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.
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Data availability
Shotgun metagenomic sequence data are available from the NCBI Sequence Read Archive under accession SRP217052. Proteomics and metabolomics data are deposited on Zenodo at https://doi.org/10.5281/zenodo.3576595. Source data for Figs. 1–5 and Extended Data Figs. 1–8 are provided with the paper.
Code availability
Source code for analysis is available on GitHub at http://github.com/kylebittinger/neonatal-gut-colonization
References
Yatsunenko, T. et al. Human gut microbiome viewed across age and geography. Nature 486, 222–227 (2012).
Stewart, C. J. et al. Temporal development of the gut microbiome in early childhood from the TEDDY study. Nature 562, 583–588 (2018).
Yassour, M. et al. Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability. Sci. Transl. Med. 8, 343ra81 (2016).
Bokulich, N. A. et al. Antibiotics, birth mode, and diet shape microbiome maturation during early life. Sci. Transl. Med. 8, 343ra82 (2016).
Wang, J. et al. Dysbiosis of maternal and neonatal microbiota associated with gestational diabetes mellitus. Gut 67, 1614–1625 (2018).
Durack, J. et al. Delayed gut microbiota development in high-risk for asthma infants is temporarily modifiable by Lactobacillus supplementation. Nat. Commun. 9, 707 (2018).
Grier, A. et al. Impact of prematurity and nutrition on the developing gut microbiome and preterm infant growth. Microbiome 5, 158 (2017).
Mueller, N. T. et al. Delivery mode and the transition of pioneering gut-microbiota structure, composition and predicted metabolic function. Genes 8, (2017).
Dobbler, P. T. et al. Low microbial diversity and abnormal microbial succession is associated with necrotizing enterocolitis in preterm infants. Front. Microbiol. 8, 2243 (2017).
Brazier, L. et al. Evolution in fecal bacterial/viral composition in infants of two central African countries (Gabon and Republic of the Congo) during their first month of life. PLoS ONE 12, e0185569 (2017).
Wampach, L. et al. Colonization and succession within the human gut microbiome by archaea, bacteria, and microeukaryotes during the first year of life. Front. Microbiol. 8, 738 (2017).
Chu, D. M. et al. Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery. Nat. Med. 23, 314–326 (2017).
Chu, D. M. et al. The early infant gut microbiome varies in association with a maternal high-fat diet. Genome Med. 8, 77 (2016).
Collado, M. C., 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. 6, 23129 (2016).
Heida, F. H. et al. A necrotizing enterocolitis-associated gut microbiota is present in the meconium: results of a prospective study. Clin. Infect. Dis. 62, 863–870 (2016).
Gómez, M. et al. Early gut colonization of preterm infants: effect of enteral feeding tubes. J. Pediatr. Gastroenterol. Nutr. 62, 893–900 (2016).
Hansen, R. et al. First-pass meconium samples from healthy term vaginally-delivered neonates: an analysis of the microbiota. PLoS ONE 10, e0133320 (2015).
Dutta, S., Ganesh, M., Ray, P. & Narang, A. Intestinal colonization among very low birth weight infants in first week of life. Indian Pediatr. 51, 807–809 (2014).
Ardissone, A. N. et al. Meconium microbiome analysis identifies bacteria correlated with premature birth. PLoS ONE 9, e90784 (2014).
Hu, J. et al. Diversified microbiota of meconium is affected by maternal diabetes status. PLoS ONE 8, e78257 (2013).
Moles, L. et al. Bacterial diversity in meconium of preterm neonates and evolution of their fecal microbiota during the first month of life. PLoS ONE 8, e66986 (2013).
Nagpal, R. et al. Sensitive quantitative analysis of the meconium bacterial microbiota in healthy term infants born vaginally or by cesarean section. Front. Microbiol. 7, (2016).
Lim, E. S. et al. Early life dynamics of the human gut virome and bacterial microbiome in infants. Nat. Med. 21, 1228–1234 (2015).
Bäckhed, F. et al. Dynamics and stabilization of the human gut microbiome during the first year of life. Cell Host Microbe 17, 690–703 (2015).
