{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T15:55:54Z","timestamp":1790178954749,"version":"4.1.0"},"reference-count":34,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2018,10,23]],"date-time":"2018-10-23T00:00:00Z","timestamp":1540252800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2018,10,23]],"date-time":"2018-10-23T00:00:00Z","timestamp":1540252800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Research on the neonatal microbiome has been performed mostly on hospital-born infants, who often undergo multiple birth-related interventions. Both the hospital environment and interventions around the time of birth may affect the neonate microbiome. In this study, we determine the structure of the microbiota in feces from babies born in the hospital or at home, and from vaginal samples of their mothers. We included 35 vaginally-born, breast-fed neonates, 14 of whom delivered at home (4 in water), and 21 who delivered in the hospital. Feces from babies and mothers and maternal vaginal swab samples were collected at enrollment, the day of birth, followed by days 1, 2, 7, 14, 21, and 28. At the time of birth, the diversity of the vaginal microbiota of mothers delivering in the hospital was lower than in mothers delivering at home, and showed higher proportion of\n                    <jats:italic>Lactobacillus<\/jats:italic>\n                    . Among 20 infants not exposed to perinatal maternal antibiotics or water birth, fecal beta diversity differed significantly by birth site, with hospital-born infants having lower\n                    <jats:italic>Bacteroides<\/jats:italic>\n                    ,\n                    <jats:italic>Bifidobacterium<\/jats:italic>\n                    ,\n                    <jats:italic>Streptococcus<\/jats:italic>\n                    , and\n                    <jats:italic>Lactobacillus<\/jats:italic>\n                    , and higher\n                    <jats:italic>Clostridium<\/jats:italic>\n                    and\n                    <jats:italic>Enterobacteriaceae<\/jats:italic>\n                    family (LDA\u2009&gt;\u20093.0), than babies born at home. At 1 month of age, feces from infants born in the hospital also induced greater pro-inflammatory gene expression (\n                    <jats:italic>TLR4<\/jats:italic>\n                    ,\n                    <jats:italic>IL-8<\/jats:italic>\n                    ,\n                    <jats:italic>occludin<\/jats:italic>\n                    and\n                    <jats:italic>TGF\u03b2<\/jats:italic>\n                    ) in human colon epithelial HT-29 cells. The results of this work suggest that hospitalization (perinatal interventions or the hospital environment) may affect the microbiota of the vaginal source and the initial colonization during labor and birth, with effects that could persist in the intestinal microbiota of infants 1 month after birth. More research is needed to determine specific factors that alter bacterial transmission between mother and baby and the long-term health implications of these differences for the developing infant.\n                  <\/jats:p>","DOI":"10.1038\/s41598-018-33995-7","type":"journal-article","created":{"date-parts":[[2018,10,17]],"date-time":"2018-10-17T10:58:52Z","timestamp":1539773932000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":49,"title":["Differences in the fecal microbiota of neonates born at home or in the hospital"],"prefix":"10.1038","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3163-9467","authenticated-orcid":false,"given":"Joan L.","family":"Combellick","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7615-9809","authenticated-orcid":false,"given":"Hakdong","family":"Shin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dongjae","family":"Shin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi","family":"Cai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Holly","family":"Hagan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Corey","family":"Lacher","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Din