted-by":"publisher","first-page":"343r","DOI":"10.1126\/scitranslmed.aad7121","volume":"8","author":"NA Bokulich","year":"2016","unstructured":"Bokulich NA, Chung J, Battaglia T, Henderson N, Jay M, Li H, et al. Antibiotics, birth mode, and diet shape microbiome maturation during early life. Sci Transl Med. 2016;8:343r\u201382r.","journal-title":"Sci Transl Med"},{"key":"729_CR33","doi-asserted-by":"publisher","first-page":"11971","DOI":"10.1073\/pnas.1002601107","volume":"107","author":"MG Dominguez-Bello","year":"2010","unstructured":"Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N, et al. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci. 2010;107:11971\u20135.","journal-title":"Proc Natl Acad Sci"},{"key":"729_CR34","doi-asserted-by":"publisher","first-page":"7486","DOI":"10.1038\/ncomms8486","volume":"6","author":"YR Nobel","year":"2015","unstructured":"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;6:7486.","journal-title":"Nat Commun."},{"key":"729_CR35","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1004903","volume":"11","author":"A Schulfer","year":"2015","unstructured":"Schulfer A, Blaser MJ. Risks of antibiotic exposures early in life on the developing microbiome. Plos Pathog. 2015;11:e1004903.","journal-title":"Plos Pathog."},{"key":"729_CR36","doi-asserted-by":"publisher","first-page":"r32","DOI":"10.1186\/gb-2012-13-4-r32","volume":"13","author":"S Schwartz","year":"2012","unstructured":"Schwartz S, Chapkin RS, Friedberg I, Ivanov IV, Davidson LA, Goldsby JS, et al. A metagenomic study of diet-dependent interaction between gut microbiota and host in infants reveals differences in immune response. Genome Biol. 2012;13:r32.","journal-title":"Genome Biol"},{"key":"729_CR37","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1038\/ismej.2015.90","volume":"10","author":"CA Merrifield","year":"2016","unstructured":"Merrifield CA, Lewis MC, Berger B, Cloarec O, Heinzmann SS, Charton F, et al. Neonatal environment exerts a sustained influence on the development of the intestinal microbiota and metabolic phenotype. ISME J. 2016;10:145\u201357.","journal-title":"ISME J."},{"key":"729_CR38","doi-asserted-by":"publisher","first-page":"647","DOI":"10.1001\/jamapediatrics.2017.0378","volume":"171","author":"PS Pannaraj","year":"2017","unstructured":"Pannaraj PS, Li F, Cerini C, Bender JM, Yang S, Rollie A, et al. Association between breast milk bacterial communities and establishment and development of the infant gut microbiome. Jama Pediatr. 2017;171:647\u201354.","journal-title":"Jama Pediatr."},{"key":"729_CR39","doi-asserted-by":"publisher","unstructured":"Shin H, Pei Z, Martinez KA, Rivera-Vinas JI, Mendez K, Cavallin H, et al. The first microbial environment of infants born by C-section: the operating room microbes. Microbiome. 2015. https:\/\/doi.org\/10.1186\/s40168-015-0126-1.","DOI":"10.1186\/s40168-015-0126-1"},{"key":"729_CR40","doi-asserted-by":"publisher","unstructured":"Brooks B, Olm MR, Firek BA, Baker R, Thomas BC, Morowitz MJ, et al. Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome. Nat Commun. 2017. https:\/\/doi.org\/10.1038\/s41467-017-02018-w.","DOI":"10.1038\/s41467-017-02018-w"},{"key":"729_CR41","doi-asserted-by":"publisher","first-page":"4578","DOI":"10.1073\/pnas.1000081107","volume":"108","author":"JE Koenig","year":"2011","unstructured":"Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J, Knight R, et al. Succession of microbial consortia in the developing infant gut microbiome. Proc Natl Acad Sci. 2011;108:4578\u201385.","journal-title":"Proc Natl Acad Sci"},{"key":"729_CR42","doi-asserted-by":"publisher","first-page":"690","DOI":"10.1016\/j.chom.2015.04.004","volume":"17","author":"F B\u00e4ckhed","year":"2015","unstructured":"B\u00e4ckhed F, Roswall J, Peng Y, Feng Q, Jia H, Kovatcheva-Datchary P, et al. Dynamics and stabilization of the human gut microbiome during the first year of life. Cell Host Microbe. 