La Rosa, P. S. et al. Patterned progression of bacterial populations in the premature infant gut. Proc. Natl Acad. Sci. USA 111, 12522–12527 (2014).
Del Chierico, F. et al. Phylogenetic and metabolic tracking of gut microbiota during perinatal development. PLoS ONE 10, e0137347 (2015).
Zwittink, R. D. et al. Metaproteomics reveals functional differences in intestinal microbiota development of preterm infants. Mol. Cell. Proteomics 16, 1610–1620 (2017).
Xiong, W., Brown, C. T., Morowitz, M. J., Banfield, J. F. & Hettich, R. L. Genome-resolved metaproteomic characterization of preterm infant gut microbiota development reveals species-specific metabolic shifts and variabilities during early life. Microbiome 5, 72 (2017).
Young, J. C. et al. Metaproteomics reveals functional shifts in microbial and human proteins during a preterm infant gut colonization case. Proteomics 15, 3463–3473 (2015).
Dominguez-Bello, M. G., Blaser, M. J., Ley, R. E. & Knight, R. Development of the human gastrointestinal microbiota and insights from high-throughput sequencing. Gastroenterology 140, 1713–1719 (2011).
Sprockett, D., Fukami, T. & Relman, D. A. Role of priority effects in the early-life assembly of the gut microbiota. Nat. Rev. Gastroenterol. Hepatol. 15, 197–205 (2018).
Campbell, J. H. et al. UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota. Proc. Natl Acad. Sci. USA 110, 5540–5545 (2013).
Sakamori, R. et al. Cdc42 and Rab8a are critical for intestinal stem cell division, survival, and differentiation in mice. J. Clin. Invest. 122, 1052–1065 (2012).
Melendez, J. et al. Cdc42 coordinates proliferation, polarity, migration, and differentiation of small intestinal epithelial cells in mice. Gastroenterology 145, 808–819 (2013).
Kolachala, V. L. et al. Epithelial-derived fibronectin expression, signaling, and function in intestinal inflammation. J. Biol. Chem. 282, 32965–32973 (2007).
Cotter, P. A., Chepuri, V., Gennis, R. B. & Gunsalus, R. P. Cytochrome o (cyoABCDE) and d (cydAB) oxidase gene expression in Escherichia coli is regulated by oxygen, pH, and the fnr gene product. J. Bacteriol. 172, 6333–6338 (1990).
Unden, G. & Bongaerts, J. Alternative respiratory pathways of Escherichia coli: energetics and transcriptional regulation in response to electron acceptors. Biochim. Biophys. Acta 1320, 217–234 (1997).
Knorr, A. L., Jain, R. & Srivastava, R. Bayesian-based selection of metabolic objective functions. Bioinformatics 23, 351–357 (2007).
Yang, Y. et al. Relation between chemotaxis and consumption of amino acids in bacteria. Mol. Microbiol. 96, 1272–1282 (2015).
Friedman, E. S. et al. Microbes vs. chemistry in the origin of the anaerobic gut lumen. Proc. Natl Acad. Sci. USA 115, 4170–4175 (2018).
Lu, W. et al. Metabolomic analysis via reversed-phase ion-pairing liquid chromatography coupled to a stand alone orbitrap mass spectrometer. Anal. Chem. 82, 3212–3221 (2010).
Clasquin, M. F., Melamud, E. & Rabinowitz, J. D. LC-MS data processing with MAVEN: a metabolomic analysis and visualization engine. Curr. Protoc. Bioinformatics 37, 14.11.1–14.11.23 (2012).
Cai, J. et al. Orthogonal comparison of GC-MS and H NMR spectroscopy for short chain fatty acid quantitation. Anal. Chem. 89, 7900–7906 (2017).
Clarke, E. L. et al. Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments. Microbiome 7, 46 (2019).
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Truong, D. T. et al. MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nat. Methods 12, 902–903 (2015).
Li, D., Liu, C.-M., Luo, R., Sadakane, K. & Lam, T.-W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31, 1674–1676 (2015).
