Bacterial colonization reprograms the neonatal gut metabolome.
Kyle Bittinger,Chunyu Zhao,Yun Li,Eileen G Ford,Elliot S. Friedman,Josephine Ni,Chiraag Kulkarni,Jingwei Cai,Yuan Tian,Qing Liu,Andrew D. Patterson,Debolina Sarkar,Siu Hung Joshua Chan,Costas D. Maranas,Anumita Saha-Shah,Peder J. Lund,Benjamin A. Garcia,Lisa M. Mattei,Jeffrey S. Gerber,Michal A. Elovitz,Andrea Kelly,Patricia A. DeRusso,Dorothy Kim,Casey E. Hofstaedter,Mark Goulian,Hongzhe Li,Frederic D. Bushman,Babette S. Zemel,Gary D. Wu +28 more
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TLDR
It is shown that the gut is detectably colonized within 16 h of birth, with Escherichia coli dominating, and that this correlates with proteome and metabolome changes including the fermentation of amino acids, which provides a mechanism for the initial growth of E. coli under anaerobic conditions.Abstract:
Initial microbial colonization and later succession in the gut of human infants are linked to health and disease later in life. The timing of the appearance of the first gut microbiome, and the consequences for the early life metabolome, are just starting to be defined. Here, we evaluated the gut microbiome, proteome and metabolome in 88 African-American newborns using faecal samples collected in the first few days of life. Gut bacteria became detectable using molecular methods by 16 h after birth. Detailed analysis of the three most common species, Escherichia coli, Enterococcus faecalis and Bacteroides vulgatus, did not suggest a genomic signature for neonatal gut colonization. The appearance of bacteria was associated with reduced abundance of approximately 50 human proteins, decreased levels of free amino acids and an increase in products of bacterial fermentation, including acetate and succinate. Using flux balance modelling and in vitro experiments, we provide evidence that fermentation of amino acids provides a mechanism for the initial growth of E. coli, the most common early colonizer, under anaerobic conditions. These results provide a deep characterization of the first microbes in the human gut and show how the biochemical environment is altered by their appearance. Using a multi-omics approach to analyse meconium and stool samples from babies during the first few days of life, the authors show that the gut is detectably colonized within 16 h of birth, with Escherichia coli dominating, and that this correlates with proteome and metabolome changes including the fermentation of amino acids.read more
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Key bacterial taxa and metabolic pathways affecting gut short-chain fatty acid profiles in early life
Naoki Tsukuda,Kana Yahagi,Taeko Hara,Yohei Watanabe,Hoshitaka Matsumoto,Hiroshi Mori,Koichi Higashi,Hirokazu Tsuji,Satoshi Matsumoto,Ken Kurokawa,Takahiro Matsuki +10 more
TL;DR: In this paper, the authors investigated dense longitudinally collected faecal samples from 12 subjects during the first 2 years to identify early life short-chain fatty acids (SCFAs) patterns and their relationships with the microbiota.
Journal ArticleDOI
Fetal meconium does not have a detectable microbiota before birth.
Katherine M. Kennedy,Max J. Gerlach,Thomas Adam,Markus M. Heimesaat,Laura Rossi,Michael G. Surette,Deborah M. Sloboda,Thorsten Braun +7 more
TL;DR: In this paper, the authors investigated whether bacteria could be detected in meconium before birth and concluded that fetal colonisation of healthy term infants does not occur before birth, indicating that colonization occurs during and after birth.
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Modulation of immune responses to vaccination by the microbiota: implications and potential mechanisms
TL;DR: In this paper, the authors synthesize this evidence, discuss the immunological mechanisms that potentially mediate these effects and consider the potential of microbiota-targeted interventions to optimize vaccine effectiveness.
Journal ArticleDOI
Oral administration of maternal vaginal microbes at birth to restore gut microbiome development in infants born by caesarean section: A pilot randomised placebo-controlled trial.
Brooke C. Wilson,Éadaoin M. Butler,Celia P. Grigg,José G. B. Derraik,Valentina Chiavaroli,Nicholas Walker,Suma Thampi,Christine Creagh,Abigail J. Reynolds,Tommi Vatanen,Tommi Vatanen,Justin M. O'Sullivan,Wayne S. Cutfield,Wayne S. Cutfield +13 more
TL;DR: In this paper, the authors investigated whether oral administration of maternal vaginal microbiota to infants born by caesarean section (CS) could restore their gut microbiome development in a pilot single-blinded, randomised placebo-controlled trial.
Journal ArticleDOI
Neonatal intestinal dysbiosis.
TL;DR: Strong circumstantial evidence and limited confirmations of causality suggest that dysbiosis early in life can influence the health of the infant acutely, as well as contribute to disease susceptibility later in life.
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