2015;17:690\u2013703.","journal-title":"Cell Host Microbe."},{"key":"729_CR43","doi-asserted-by":"publisher","first-page":"814","DOI":"10.1038\/nbt.2676","volume":"31","author":"MGI Langille","year":"2013","unstructured":"Langille MGI, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol. 2013;31:814\u201321.","journal-title":"Nat Biotechnol."},{"key":"729_CR44","doi-asserted-by":"publisher","first-page":"761","DOI":"10.1038\/nmeth.1650","volume":"8","author":"D Knights","year":"2011","unstructured":"Knights D, Kuczynski J, Charlson ES, Zaneveld J, Mozer MC, Collman RG, et al. Bayesian community-wide culture-independent microbial source tracking. Nat Methods. 2011;8:761\u20133.","journal-title":"Nat Methods."},{"key":"729_CR45","doi-asserted-by":"publisher","first-page":"789","DOI":"10.1016\/j.cell.2014.09.053","volume":"159","author":"JK Goodrich","year":"2014","unstructured":"Goodrich JK, Waters JL, Poole AC, Sutter JL, Koren O, Blekhman R, et al. Human genetics shape the gut microbiome. Cell. 2014;159:789\u201399.","journal-title":"Cell."},{"issue":"3","key":"729_CR46","doi-asserted-by":"publisher","first-page":"805","DOI":"10.1038\/s41396-018-0312-9","volume":"13","author":"Wei Zhou","year":"2018","unstructured":"Zhou W, Chow K, Fleming E, Oh J. Selective colonization ability of human fecal microbes in different mouse gut environments. ISME J. 2018. https:\/\/doi.org\/10.1038\/s41396-018-0312-9.","journal-title":"The ISME Journal"},{"key":"729_CR47","doi-asserted-by":"publisher","first-page":"E9105","DOI":"10.1073\/pnas.1711596114","volume":"114","author":"JL Mark Welch","year":"2017","unstructured":"Mark Welch JL, Hasegawa Y, McNulty NP, Gordon JI, Borisy GG. Spatial organization of a model 15-member human gut microbiota established in gnotobiotic mice. Proc Natl Acad Sci. 2017;114:E9105\u201314.","journal-title":"Proc Natl Acad Sci"},{"key":"729_CR48","doi-asserted-by":"publisher","first-page":"334","DOI":"10.1016\/j.dci.2008.05.006","volume":"33","author":"Y Sang","year":"2009","unstructured":"Sang Y, Blecha F. Porcine host defense peptides: expanding repertoire and functions. Dev Comparative Immunol. 2009;33:334\u201343.","journal-title":"Dev Comparative Immunol"},{"key":"729_CR49","doi-asserted-by":"publisher","first-page":"255","DOI":"10.1126\/science.1209791","volume":"334","author":"S Vaishnava","year":"2011","unstructured":"Vaishnava S, Yamamoto M, Severson KM, Ruhn KA, Yu X, Koren O, et al. The antibacterial lectin RegIIIgamma promotes the spatial segregation of microbiota and host in the intestine. Science. 2011;334:255\u20138.","journal-title":"Science."},{"key":"729_CR50","doi-asserted-by":"publisher","first-page":"639","DOI":"10.1038\/nri.2016.88","volume":"16","author":"ME Johansson","year":"2016","unstructured":"Johansson ME, Hansson GC. Immunological aspects of intestinal mucus and mucins. Nat Rev Immunol. 2016;16:639\u201349.","journal-title":"Nat Rev Immunol."},{"key":"729_CR51","doi-asserted-by":"publisher","first-page":"636","DOI":"10.4049\/jimmunol.182.1.636","volume":"182","author":"SC Gribar","year":"2009","unstructured":"Gribar SC, Sodhi CP, Richardson WM, Anand RJ, Gittes GK, Branca MF, et al. Reciprocal expression and signaling of TLR4 and TLR9 in the pathogenesis and treatment of necrotizing enterocolitis. J Immunol. 2009;182:636\u201346.","journal-title":"J Immunol."},{"key":"729_CR52","doi-asserted-by":"publisher","first-page":"372","DOI":"10.1016\/j.immuni.2013.08.003","volume":"39","author":"T Zelante","year":"2013","unstructured":"Zelante T, Iannitti RG, Cunha C, De Luca A, Giovannini G, Pieraccini G, et al. Tryptophan catabolites from microbiota engage aryl hydrocarbon receptor and balance mucosal reactivity via interleukin-22. Immunity. 