L.","family":"Lin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kathryn","family":"McCauley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susan V.","family":"Lynch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria Gloria","family":"Dominguez-Bello","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2018,10,23]]},"reference":[{"key":"33995_CR1","doi-asserted-by":"publisher","first-page":"11971","DOI":"10.1073\/pnas.1002601107","volume":"107","author":"MG Dominguez-Bello","year":"2010","unstructured":"Dominguez-Bello, M. G. et al. Delivery mode shapes the acquisition and structure of the primordial microbiota across multiple body habitats in newborns. Proceedings of the National Academy of Sciences of the United States of America 107, 11971\u201311975, https:\/\/doi.org\/10.1073\/pnas.1002601107 (2010).","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"33995_CR2","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-015-0126-1","volume":"3","author":"H Shin","year":"2015","unstructured":"Shin, H. et al. The first microbial environment of infants born by C-section: the operating room microbes. Microbiome 3, 59, https:\/\/doi.org\/10.1186\/s40168-015-0126-1 (2015).","journal-title":"Microbiome"},{"key":"33995_CR3","doi-asserted-by":"publisher","first-page":"629","DOI":"10.1111\/j.1365-2222.2007.02780.x","volume":"38","author":"S Thavagnanam","year":"2007","unstructured":"Thavagnanam, S., Fleming, J., Bromely, A., Shields, M. D. & Cardwell, C. R. A meta-analysis of the association between Caesarean section and childhood asthma. Clinical and Experimental Allergy 38, 629\u2013633 (2007).","journal-title":"Clinical and Experimental Allergy"},{"key":"33995_CR4","doi-asserted-by":"crossref","unstructured":"Azad, M. B. & Kozyrskyj, A. L. Perinatal programming of asthma: the role of gut microbiota. Clinical and Developmental Immunology, 1\u20139 (2012).","DOI":"10.1155\/2012\/932072"},{"key":"33995_CR5","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1053\/j.gastro.2011.09.047","volume":"142","author":"K Marild","year":"2012","unstructured":"Marild, K., Stephansson, O., Montgomery, S., Murray, J. A. & Ludvigsson, J. F. Pregnancy outcome and risk of celiac disease in offspring: a nationwide case-control study. Gastroenterology 142, 39\u201345 e33, https:\/\/doi.org\/10.1053\/j.gastro.2011.09.047 (2012).","journal-title":"Gastroenterology"},{"key":"33995_CR6","doi-asserted-by":"publisher","first-page":"601","DOI":"10.1016\/j.jaci.2013.05.043","volume":"132","author":"J Penders","year":"2013","unstructured":"Penders, J. et al. Establishment of the intestinal microbiota and its role for atopic dermatitis in early childhood. The Journal of allergy and clinical immunology 132, 601\u2013607.e608, https:\/\/doi.org\/10.1016\/j.jaci.2013.05.043 (2013).","journal-title":"The Journal of allergy and clinical immunology"},{"key":"33995_CR7","doi-asserted-by":"publisher","first-page":"e87896","DOI":"10.1371\/journal.pone.0087896","volume":"9","author":"K Darmasseelane","year":"2014","unstructured":"Darmasseelane, K., Hyde, M. J., Santhakumaran, S., Gale, C. & Modi, N. Mode of delivery and offspring body mass index, overweight and obesity in adult life: a systematic review and meta-analysis. PloS one 9, e87896, https:\/\/doi.org\/10.1371\/journal.pone.0087896 (2014).","journal-title":"PloS one"},{"key":"33995_CR8","doi-asserted-by":"publisher","first-page":"665","DOI":"10.1038\/ijo.2014.180","volume":"39","author":"NT Mueller","year":"2015","unstructured":"Mueller, N. T. et al. Prenatal exposure to antibiotics, cesarean section and risk of childhood obesity. Int J Obes (Lond) 39, 665\u2013670, https:\/\/doi.org\/10.1038\/ijo.2014.180 (2015).","journal-title":"Int J Obes (Lond)"},{"key":"33995_CR9","doi-asserted-by":"crossref","unstructured":"Lax, S. et