Eren, A. M. et al. Anvi’o: an advanced analysis and visualization platform for ‘omics data. PeerJ 3, e1319 (2015).
Scholz, M. et al. Strain-level microbial epidemiology and population genomics from shotgun metagenomics. Nat. Methods 13, 435–438 (2016).
Delmont, T. O. & Eren, A. M. Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies. PeerJ 4, e1839 (2016).
Li, J. et al. An integrated catalog of reference genes in the human gut microbiome. Nat. Biotechnol. 32, 834–841 (2014).
Apweiler, R. et al. UniProt: the Universal Protein knowledgebase. Nucleic Acids Res. 32, D115–D119 (2004).
Zhang, X. et al. MetaPro-IQ: a universal metaproteomic approach to studying human and mouse gut microbiota. Microbiome 4, 31 (2016).
Szklarczyk, D. et al. The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible. Nucleic Acids Res. 45, D362–D368 (2017).
Anderson, M. J. A new method for non-parametric multivariate analysis of variance. Austral Ecol. 26, 32–46 (2008).
Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. Royal Stat. Soc. Series B. 57, 289–300 (1995).
Acknowledgements
Partial funding was provided by an unrestricted donation from the American Beverage Foundation for a Healthy America to the Children’s Hospital of Philadelphia to support the Healthy Weight Program. This study was also supported by the Research Institute of the Children’s Hospital of Philadelphia, The PennCHOP Microbiome Program, the Pennsylvania State University Department of Chemical Engineering, the USDA National Institute of Food and Agriculture (project no. PEN04607, accession no. 1009993; to A.D.P.), the Pennsylvania Department of Health using Tobacco C.U.R.E. Funds (to A.D.P.), the NIH National Center for Research Resources Clinical and Translational Science Program (grant no. UL1TR001878), the National Institute of Digestive Diseases and Disorders of the Kidney (grant no. R01DK107565), a Tobacco Formula grant under the Commonwealth Universal Research Enhancement program (grant no. SAP 4100068710), Research Electronic Data Capture (REDCap), the Human-Microbial Analytic and Repository Core of the Center for Molecular Studies in Digestive and Liver Disease (grant no. P30 DK050306), the Research Scholar Award from the American Gastroenterological Association, the Howard Hughes Medical Institute Medical Fellowship, NIH 2T32CA009140 and Crohn’s and Colitis Foundation, and the Center for Bioenergy Innovation (grant no. DE-AC05-00OR22725). Special thanks go to the mothers and their infants who participated in this research study.
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Authors and Affiliations
Contributions
B.Z., G.D.W., M.A.E. and P.D. are responsible for the overall study design. E.F., A.K. and B.Z. performed clinical sampling. L.M.M., D.K. and C.E.H. carried out DNA sequencing and qPCR experiments. C.Z., K.B. and M.G. carried out bioinformatics analysis. A.S.-S., P.L. and B.A.G. carried out proteomics experiments and performed data analysis. J.C., Y.T., Q.L. and A.D.P. carried out metabolomics experiments and performed data analysis. D.S., S.H.J.C. and C.M. carried out metabolomic flux modelling. J.N. and E.S.F. carried out bacterial culture experiments and performed data analysis. K.B., Y.L., C.Z. and H.L. carried out statistical analysis. J.S.G., M.A.E., F.D.B., A.K. and P.D. provided critical guidance in the analysis and interpretation of results. K.B. and G.D.W. wrote the manuscript. F.D.B., B.Z., C.Z., Y.L., A.K., J.S.G., E.F., J.N., E.S.F., A.D.P., D.S., C.M. and L.M.M. revised the manuscript. B.Z. and G.D.W. managed the project.