2013;39:372\u201385.","journal-title":"Immunity."},{"key":"729_CR53","doi-asserted-by":"publisher","first-page":"1943","DOI":"10.1073\/pnas.0711734105","volume":"105","author":"A Are","year":"2008","unstructured":"Are A, Aronsson L, Wang S, Greicius G, Lee YK, Gustafsson JA, et al. Enterococcus faecalis from newborn babies regulate endogenous PPARgamma activity and IL-10 levels in colonic epithelial cells. Proc Natl Acad Sci U S A. 2008;105:1943\u20138.","journal-title":"Proc Natl Acad Sci U S A."},{"key":"729_CR54","doi-asserted-by":"publisher","first-page":"667","DOI":"10.1038\/nri3738","volume":"14","author":"AM Mowat","year":"2014","unstructured":"Mowat AM, Agace WW. Regional specialization within the intestinal immune system. Nat Rev Immunol. 2014;14:667\u201385.","journal-title":"Nat Rev Immunol."},{"key":"729_CR55","doi-asserted-by":"publisher","unstructured":"Milani C, Duranti S, Bottacini F, Casey E, Turroni F, Mahony J, et al. The first microbial colonizers of the human gut: composition, activities, and health implications of the infant gut microbiota. Microbiol Mol Biol Rev. 2017. https:\/\/doi.org\/10.1128\/MMBR.00036-17.","DOI":"10.1128\/MMBR.00036-17"},{"key":"729_CR56","doi-asserted-by":"publisher","first-page":"314","DOI":"10.1038\/nm.4272","volume":"23","author":"DM Chu","year":"2017","unstructured":"Chu DM, Ma J, Prince AL, Antony KM, Seferovic MD, Aagaard KM. Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery. Nat Med. 2017;23:314\u201326.","journal-title":"Nat Med."},{"key":"729_CR57","doi-asserted-by":"publisher","first-page":"343r","DOI":"10.1126\/scitranslmed.aad0917","volume":"8","author":"M Yassour","year":"2016","unstructured":"Yassour M, Vatanen T, Siljander H, Hamalainen AM, Harkonen T, Ryhanen SJ, et al. Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability. Sci Transl Med. 2016;8:343r\u201381r.","journal-title":"Sci Transl Med"},{"key":"729_CR58","doi-asserted-by":"publisher","unstructured":"Liu Y, Zheng Z, Yu L, Wu S, Sun L, Wu S, et al. Examination of the temporal and spatial dynamics of the gut microbiome in newborn piglets reveals distinct microbial communities in six intestinal segments. Sci Rep-UK. 2019. https:\/\/doi.org\/10.1038\/s41598-019-40235-z.","DOI":"10.1038\/s41598-019-40235-z"},{"key":"729_CR59","doi-asserted-by":"publisher","first-page":"1055","DOI":"10.1053\/j.gastro.2014.07.020","volume":"147","author":"L Albenberg","year":"2014","unstructured":"Albenberg L, Esipova TV, Judge CP, Bittinger K, Chen J, Laughlin A, et al. Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota. Gastroenterology. 2014;147:1055\u201363.","journal-title":"Gastroenterology."},{"key":"729_CR60","volume":"10","author":"R Hansen","year":"2015","unstructured":"Hansen R, Scott KP, Khan S, Martin JC, Berry SH, Stevenson M, et al. First-pass meconium samples from healthy term vaginally-delivered neonates: an analysis of the microbiota. Plos One. 2015;10:e133320.","journal-title":"Plos One."},{"key":"729_CR61","doi-asserted-by":"publisher","unstructured":"Nagpal R, Tsuji H, Takahashi T, Kawashima K, Nagata S, Nomoto K, et al. Sensitive quantitative analysis of the meconium bacterial microbiota in healthy term infants born vaginally or by cesarean section. Front Microbiol. 2016. https:\/\/doi.org\/10.3389\/fmicb.2016.01997.","DOI":"10.3389\/fmicb.2016.01997"},{"key":"729_CR62","first-page":"237r","volume":"6","author":"K Aagaard","year":"2014","unstructured":"Aagaard K, Ma J, Antony KM, Ganu R, Petrosino J, Versalovic J. The placenta harbors a unique microbiome. Sci Transl Med. 2014;6:237r\u201365r.","journal-title":"Sci Transl Med"},{"key":"729_CR63","doi-asserted-by":"publisher","first-page":"23129","DOI":"10.1038\/srep23129","volume":"6","author":"MC Collado","year":"2016","unstructured":"Collado MC, Rautava S, Aakko J, Isolauri E, Salminen S. Human gut colonisation may be initiated in utero by distinct microbial communities in the placenta and amniotic fluid. Sci Rep-UK. 2016;6:23129.","journal-title":"Sci Rep-UK."},{"key":"729_CR64","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0090784","volume":"9","author":"AN Ardissone","year":"2014","unstructured":"Ardissone AN, de la Cruz DM, Davis-Richardson AG, Rechcigl KT, Li N, Drew JC, et al. Meconium microbiome analysis identifies bacteria correlated with premature birth. Plos One. 2014;9:e90784.","journal-title":"Plos One."},{"key":"729_CR65","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1016\/j.resmic.2007.12.007","volume":"159","author":"E Jimenez","year":"2008","unstructured":"Jimenez E, Marin ML, Martin R, Odriozola JM, Olivares M, Xaus J, et al. Is meconium from healthy newborns actually sterile? Res Microbiol. 2008;159:187\u201393.","journal-title":"Res Microbiol."},{"key":"729_CR66","doi-asserted-by":"publisher","first-page":"120r","DOI":"10.1126\/scitranslmed.3008791","volume":"6","author":"A Ardeshir","year":"2014","unstructured":"Ardeshir A, Narayan NR, Mendez-Lagares G, Lu D, Rauch M, Huang Y, et al. Breast-fed and bottle-fed infant rhesus macaques develop distinct gut microbiotas and immune systems. Sci Transl Med. 2014;6:120r\u2013252r.","journal-title":"Sci Transl Med"},{"key":"729_CR67","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1016\/j.chom.2018.06.005","volume":"24","author":"P Ferretti","year":"2018","unstructured":"Ferretti P, Pasolli E, Tett A, Asnicar F, Gorfer V, Fedi S, et al. Mother-to-infant microbial transmission from different body sites shapes the developing infant gut microbiome. Cell Host Microbe. 2018;24:133\u201345.","journal-title":"Cell Host Microbe."},{"key":"729_CR68","doi-asserted-by":"publisher","first-page":"1112","DOI":"10.1038\/ismej.2013.15","volume":"7","author":"IG Pantoja-Feliciano","year":"2013","unstructured":"Pantoja-Feliciano IG, Clemente JC, Costello EK, Perez ME, Blaser MJ, Knight R, et al. Biphasic assembly of the murine intestinal microbiota during early development. ISME J. 2013;7:1112\u20135.","journal-title":"ISME J."},{"key":"729_CR69","doi-asserted-by":"publisher","first-page":"419","DOI":"10.1146\/annurev-animal-022114-111112","volume":"3","author":"AR Pacheco","year":"2015","unstructured":"Pacheco AR, Barile D, Underwood MA, Mills DA. The impact of the milk glycobiome on the neonate gut microbiota. Annu Rev Anim Biosci. 2015;3:419\u201345.","journal-title":"Annu Rev Anim Biosci."},{"issue":"7","key":"729_CR70","doi-asserted-by":"publisher","first-page":"1578","DOI":"10.1016\/j.cell.2012.04.037","volume":"149","author":"Hachung Chung","year":"2012","unstructured":"Chung H, Pamp S, Hill J, Surana N, Edelman S. Gut immune maturation depends on colonization with a host-specific microbiota. Cell. 2012. https:\/\/doi.org\/10.1016\/j.cell.2012.04.037.","journal-title":"Cell"},{"key":"729_CR71","doi-asserted-by":"publisher","first-page":"1126","DOI":"10.1126\/science.1127119","volume":"313","author":"HL Cash","year":"2006","unstructured":"Cash HL, Whitham CV, Behrendt CL, Hooper LV. Symbiotic bacteria direct expression of an intestinal bactericidal lectin. Science. 2006;313:1126\u201330.","journal-title":"Science."