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The mode of delivery shows significant impact on microbial development and, thus, the initiation of the tryptophan catabolism pathway. Further antibiotics (ATB) treatment of mothers before or during delivery affects the microbial and tryptophan metabolite composition of stool of the caesarean- and vaginal-delivered newborns. The determination of microbiome and levels of tryptophan microbial metabolites in meconium and stool can characterize intestinal colonization of a newborn. From 134 samples from the Central European Longitudinal Studies of Parents and Children: The Next Generation (CELSPAC: TNG) cohort study, 16S rRNA gene sequencing was performed, and microbial tryptophan metabolites were quantified using ultra-high-performance liquid chromatography with triple-quadrupole mass spectrometry. Microbial diversity and concentrations of tryptophan metabolites were significantly higher in stool compared to meconium. Treatment of mothers with ATB before or during delivery affects metabolite composition and microbial diversity in stool of vaginal- and caesarean-delivered newborns. Correlation of microbial and metabolite composition shows significant positive correlations of indol-3-lactic acid, <jats:italic>N<\/jats:italic>-acetyl-tryptophan and indol-3-acetic acid with <jats:italic>Bifidobacterium<\/jats:italic>, <jats:italic>Bacteroides<\/jats:italic> and <jats:italic>Peptoclostridium<\/jats:italic>. The positive effect of vaginal delivery on newborns\u2019 microbiome development is degraded when mother is treated with ATB before or during delivery.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Key points<\/jats:title>\n            <jats:p>\u2022 <jats:italic>Antibiotic treatment diminishes the positive effects of vaginal delivery.<\/jats:italic>\n            <\/jats:p>\n            <jats:p>\u2022 <jats:italic>Antibiotic treatment affects metabolite and microbial composition in newborns.<\/jats:italic>\n            <\/jats:p>\n            <jats:p>\u2022 <jats:italic>Bifidobacterium and Peptoclostridium could be the producer of indole-lactic acid.<\/jats:italic>\n            <\/jats:p>\n          <\/jats:sec>","DOI":"10.1007\/s00253-024-13339-4","type":"journal-article","created":{"date-parts":[[2024,11,5]],"date-time":"2024-11-05T19:01:42Z","timestamp":1730833302000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Fecal tryptophan metabolite profiling in newborns in relation to microbiota and antibiotic treatment"],"prefix":"10.1007","volume":"108","author":[{"given":"Anne-Christine","family":"Aust","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Veronika","family":"Vidova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katerina","family":"Coufalikova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sona","family":"Smetanova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kristyna","family":"Kozeluhova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lenka","family":"Micenkova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Petra","family":"Videnska","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stanislav","family":"Smatana","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eva","family":"Budinska","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ivo","family":"Borek","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Petr","family":"Janku","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jana","family":"Klanova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zdenek","family":"Spacil","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9474-2133","authenticated-orcid":false,"given":"Vojtech","family":"Thon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,11,5]]},"reference":[{"key":"13339_CR1","doi-asserted-by":"publisher","DOI":"10.1007\/978-94-009-4109-0","volume-title":"The statistical analysis of compositional data","author":"J Aitchison","year":"1986","unstructured":"Aitchison J (1986) The statistical analysis of compositional data. 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