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Extended data
Extended Data Fig. 1 Microbiota differences between birth and 1 month.
a, The number of bacterial species increased in the 1 month samples (P = 8×10−16, two-sided Wilcoxon signed-rank test, n = 88 per group). Boxes indicate the median and interquartile distance, whiskers indicate maximum and minimum data points within 1.5 times the interquartile range, points represent values outside this range. b, The identity of bacterial species was different in samples at 1 month, as quantified by Jaccard distance (R2 = 0.09, P = 0.001, PERMANOVA test with restricted permutations, n1 = 81 samples from birth, n2 = 88 samples from 1 month, 7 birth samples excluded due to no taxonomic assignments). c, Heatmap of taxa detected in samples collected at 1 month. Taxa were included if the relative abundance was greater than 10% in any sample. d, Prevalence of bacterial taxa in samples collected at birth and 1 month. Taxa shown were determined to be differentially present or absent by Fisher’s exact test, P < 0.05 after correction for false discovery rate (n = 88 per group, 482 taxa tested, two-sided test).
Extended Data Fig. 2 Abundance of bacterial gene orthologs at birth and 1 month.
a, The total number of KEGG gene orthologs per sample was higher at 1 month relative to birth (P = 9×10−16, two-sided Wilcoxon signed-rank test, n = 88 per group). b, Genes increasing in abundance at 1 month relative to birth (top 100 shown, P < 0.001 after correction for false discovery rate, two-sided Wilcoxon signed-rank test, n = 88 per group). Points show the median value, error bars show the interquartile range. c, The number of glycoside hydrolase gene types per sample (P = 9×10−16) and total abundance of glycoside hydrolase genes (P = 7×10−13) in each sample increased from birth to 1 month (two-sided Wilcoxon signed-rank test, n = 88 per group). Boxes indicate the median and interquartile distance, whiskers indicate maximum and minimum data points within 1.5 times the interquartile range, points represent values outside this range.
Extended Data Fig. 3 Correlation of microbiota with mode of delivery.
a, The mode of delivery was not associated with differences in the number of bacterial species per sample at birth or 1 month (two-sided Mann-Whitney test). b, The mode of delivery had a small effect on the composition of bacteria present at 1 month, as measured by Jaccard distance (R2 = 0.02, PERMANOVA test), but no effect at birth. c, Several taxa differed in prevalence according to mode of delivery at 1 month, but were not statistically significant after correction for multiple comparisons (two-sided Fisher’s exact test). No taxa differed in abundance at either time point (two-sided Mann-Whitney test). d, KEGG gene orthologs associated with mode of delivery in 1 month samples (two-sided Mann-Whitney test, P < 0.05 after correction for false discovery rate). Points with error bars in (d) indicate the median and interquartile range. Boxes in (a) and (c) indicate the median and interquartile distance, whiskers indicate maximum and minimum data points within 1.5 times the interquartile range, points represent values outside this range. Sample size in all tests was n1 = 64 vaginal birth, n2 = 24 c-section.
Extended Data Fig. 4 Association of breastfeeding with bacterial taxa and gene function.
a, The number of bacterial species decreased with breastfeeding at 1 month, but not at birth (two-sided Mann-Whitney test). Boxes in indicate the median and interquartile distance, whiskers indicate maximum and minimum data points within 1.5 times the interquartile range, points represent values outside this range. b, Breastfeeding altered the composition of bacterial species present at 1 month but not at birth (PERMANOVA test). c, The abundance of Bifidobacterium increased with breastfeeding at birth and 1 month (one-sided Mann-Whitney test). d, Other genera found to differ in abundance with breastfeeding at 1 month (two-sided Mann-Whitney test, corrected for false discovery rate). e, KEGG gene orthologs differing in abundance with breastfeeding (two-sided Mann-Whitney test, corrected for false discovery rate). Corrected p-values are shown for statistically significant differences. Points with error bars in (e) indicate the median and interquartile range. Sample size at birth was n1 = 19 formula, n2 = 61 breastfed; sample size at 1 month was n1 = 36 formula, n2 = 52 breastfed.
Extended Data Fig. 5 Negative control samples used in metagenomic DNA sequencing.
a, Bacterial species abundance in negative control samples. b, Jaccard distance between negative control samples and meconium samples (n1 = 81 meconium samples, n2 = 15 negative control samples, 7 meconium samples excluded due to no taxonomic assignments). c, Jaccard distance to centroid of negative control samples. The 95% quantile for distance of negative control samples to their own centroid is indicated with a dashed line; 32 meconium samples fell within this distance. d, Prevalence of species commonly detected in negative controls. For all but E. coli, the species were more prevalent in negative controls than in meconium samples. e, Stacked bar charts showing prominent taxa in negative controls, birth, and 1 month samples.