},{"key":"729_CR72","doi-asserted-by":"publisher","first-page":"20858","DOI":"10.1073\/pnas.0808723105","volume":"105","author":"S Vaishnava","year":"2008","unstructured":"Vaishnava S, Behrendt CL, Ismail AS, Eckmann L, Hooper LV. Paneth cells directly sense gut commensals and maintain homeostasis at the intestinal host-microbial interface. Proc Natl Acad Sci U S A. 2008;105:20858\u201363.","journal-title":"Proc Natl Acad Sci U S A."},{"key":"729_CR73","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1038\/nrgastro.2017.173","volume":"15","author":"D Sprockett","year":"2018","unstructured":"Sprockett D, Fukami T, Relman DA. Role of priority effects in the early-life assembly of the gut microbiota. Nat Rev Gastro Hepat. 2018;15:197\u2013205.","journal-title":"Nat Rev Gastro Hepat."},{"key":"729_CR74","doi-asserted-by":"publisher","unstructured":"Sommer F, Nookaew I, Sommer N, Fogelstrand P, B\u00e4ckhed F. Site-specific programming of the host epithelial transcriptome by the gut microbiota. Genome Biol. 2015. https:\/\/doi.org\/10.1186\/s13059-015-0614-4.","DOI":"10.1186\/s13059-015-0614-4"},{"key":"729_CR75","doi-asserted-by":"publisher","first-page":"1170","DOI":"10.1038\/ismej.2015.187","volume":"10","author":"JS Lichtman","year":"2016","unstructured":"Lichtman JS, Alsentzer E, Jaffe M, Sprockett D, Masutani E, Ikwa E, et al. The effect of microbial colonization on the host proteome varies by gastrointestinal location. Isme J. 2016;10:1170\u201381.","journal-title":"Isme J."},{"key":"729_CR76","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1111\/j.1365-2672.2006.03102.x","volume":"102","author":"MP Diaz-Ropero","year":"2007","unstructured":"Diaz-Ropero MP, Martin R, Sierra S, Lara-Villoslada F, Rodriguez JM, Xaus J, et al. Two Lactobacillus strains, isolated from breast milk, differently modulate the immune response. J Appl Microbiol. 2007;102:337\u201343.","journal-title":"J Appl Microbiol."},{"key":"729_CR77","doi-asserted-by":"publisher","first-page":"700","DOI":"10.1016\/j.jff.2013.12.015","volume":"7","author":"Y Chiu","year":"2014","unstructured":"Chiu Y, Tsai J, Lin S, Chotirosvakin C, Lin M. Characterisation of bifidobacteria with immunomodulatory properties isolated from human breast milk. J Funct Foods. 2014;7:700\u20138.","journal-title":"J Funct Foods."},{"key":"729_CR78","doi-asserted-by":"publisher","first-page":"900","DOI":"10.1038\/ijo.2013.49","volume":"37","author":"J Blustein","year":"2013","unstructured":"Blustein J, Attina T, Liu M, Ryan AM, Cox LM, Blaser MJ, et al. Association of caesarean delivery with child adiposity from age 6 weeks to 15 years. Int J Obes (Lond). 2013;37:900\u20136.","journal-title":"Int J Obes (Lond)."},{"key":"729_CR79","doi-asserted-by":"publisher","first-page":"1369","DOI":"10.1111\/j.1365-2222.2012.04021.x","volume":"42","author":"C Almqvist","year":"2012","unstructured":"Almqvist C, Cnattingius S, Lichtenstein P, Lundholm C. The impact of birth mode of delivery on childhood asthma and allergic diseases--a sibling study. Clin Exp Allergy. 2012;42:1369\u201376.","journal-title":"Clin Exp Allergy."},{"key":"729_CR80","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pmed.1001973","volume":"13","author":"M Black","year":"2016","unstructured":"Black M, Bhattacharya S, Philip S, Norman JE, McLernon DJ. Planned repeat cesarean section at term and adverse childhood health outcomes: a record-linkage study. Plos Med. 2016;13:e1001973.","journal-title":"Plos Med."},{"key":"729_CR81","doi-asserted-by":"publisher","DOI":"10.1001\/jamapediatrics.2017.0698","volume":"171","author":"RM Martin","year":"2017","unstructured":"Martin RM, Kramer MS, Patel R, Rifas-Shiman SL, Thompson J, Yang S, et al. Effects of promoting long-term, exclusive breastfeeding on adolescent adiposity, blood pressure, and growth trajectories: a secondary analysis of a randomized clinical trial. Jama Pediatr. 2017;171:e170698.","journal-title":"Jama Pediatr."