al. Bacterial colonization and succession in a newly opened hospital. Science Translational Medicine 9 (2017).","DOI":"10.1126\/scitranslmed.aah6500"},{"key":"33995_CR10","doi-asserted-by":"publisher","first-page":"511","DOI":"10.1542\/peds.2005-2824","volume":"118","author":"J Penders","year":"2006","unstructured":"Penders, J. et al. Factors influencing the composition of the intestinal microbiota in early infancy. Pediatrics 118, 511\u2013521, https:\/\/doi.org\/10.1542\/peds.2005-2824 (2006).","journal-title":"Pediatrics"},{"key":"33995_CR11","doi-asserted-by":"publisher","first-page":"250","DOI":"10.1038\/nm.4039","volume":"22","author":"MG Dominguez-Bello","year":"2016","unstructured":"Dominguez-Bello, M. G. et al. Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. Nat Med 22, 250\u2013253, https:\/\/doi.org\/10.1038\/nm.4039 (2016).","journal-title":"Nat Med"},{"key":"33995_CR12","doi-asserted-by":"publisher","first-page":"343ra382","DOI":"10.1126\/scitranslmed.aad7121","volume":"8","author":"NA Bokulich","year":"2016","unstructured":"Bokulich, N. A. et al. Antibiotics, birth mode, and diet shape microbiome maturation during early life. Sci Transl Med 8, 343ra382, https:\/\/doi.org\/10.1126\/scitranslmed.aad7121 (2016).","journal-title":"Sci Transl Med"},{"key":"33995_CR13","doi-asserted-by":"publisher","first-page":"332","DOI":"10.1007\/BF01647733","volume":"15","author":"R Bennet","year":"1987","unstructured":"Bennet, R. & Nord, C. E. Development of the faecal anaerobic microflora after caesarean section and treatment with antibiotics in newborn infants. Infection 15, 332\u2013336 (1987).","journal-title":"Infection"},{"key":"33995_CR14","doi-asserted-by":"publisher","first-page":"6051","DOI":"10.1007\/s00253-014-5712-9","volume":"98","author":"I Aloisio","year":"2014","unstructured":"Aloisio, I. et al. Influence of intrapartum antibiotic prophylaxis against group B Streptococcus on the early newborn gut composition and evaluation of the anti-Streptococcus activity of Bifidobacterium strains. Applied microbiology and biotechnology 98, 6051\u20136060, https:\/\/doi.org\/10.1007\/s00253-014-5712-9 (2014).","journal-title":"Applied microbiology and biotechnology"},{"key":"33995_CR15","doi-asserted-by":"publisher","first-page":"212","DOI":"10.1001\/jamapediatrics.2015.3732","volume":"170","author":"JC Madan","year":"2016","unstructured":"Madan, J. C. et al. Association of Cesarean Delivery and Formula Supplementation With the Intestinal Microbiome of 6-Week-Old Infants. JAMA pediatrics 170, 212\u2013219, https:\/\/doi.org\/10.1001\/jamapediatrics.2015.3732 (2016).","journal-title":"JAMA pediatrics"},{"key":"33995_CR16","doi-asserted-by":"publisher","first-page":"478","DOI":"10.1016\/j.anaerobe.2011.03.009","volume":"17","author":"E Bezirtzoglou","year":"2011","unstructured":"Bezirtzoglou, E., Tsiotsias, A. & Welling, G. W. Microbiota profile in feces of breast- and formula-fed newborns by using fluorescence in situ hybridization (FISH). Anaerobe 17, 478\u2013482, https:\/\/doi.org\/10.1016\/j.anaerobe.2011.03.009 (2011).","journal-title":"Anaerobe"},{"key":"33995_CR17","doi-asserted-by":"publisher","first-page":"2199","DOI":"10.1042\/cs20160349","volume":"130","author":"LT Stiemsma","year":"2016","unstructured":"Stiemsma, L. T. et al. Shifts in Lachnospira and Clostridium sp. in the 3-month stool microbiome are associated with preschool age asthma. Clinical science (London, England: 1979) 130, 2199\u20132207, https:\/\/doi.org\/10.1042\/cs20160349 (2016).","journal-title":"Clinical science (London, England: 1979)"},{"issue":"5","key":"33995_CR18","doi-asserted-by":"publisher","first-page":"948-955.e3","DOI":"10.1016\/j.jaci.2011.07.027","volume":"128","author":"Frederika A. van Nimwegen","year":"2011","unstructured":"van Nimwegen, F. A. et al. Mode and place of delivery, gastrointestinal microbiota, and their influence on asthma and atopy. The Journal of allergy and clinical immunology 128, 