Host and gut microbiota symbiotic factors: lessons from inflammatory bowel disease and successful symbionts
ABSTRACT Humans are colonized by a diverse collection of microbes, the largest numbers of which reside in the distal gut. The vast majority of humans coexist in a beneficial equilibrium with these microbes. However, disruption of this mutualistic relationship can manifest itself in human diseases such as inflammatory bowel disease. Thus the study of inflammatory bowel disease and its genetics can provide insight into host pathways that mediate host-microbiota symbiosis. Bacteria of the human intestinal ecosystem face numerous challenges imposed by human dietary intake, the mucosal immune system, competition from fellow members of the gut microbiota, transient ingested microbes and invading pathogens. Considering features of human resident gut bacteria provides the opportunity to understand how microbes have achieved their symbiont status. While model symbionts have provided perspective into host-microbial homeostasis, high-throughput approaches are becoming increasingly practical for functionally characterizing the gut microbiota as a community.
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ABSTRACT: A central challenge in microbial community ecology is the delineation of appropriate units of biodiversity, which can be taxonomic, phylogenetic or functional in nature. The term "community" is applied ambiguously; in some cases the term refers simply to a set of observed entities, while in other cases it requires that these entities interact with one another. Microbes can rapidly gain and lose genes, potentially decoupling community roles from taxonomic and phylogenetic groupings. Trait-based approaches offer a useful alternative, but many traits can be defined based on gene functions, metabolic modules, and genomic properties, and the optimal set of traits to choose is often not obvious. An analysis that considers taxon assignment and traits in concert may be ideal, with the strengths of each approach offsetting the weaknesses of the other. Individual genes also merit consideration as entities in an ecological analysis, with characteristics such as diversity, turnover, and interactions modeled using genes rather than organisms as entities. We identify some promising avenues of research that are likely to yield a deeper understanding of microbial communities that shift from observation-based questions of "Who is There?" and "What Are They Doing?" to the mechanistically driven "How Will They Respond?" This article is protected by copyright. All rights reserved.FEMS microbiology reviews 08/2013; 38(1). DOI:10.1111/1574-6976.12035 · 13.81 Impact Factor
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ABSTRACT: Molecular analyses of symbiotic relationships are challenging our biological definitions of individuality and supplanting them with a new notion of normal part-whole relationships. This new notion is that of a 'holobiont', a consortium of organisms that becomes a functionally integrated 'whole'. This holobiont includes the zoological organism (the 'animal') as well as its persistent microbial symbionts. This new individuality is seen on anatomical and physiological levels, where a diversity of symbionts form a new 'organ system' within the zoological organism and become integrated into its metabolism and development. Moreover, as in normal development, there are reciprocal interactions between the 'host' organism and its symbionts that alter gene expression in both sets of cells. The immune system, instead of being seen as functioning solely to keep microbes out of the body, is also found to develop, in part, in dialogue with symbionts. Moreover, the immune system is actively involved in the colonization of the zoological organism, functioning as a mechanism for integrating microbes into the animal-cell community. Symbionts have also been found to constitute a second mode of genetic inheritance, providing selectable genetic variation for natural selection. We develop, grow and evolve as multi-genomic consortia/teams/ecosystems.Journal of Biosciences 04/2014; 39(2):201-9. DOI:10.1007/s12038-013-9343-6 · 1.94 Impact Factor
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ABSTRACT: Background: Eczema affects 3.5% of the global population, with peak prevalence during infancy. Eczema has no cure, but probiotics have been suggested as a preventative measure. Objective: To comprehensively analyze the impact of prenatal and postnatal probiotic supplementation on the prevention of infantile and childhood eczema. Methods: MEDLINE, EMBASE, Cochrane Central Register of Controlled Trials, and PubMed were searched for randomized controlled trials regarding probiotic usage and eczema development from 1945 to 2013. Participants included were 7 years old or younger with probiotic exposure in utero or below 6 months of age and who was not diagnosed previously. Results: 27 publications describing 16 studies assessing 10 probiotics in 2,797 participants met our criterion. The pooled relative risk of all the studies, 0.74 (95% confidence interval 0.67, 0.82), indicated that probiotic supplementation in the first several years of life did have a significant impact on development of eczema. During evaluation of the studies, heterogeneity of terms and definitions for similar primary and secondary outcomes were identified. Conclusion: The use of probiotic supplements during pregnancy and/or during infancy creates a statistically significant decline in the incidence of eczema. The heterogeneity of terms and definitions regarding eczema is the major limitation of these studies.Military medicine 06/2014; 179(6):580-592. DOI:10.7205/MILMED-D-13-00546 · 0.77 Impact Factor