},{"key":"729_CR82","doi-asserted-by":"publisher","first-page":"475","DOI":"10.1016\/S0140-6736(15)01024-7","volume":"387","author":"CG Victora","year":"2016","unstructured":"Victora CG, Bahl R, Barros AJ, Franca GV, Horton S, Krasevec J, et al. Breastfeeding in the 21st century: epidemiology, mechanisms, and lifelong effect. Lancet. 2016;387:475\u201390.","journal-title":"Lancet."},{"key":"729_CR83","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, et al. Bacteria, phages and pigs: the effects of in-feed antibiotics on the microbiome at different gut locations. Isme J. 2014;8:1566\u201376.","journal-title":"Isme J."},{"key":"729_CR84","doi-asserted-by":"publisher","first-page":"1222","DOI":"10.1038\/ismej.2011.181","volume":"6","author":"L Behrendt","year":"2012","unstructured":"Behrendt L, Larkum AW, Trampe E, Norman A, Sorensen SJ, Kuhl M. Microbial diversity of biofilm communities in microniches associated with the didemnid ascidian Lissoclinum patella. Isme J. 2012;6:1222\u201337.","journal-title":"Isme J."},{"key":"729_CR85","doi-asserted-by":"publisher","first-page":"D590","DOI":"10.1093\/nar\/gks1219","volume":"41","author":"C Quast","year":"2013","unstructured":"Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590\u20136.","journal-title":"Nucleic Acids Res."},{"key":"729_CR86","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1038\/nmeth.f.303","volume":"7","author":"JG Caporaso","year":"2010","unstructured":"Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335\u20136.","journal-title":"Nat Methods."},{"key":"729_CR87","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0009490","volume":"5","author":"MN Price","year":"2010","unstructured":"Price MN, Dehal PS, Arkin AP. FastTree 2--approximately maximum-likelihood trees for large alignments. Plos One. 2010;5:e9490.","journal-title":"Plos One."},{"key":"729_CR88","doi-asserted-by":"publisher","first-page":"169","DOI":"10.1038\/ismej.2010.133","volume":"5","author":"C Lozupone","year":"2011","unstructured":"Lozupone C, Lladser ME, Knights D, Stombaugh J, Knight R. UniFrac: an effective distance metric for microbial community comparison. Isme J. 2011;5:169\u201372.","journal-title":"Isme J."},{"key":"729_CR89","doi-asserted-by":"publisher","first-page":"559","DOI":"10.3390\/nu9060559","volume":"9","author":"H Liu","year":"2017","unstructured":"Liu H, Hou C, Wang G, Jia H, Yu H, Zeng X, et al. Lactobacillus reuteri I5007 modulates intestinal host defense peptide expression in the model of IPEC-J2 cells and neonatal piglets. Nutrients. 2017;9:559.","journal-title":"Nutrients."},{"key":"729_CR90","doi-asserted-by":"publisher","first-page":"402","DOI":"10.1006\/meth.2001.1262","volume":"25","author":"KJ Livak","year":"2001","unstructured":"Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2\u2212\u0394\u0394CT method. Methods. 2001;25:402\u20138.","journal-title":"Methods."},{"key":"729_CR91","doi-asserted-by":"publisher","first-page":"3123","DOI":"10.1093\/bioinformatics\/btu494","volume":"30","author":"DH Parks","year":"2014","unstructured":"Parks DH, Tyson GW, Hugenholtz P, Beiko RG. STAMP: statistical analysis of taxonomic and functional profiles. Bioinformatics. 2014;30:3123\u20134.","journal-title":"Bioinformatics."},{"key":"729_CR92","doi-asserted-by":"publisher","first-page":"1764","DOI":"10.1111\/j.1365-2222.2007.02849.x","volume":"37","author":"MM Gr\u00f6nlund","year":"2007","unstructured":"Gr\u00f6nlund MM, Gueimonde M, Laitinen K, Kociubinski G, Gr\u00f6nroos T, Salminen S, et al. Maternal breast-milk and intestinal bifidobacteria guide the compositional development of the Bifidobacterium microbiota in infants at risk of allergic disease. Clin Exper Allergy. 2007;37:1764\u201372.","journal-title":"Clin Exper Allergy."