948\u2013955. e941\u2013943, https:\/\/doi.org\/10.1016\/j.jaci.2011.07.027 (2011).","journal-title":"Journal of Allergy and Clinical Immunology"},{"key":"33995_CR19","doi-asserted-by":"publisher","first-page":"1187","DOI":"10.1038\/nm.4176","volume":"22","author":"KE Fujimura","year":"2016","unstructured":"Fujimura, K. E. et al. Neonatal gut microbiota associates with childhood multisensitized atopy and T cell differentiation. Nat Med 22, 1187\u20131191, https:\/\/doi.org\/10.1038\/nm.4176 (2016).","journal-title":"Nat Med"},{"key":"33995_CR20","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1111\/j.1753-4887.2011.00388.x","volume":"69","author":"E Hosseini","year":"2011","unstructured":"Hosseini, E., Grootaert, C., Verstraete, W. & Van de Wiele, T. Propionate as a health-promoting microbial metabolite in the human gut. Nutrition reviews 69, 245\u2013258, https:\/\/doi.org\/10.1111\/j.1753-4887.2011.00388.x (2011).","journal-title":"Nutrition reviews"},{"key":"33995_CR21","unstructured":"NICE. Intrapartum care: care of healthy women and babies during childbirth. (United Kingdom 2014)."},{"key":"33995_CR22","doi-asserted-by":"publisher","first-page":"473","DOI":"10.1111\/ped.13168","volume":"59","author":"K Hasegawa","year":"2017","unstructured":"Hasegawa, K. et al. Household siblings and nasal and fecal microbiota in infants. Pediatrics international: official journal of the Japan Pediatric Society 59, 473\u2013481, https:\/\/doi.org\/10.1111\/ped.13168 (2017).","journal-title":"Pediatrics international: official journal of the Japan Pediatric Society"},{"key":"33995_CR23","first-page":"352","volume":"11","author":"DK Gardner","year":"1992","unstructured":"Gardner, D. K., Gabbe, S. G. & Harter, C. Simultaneous concentrations of ciprofloxacin in breast milk and in serum in mother and breast-fed infant. Clinical pharmacy 11, 352\u2013354 (1992).","journal-title":"Clinical pharmacy"},{"key":"33995_CR24","doi-asserted-by":"publisher","DOI":"10.1038\/srep08988","volume":"5","author":"DA MacIntyre","year":"2015","unstructured":"MacIntyre, D. A. et al. The vaginal microbiome during pregnancy and the postpartum period in a European population. Scientific Reports 5, 8988, https:\/\/doi.org\/10.1038\/srep08988 (2015).","journal-title":"Scientific Reports"},{"key":"33995_CR25","doi-asserted-by":"publisher","first-page":"361","DOI":"10.2147\/IJWH.S55561","volume":"7","author":"R Zielinski","year":"2015","unstructured":"Zielinski, R., Ackerson, K. & Kane Low, L. Planned home birth: benefits, risks, and opportunities. International Journal of Women\u2019s Health 7, 361\u2013377, https:\/\/doi.org\/10.2147\/IJWH.S55561 (2015).","journal-title":"International Journal of Women\u2019s Health"},{"key":"33995_CR26","doi-asserted-by":"publisher","first-page":"307ra152","DOI":"10.1126\/scitranslmed.aab2271","volume":"7","author":"MC Arrieta","year":"2015","unstructured":"Arrieta, M. C. et al. Early infancy microbial and metabolic alterations affect risk of childhood asthma. Sci Transl Med 7, 307ra152, https:\/\/doi.org\/10.1126\/scitranslmed.aab2271 (2015).","journal-title":"Sci Transl Med"},{"issue":"7681","key":"33995_CR27","doi-asserted-by":"publisher","first-page":"457","DOI":"10.1038\/nature24621","volume":"551","author":"Luke R. Thompson","year":"2017","unstructured":"Thompson, L. R. et al. A communal catalogue reveals Earth\u2019s multiscale microbial diversity. Nature, https:\/\/doi.org\/10.1038\/nature24621 (2017).","journal-title":"Nature"},{"key":"33995_CR28","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1038\/Nmeth.F.303","volume":"7","author":"JG Caporaso","year":"2010","unstructured":"Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7, 335\u2013336, https:\/\/doi.org\/10.1038\/Nmeth.F.303 (2010).","journal-title":"Nat Methods"},{"key":"33995_CR29","doi-asserted-by":"publisher","first-page":"5069","DOI":"10.1128\/AEM.03006-05","volume":"72","author":"TZ DeSantis","year":"2006","unstructured":"DeSantis, T. Z. et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72, 5069\u20135072 (2006).","journal-title":"Appl Environ Microbiol"},{"key":"33995_CR30","doi-asserted-by":"publisher","first-page":"2460","DOI":"10.1093\/bioinformatics\/btq461","volume":"26","author":"RC Edgar","year":"2010","unstructured":"Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460\u20132461, https:\/\/doi.org\/10.1093\/bioinformatics\/btq461 (2010).","journal-title":"Bioinformatics"},{"key":"33995_CR31","doi-asserted-by":"publisher","first-page":"266","DOI":"10.1093\/bioinformatics\/btp636","volume":"26","author":"JG Caporaso","year":"2010","unstructured":"Caporaso, J. G. et al. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26, 266\u2013267, https:\/\/doi.org\/10.1093\/bioinformatics\/btp636 (2010).","journal-title":"Bioinformatics"},{"key":"33995_CR32","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2011-12-6-r60","volume":"12","author":"N Segata","year":"2011","unstructured":"Segata, N. et al. Metagenomic biomarker discovery and explanation. Genome biology 12, R60, https:\/\/doi.org\/10.1186\/gb-2011-12-6-r60 (2011).","journal-title":"Genome biology"},{"key":"33995_CR33","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-03157-4","volume":"9","author":"J Durack","year":"2018","unstructured":"Durack, J. et al. Delayed gut microbiota development in high-risk for asthma infants is temporarily modifiable by Lactobacillus supplementation. Nature communications 9, 707, https:\/\/doi.org\/10.1038\/s41467-018-03157-4 (2018).","journal-title":"Nature communications"},{"key":"33995_CR34","doi-asserted-by":"publisher","first-page":"402","DOI":"10.1006\/meth.2001.1262","volume":"25","author":"KJ Livak","year":"2001","unstructured":"Livak, K. J. & Schmittgen, T. D. Analysis of relative gene expression data using real-time quantitative PCR and the 2(\u2212Delta Delta C(T)) Method. Methods (San Diego, Calif.) 25, 402\u2013408, https:\/\/doi.org\/10.1006\/meth.2001.1262 (2001).","journal-title":"Methods (San Diego, Calif.)"}],"updated-by":[{"DOI":"10.1038\/s41598-019-44426-6","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2019,6,18]],"date-time":"2019-06-18T00:00:00Z","timestamp":1560816000000}}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41598-018-33995-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-018-33995-7","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-018-33995-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,12,21]],"date-time":"2022-12-21T05:47:37Z","timestamp":1671601657000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41598-018-33995-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,10,23]]},"references-count":34,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2018,12]]}},"alternative-id":["33995"],"URL":"https:\/\/doi.org\/10.1038\/s41598-018-33995-7","relation":{"is-basis-for":[{"id-type":"doi","id":"10.52843\/cassyni.rl5mr2","asserted-by":"object"}]},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,10,23]]},"assertion":[{"value":"24 April 2018","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 October 2018","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 October 2018","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 June 2019","order":4,"name":"change_date","label":"Change Date","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Correction","order":5,"name":"change_type","label":"Change Type","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.","order":6,"name":"change_details","label":"Change Details","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"M.G.D.B. has intellectual property, equity and is a SAB member of CommenSe. Other authors have no competing interests as defined by Nature Research, or other interests that might be perceived to influence the results and\/or discussion reported in this paper.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing Interests"}}],"article-number":"15660"}}