Extended Data Fig. 6 Estimation of bacterial-to-human DNA ratio by qPCR.
a, Absolute quantification of bacterial DNA by 16 S qPCR in meconium and negative control samples. b, Negative correlation of 16 S copy number and human DNA percentage in metagenomic sequencing (two-sided test of Spearman correlation, ρ = −0.6, P = 2×10−9, n = 88). c, Positive correlation between beta-actin copy number and human DNA percentage (two-sided test of Spearman correlation, ρ = 0.4, P = 3×10−4, n = 88). d, Negative correlation between estimated bacterial-to-human DNA ratio and human DNA percentage (two-sided test of Spearman correlation, ρ = −0.8, P = 2×10−16, n = 48, samples were excluded if either measurement was below the limit of detection). The linear regression estimate is indicated with a solid black line and the 95% confidence interval is indicated by the grey area.
Extended Data Fig. 7 Bacterial-to-human DNA ratio associated with time since birth.
a, Bacterial 16 S copy number per gram feces increased with time since birth (two-sided test of Spearman correlation, ρ = 0.5, P = 6×10−6, n = 85, 3 samples excluded due to no data on time since birth). b, Bacterial 16 S copy number per μL extracted DNA increases with time since birth (two-sided test of Spearman correlation, ρ = 0.5, P = 7×10−6, n = 85). c, The bacterial-to-human DNA ratio is higher in samples collected after 16 hours with low human DNA relative to others (two-sided Mann-Whitney test, P = 4×10−11, n1 = 32 samples collected after 16 hours with low human DNA, n2 = 53 others). Samples with a bacterial-to-human DNA ratio above unity are labeled with the subject ID. d, The bacterial-to-human DNA ratio is higher in samples collected.
Extended Data Fig. 8 Acetate concentration in meconium samples.
a, The acetate concentration was higher in samples obtained after 16 hours with low human DNA and other groups, and was not different in samples collected before vs. after 16 hours with high human DNA (two-sided Mann-Whitney test, p-values indicated above bars, n1 = 30 collected before 16 hours, n2 = 21 after 16 hours with human DNA > 75%, n3 = 30 after 16 hours with human DNA < 75%). Boxes in indicate the median and interquartile distance, whiskers indicate maximum and minimum data points within 1.5 times the interquartile range, points represent values outside this range. b, Acetate concentration increased with 16 S copy number per gram feces (two-sided test of Spearman correlation, ρ = 0.33, P = 0.002, n = 84). The blue line indicates the linear regression estimate, and the grey area indicates the 95% confidence interval. The dashed vertical line indicates the lower limit of detection for 16 S qPCR measurements. Samples with high acetate concentration are labeled. c, Acetate concentration increased with time since birth (two-sided test of Spearman correlation, ρ = 0.27, P = 0.02, n = 81). The dashed vertical line indicates 16 hours after birth.
Extended Data Fig. 9 Products of aerobic and anaerobic amino acid metabolism in E. coli.
Simulated metabolic flux in E. coli under aerobic and anaerobic conditions. The arrow thickness for a reaction is proportional to the flux flowing through it, with red being the maximum and grey the minimum (equivalent to zero flux).
Extended Data Fig. 10 Summary of data presented for meconium samples and negative controls.
Samples are ordered from top to bottom by time of collection. An empty set symbol (∅) indicates samples that were not submitted for proteomic and metabolomic analysis, due to availability of specimen. The dashed horizontal line indicates 16 hours after birth.
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Bittinger, K., Zhao, C., Li, Y. et al. Bacterial colonization reprograms the neonatal gut metabolome. Nat Microbiol 5, 838–847 (2020). https://doi.org/10.1038/s41564-020-0694-0
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DOI: https://doi.org/10.1038/s41564-020-0694-0
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