期刊
NATURE MICROBIOLOGY
卷 5, 期 6, 页码 838-+出版社
NATURE PORTFOLIO
DOI: 10.1038/s41564-020-0694-0
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资金
- American Beverage Foundation for a Healthy America
- Research Institute of the Children's Hospital of Philadelphia
- PennCHOP Microbiome Program
- Pennsylvania State University Department of Chemical Engineering
- USDA National Institute of Food and Agriculture [PEN04607, 1009993]
- Pennsylvania Department of Health
- NIH National Center for Research Resources Clinical and Translational Science Program [UL1TR001878]
- National Institute of Digestive Diseases and Disorders of the Kidney [R01DK107565]
- Tobacco Formula grant under the Commonwealth Universal Research Enhancement program [SAP 4100068710]
- Human-Microbial Analytic and Repository Core of the Center for Molecular Studies in Digestive and Liver Disease [P30 DK050306]
- American Gastroenterological Association
- Howard Hughes Medical Institute Medical Fellowship
- Crohn's and Colitis Foundation
- Center for Bioenergy Innovation [DE-AC05-00OR22725]
- Research Electronic Data Capture (REDCap)
- NIH [2T32CA009140]
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.
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