},{"key":"729_CR93","doi-asserted-by":"publisher","first-page":"2688","DOI":"10.1093\/bioinformatics\/btl446","volume":"22","author":"A Stamatakis","year":"2006","unstructured":"Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006;22:2688\u201390.","journal-title":"Bioinformatics."},{"key":"729_CR94","doi-asserted-by":"crossref","unstructured":"Flemer B, Lynch DB, Brown JMR, Jeffery IB, Ryan FJ, Claesson MJ, et al. Tumour-associated and non-tumour-associated microbiota in colorectal cancer. Gut. 2016:2015\u2013309595.","DOI":"10.1136\/gutjnl-2015-309595"},{"key":"729_CR95","doi-asserted-by":"publisher","first-page":"208","DOI":"10.1164\/rccm.201607-1525OC","volume":"196","author":"Y Huang","year":"2017","unstructured":"Huang Y, Ma SF, Espindola MS, Vij R, Oldham JM, Huffnagle GB, et al. Microbes are associated with host innate immune response in idiopathic pulmonary fibrosis. Am J Respir Crit Care Med. 2017;196:208\u201319.","journal-title":"Am J Respir Crit Care Med."},{"key":"729_CR96","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1004226","volume":"11","author":"ZD Kurtz","year":"2015","unstructured":"Kurtz ZD, M\u00fcller CL, Miraldi ER, Littman DR, Blaser MJ, Bonneau RA. Sparse and compositionally robust inference of microbial ecological networks. Plos Comput Biol. 2015;11:e1004226.","journal-title":"Plos Comput Biol."},{"key":"729_CR97","unstructured":"Bastian M, Heymann S, Jacomy M. Gephi: an open source software for exploring and manipulating networks. International AAAI Conference on Web and Social Nedia. 2014; https:\/\/www.aaai.org\/ocs\/index.php\/ICWSM\/09\/paper\/view\/154."},{"key":"729_CR98","unstructured":"Liu H, Zeng X, Zhang G, Hou C, Li N, Yu H, Shang L, Zhang X, Paolo T, Yang F, Liu Z, Qiao S, Biehl LM, Vogel W, D\u00f6rfel D, Hamprecht A, Seifert H, Autenrieth IB, Peter S. Maternal milk and fecal microbes guide the spatiotemporal development of mucosa-associated microbiota and barrier function in the neonatal gut. NCBI repository with study accession number PRJNA524979."},{"key":"729_CR99","unstructured":"Liu H, Zeng X, Zhang G, Hou C, Li N, Yu H, Shang L, Zhang X, Paolo T, Yang F, Liu Z, Qiao S. Biehl LM, Vogel W, D\u00f6rfel D, Hamprecht A, Seifert H, Autenrieth IB, Peter S. Maternal milk and fecal microbes guide the spatiotemporal development of mucosa-associated microbiota and barrier function in the neonatal gut. NCBI repository with study accession number PRJNA480348."}],"container-title":["BMC Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12915-019-0729-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12915-019-0729-2\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12915-019-0729-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,12,16]],"date-time":"2020-12-16T19:30:21Z","timestamp":1608147021000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbiol.biomedcentral.com\/articles\/10.1186\/s12915-019-0729-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,12]]},"references-count":99,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2019,12]]}},"alternative-id":["729"],"URL":"https:\/\/doi.org\/10.1186\/s12915-019-0729-2","relation":{},"ISSN":["1741-7007"],"issn-type":[{"value":"1741-7007","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,12]]},"assertion":[{"value":"15 July 2019","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"28 November 2019","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 December 2019","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"All animal procedures reported in this study were approved by the China Agricultural University Institutional Animal Care and Use Committee under Protocol number CAU20161110-2.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"106"}}