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BACKGROUND: The compromised gut microbiome that results from C-section birth has been hypothesized as a risk factor for the development of non-communicable diseases (NCD). In a double-blind randomized controlled study, 153 infants born by elective C-section received an infant formula supplemented with either synbiotic, prebiotics, or unsupplemented from birth until 4 months old. Vaginally born infants were included as a reference group. Stool samples were collected from day 3 till week 22. Multi-omics were deployed to investigate the impact of mode of delivery and nutrition on the development of the infant gut microbiome, and uncover putative biological mechanisms underlying the role of a compromised microbiome as a risk factor for NCD. RESULTS: As early as day 3, infants born vaginally presented a hypoxic and acidic gut environment characterized by an enrichment of strict anaerobes (Bifidobacteriaceae). Infants born by C-section presented the hallmark of a compromised microbiome driven by an enrichment of Enterobacteriaceae. This was associated with meta-omics signatures characteristic of a microbiome adapted to a more oxygen-rich gut environment, enriched with genes associated with reactive oxygen species metabolism and lipopolysaccharide biosynthesis, and depleted in genes involved in the metabolism of milk carbohydrates. The synbiotic formula modulated expression of microbial genes involved in (oligo)saccharide metabolism, which emulates the eco-physiological gut environment observed in vaginally born infants. The resulting hypoxic and acidic milieu prevented the establishment of a compromised microbiome. CONCLUSIONS: This study deciphers the putative functional hallmarks of a compromised microbiome acquired during C-section birth, and the impact of nutrition that may counteract disturbed microbiome development. TRIAL REGISTRATION: The study was registered in the Dutch Trial Register (Number: 2838 ) on 4th April 2011.

Additional file 1: Figure S1. Prevalence of Bifidobacterium and Bacteroides per intervention group from day 3 till week 22. Figure S2a. Box-plots representing the distribution of samples along db-RDA1 at week 2. Non-parametric Mann-Whitney U tests P 0.6 against the metagenomics reads assigned to the two species are mapped onto the KEGG metabolism pathway map. Figure S6. Metabolic pathway derived from the metatranscriptomics dataset depicting correlations with Bifidobacterium breve (blue) and Klebsiella (red). KEGG genes which exhibit Pearson correlation coefficients > 0.6 against the metatranscriptomic reads assigned to the two species are mapped onto the KEGG metabolism pathway map. Figure S7. Correlation between Bifidobacterium breve and HMOs metabolism. Linear model plot depicting correlation between Bifidobacterium breve and Lacto-N I Galacto-N-biose metabolism (SEED data). Figure S8. Heat map of lactose and HMO species present in the pooled samples for the synbiotic, prebiotics, control and reference groups (in triplicate). The colour scale is based on the row z-score. Figure S9. Abundance patterns of Bifidobacterium (16S rRNA), milk sugars, acetate and lactic acid as emerged from biological pools and corresponding groups. Bifidobacterium and acetic acid were detected at their highest levels of abundance in correspondence to lactose and HMOs being detected at their lowest, and vice-versa. Raw intensities (for milk sugars), amounts (for organic acid) and relative abundances (for Bifidobacterium) were normalized between 0 and 1 to allow for a visual comparison. Figure S10a. Correlation between Klebsiella and respiration. Linear model plot depicting correlation between Klebsiella and Formate deshydrogenase (SEED data). Figure S10b. Correlation between Klebsiella and reactive oxygen species metabolism. Linear model plot depicting correlation between Klebsiella and Glutathion-S-transferase (SEED data). Figure S10c. Correlation between Klebsiella and lipopolysaccharide biosynthesis (LPS). Linear model plot depicting correlation between Klebsiella and KDO2-Lipid A biosynthesis (SEED data). Figure S11. Prevalence of human infant type Bifidobacterium species per group from day 3 till week 22. Figure S12. Infographic depicting the functional impact of vaginal birth on the infant gut microbiome. The acquisition of Bifidobacterium during birth allows the establishment of a hypoxic and acidic gut environment that prevents the growth of opportunistic pathogens (Enterobacteriacae). Bifidobacterium metabolizes the human milk oligosaccharides present in human milk through a fermentative metabolism, and acetate, one of the major end-products of the pathway, is oxidized by the colonocytes (β oxidation) as a source of energy. This biological phenomenon prevents the increase in oxygenation in colonic epithelial cells and contributes towards reducing and acidifying the colonic environment. Figure S13. Infographic depicting the functional impact of C-section birth on the infant gut microbiome. C-section birth is characterized by an enrichment of facultative anaerobes and aerobes (Enterobacteriaceae). The delayed colonization by Bifidobacterium prevents the establishment of a reduced and acidic gut environment leading to an increase in oxygenation in colonic epithelial cells and expansion of Enterobacteriaceae. Members of Enterobacteriaceae such as Klebsiella pneumoniae, uses oxygen to thrive in the colonic environment. They express lipopolysaccharide (LPS) and metabolize reactive oxygen species in the colonic environment.

presented in: ASMS 2010 in Salt Lake City, Utah “Are iPS cells indistinguishable from ES cells?”We pro le the proteomes of human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSCs) with quantitative dimethyllabeling developed in-house to unravel the similarities and di erences between the two cell lines. Our results show that both pluripotent cell lines are nearly indistinguishable at the proteome level. Being self-renewing and pluripotent, hESCs hold great promise for cell transplantation therapies to cure degenerative diseases such as Parkinson’s disease or heart failures. However, this technology is limited by ethical issues since embryos are inevitably destroyed upon derivation of hESCs. Besides, potential risks do exist for immune rejection posttransplantion. These issues can probably be addressed now by the reprogrammingtechnology where adult somatic cells are induced to become hESC-like by the ectopic expression of de ned transcription factors . These induced pluripotent stem cells (hiPSCs) closely resemble hESCs in many aspects, such as the expression of certain stem cell markers. More importantly, they are also capable of pluripotency and self-renewal. Being patient-derived and thus patient-speci c, hiPSCs are ideal replacements for hESCs in cell transplantation therapies. However, before any clinical applications, they need to be characterized extensively so as to evaluate their abilities for replication and di erentiation in comparison to the actual hESCs. More recently, transcriptomic approaches have been used to assess the gene expression pro les of both cell types . We argue that mRNA levels are not truly representative of the true character of a cell as proteins are the actual functional entities. Therefore, we used “proteomics profi ling” instead and ask “Are iPS cells indistinguishable from ES cells?”