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Available from: Se Jin Song, Nov 11, 2014
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    • "For example, infants born vaginally acquire a community more similar to the mother's vaginal and fecal microbiota, whereas infants born by cesarean section have a microbiome that is more similar to those of skin and hospital environments (Dominguez-Bello et al., 2010; Brooks et al., 2014). Cesarean section infants appear to have lower microbial richness and diversity relative to vaginally born infants at 4 months of age (Song et al., 2013). Throughout the first year of life the microbial community increases in diversity, reaching an adult-like state around 2.5 years of life (Koenig et al., 2011). "
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    ABSTRACT: While there has been growing interest in the gut microbiome in recent years, it remains unclear whether closely related species and strains have similar or distinct functional roles and if organisms capable of both aerobic and anaerobic growth do so simultaneously. To investigate these questions, we implemented a high-throughput mass spectrometry-based proteomics approach to identify proteins in fecal samples collected on days of life 13-21 from an infant born at 28 weeks gestation. No prior studies have coupled strain-resolved community metagenomics to proteomics for such a purpose. Sequences were manually curated to resolve the genomes of two strains of Citrobacter that were present during the later stage of colonization. Proteome extracts from fecal samples were processed via a nano-2D-LC-MS/MS and peptides were identified based on information predicted from the genome sequences for the dominant organisms, Serratia and the two Citrobacter strains. These organisms are facultative anaerobes, and proteomic information indicates the utilization of both aerobic and anaerobic metabolisms throughout the time series. This may indicate growth in distinct niches within the gastrointestinal tract. We uncovered differences in the physiology of coexisting Citrobacter strains, including differences in motility and chemotaxis functions. Additionally, for both Citrobacter strains we resolved a community-essential role in vitamin metabolism and a predominant role in propionate production. Finally, in this case study we detected differences between genome abundance and activity levels for the dominant populations. This underlines the value in layering proteomic information over genetic potential.
    Frontiers in Microbiology 07/2015; 6:654. DOI:10.3389/fmicb.2015.00654 · 3.99 Impact Factor
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    Food Reviews International 01/2013; 5(1):1-13. DOI:10.2310/6180.2009.00035 · 2.21 Impact Factor
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    ABSTRACT: Among mammals, milk constituents directly influence the ecology of the infant's commensal microbiota. The immunological and nutritional impacts of breast milk and microbiota are increasingly well-understood; less clear are the consequences for infant behavior. Here we propose that interactions among bioactives in mother's milk and microbes in the infant gut contribute to infant behavioral phenotype and, in part, have the potential to mediate parent-offspring conflict. We hypothesize that infant behavior likely varies as a function of their mother's milk composition interacting with the infant's neurobiology directly and indirectly through the commensal gut bacteria. In this paper, we will explore our hypothesis of a milk-microbiota-brain-behavior dynamic in the context of the co-evolution between human milk oligosaccharides (HMO), bacteria, the gut-brain axis, and behavior. Integrating established features of these systems allows us to generate novel hypotheses to motivate future research and consider potential implications of current and emerging clinical treatments. © The Author(s) 2015. Published by Oxford University Press on behalf of the Foundation for Evolution, Medicine, and Public Health.
    04/2015; 2015(1). DOI:10.1093/emph/eov007
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