The gut microbiota—Masters of host development and physiology

1] Wallenberg Laboratory for Cardiovascular and Metabolic Research, Sahlgrenska University Hospital, Department of Molecular and Clinical Medicine, University of Gothenburg, SE-413 45 Gothenburg, Sweden. [2] Sahlgrenska Center for Cardiovascular and Metabolic Research, Department of Molecular and Clinical Medicine, University of Gothenburg, SE-413 45 Gothenburg, Sweden.
Nature Reviews Microbiology (Impact Factor: 23.57). 02/2013; 11(4). DOI: 10.1038/nrmicro2974
Source: PubMed

ABSTRACT Establishing and maintaining beneficial interactions between the host and its associated microbiota are key requirements for host health. Although the gut microbiota has previously been studied in the context of inflammatory diseases, it has recently become clear that this microbial community has a beneficial role during normal homeostasis, modulating the host's immune system as well as influencing host development and physiology, including organ development and morphogenesis, and host metabolism. The underlying molecular mechanisms of host-microorganism interactions remain largely unknown, but recent studies have begun to identify the key signalling pathways of the cross-species homeostatic regulation between the gut microbiota and its host.

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Available from: Felix Sommer, Mar 11, 2015
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    • "The resulting associations between animals and microbes profoundly influence the maturation of their tissues and the function of adult organs. In particular, the development of the vertebrate digestive tract, which harbors the vast majority of microbial cells in the body, is strongly influenced by the presence and composition of the gut microbiota (Bates et al., 2006; Olszak et al., 2012; Semova et al., 2012; Sommer and Bäckhed, 2013). A comprehensive description of animal development must, therefore, include not only a catalog of the birth, specification and differentiation of the animal cells that comprise the body but also the associated microbial cells (McFall-Ngai et al., 2013). "
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    ABSTRACT: The assembly of resident microbial communities is an important event in animal development; however, the extent to which this process mirrors the developmental programs of host tissues is unknown. Here we surveyed the intestinal bacteria at key developmental time points in a sibling group of 135 individuals of a model vertebrate, the zebrafish (Danio rerio). Our survey revealed stage-specific signatures in the intestinal microbiota and extensive interindividual variation, even within the same developmental stage. Microbial community shifts were apparent during periods of constant diet and environmental conditions, as well as in concert with dietary and environmental change. Interindividual variation in the intestinal microbiota increased with age, as did the difference between the intestinal microbiota and microbes in the surrounding environment. Our results indicate that zebrafish intestinal microbiota assemble into distinct communities throughout development, and that these communities are increasingly different from the surrounding environment and from one another.The ISME Journal advance online publication, 4 September 2015; doi:10.1038/ismej.2015.140.
    The ISME Journal 09/2015; DOI:10.1038/ismej.2015.140 · 9.30 Impact Factor
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    • "The microorganisms that reside on and inside humans and other vertebrate animals are remarkable, not only because of their importance to host health and development (Bates et al., 2006; Fraune and Bosch, 2010; Sommer and Bäckhed, 2013), but also because they assemble into complex communities de novo in every new hatchling or infant host. The processes responsible for structuring these complex systems, often referred to as a host's microbiota, are not well understood despite a strong interest in manipulating them to improve human health. "
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    ABSTRACT: Despite their importance to host health and development, the communities of microorganisms associated with humans and other animals are characterized by a large degree of unexplained variation across individual hosts. The processes that drive such inter-individual variation are not well understood. To address this, we surveyed the microbial communities associated with the intestine of the zebrafish, Danio rerio, over developmental time. We compared our observations of community composition and distribution across hosts with that predicted by a neutral assembly model, which assumes that community assembly is driven solely by chance and dispersal. We found that as hosts develop from larvae to adults, the fit of the model to observed microbial distributions decreases, suggesting that the relative importance of non-neutral processes, such as microbe-microbe interactions, active dispersal, or selection by the host, increases as hosts mature. We also observed that taxa which depart in their distributions from the neutral prediction form ecologically distinct sub-groups, which are phylogenetically clustered with respect to the full metacommunity. These results demonstrate that neutral processes are sufficient to generate substantial variation in microbiota composition across individual hosts, and suggest that potentially unique or important taxa may be identified by their divergence from neutral distributions.The ISME Journal advance online publication, 21 August 2015; doi:10.1038/ismej.2015.142.
    The ISME Journal 08/2015; DOI:10.1038/ismej.2015.142 · 9.30 Impact Factor
    • "Considering that the human digestive tract is estimated to contain up to 10 14 bacterial cells [66], pathogens face fierce competition for available nutrients. In addition , some gut microbiota species engage in interbacterial warfare, using weapons such as bacteriocins and type VI secretion systems to kill competitors, including pathogens [56] [61]. "
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    ABSTRACT: Gastrointestinal pathogens must overcome many obstacles in order to successfully colonize a host, not the least of which is the presence of the gut microbiota, the trillions of commensal microorganisms inhabiting mammals' digestive tracts, and their products. It is well established that a healthy gut microbiota provides its host with protection from numerous pathogens, including Salmonella species, Clostridium difficile, diarrheagenic Escherichia coli, and Vibrio cholerae. Conversely, pathogenic bacteria have evolved mechanisms to establish an infection and thrive in the face of fierce competition from the microbiota for space and nutrients. Here, we review the evidence that gut microbiota-generated metabolites play a key role in determining the outcome of infection by bacterial pathogens. By consuming and transforming dietary and host-produced metabolites, as well as secreting primary and secondary metabolites of their own, the microbiota define the chemical environment of the gut and often determine specific host responses. Although most gut microbiota-produced metabolites are currently uncharacterized, several well-studied molecules made or modified by the microbiota are known to affect the growth and virulence of pathogens, including short-chain fatty acids, succinate, mucin O-glycans, molecular hydrogen, secondary bile acids, and the AI-2 quorum sensing autoinducer. We also discuss challenges and possible approaches to further study of the chemical interplay between microbiota and gastrointestinal pathogens. Copyright © 2015. Published by Elsevier Ltd.
    Anaerobe 05/2015; 34. DOI:10.1016/j.anaerobe.2015.05.002 · 2.48 Impact Factor
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