Experimental Approaches for Defining Functional Roles of Microbes in the Human Gut

Center for Genome Sciences & Systems Biology and Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri 63108
Annual review of microbiology (Impact Factor: 13.02). 09/2013; 67:459-75. DOI: 10.1146/annurev-micro-092412-155642
Source: PubMed

ABSTRACT The complex and intimate relationship between humans and their gut microbial communities is becoming less obscure, due in part to large-scale gut microbial genome-sequencing projects and culture-independent surveys of the composition and gene content of these communities. These studies build upon, and are complemented by, experimental efforts to define underlying mechanisms of host-microbe interactions in simplified model systems. This review highlights the intersection of these approaches. Experimental studies now leverage the advances in high-throughput DNA sequencing that have driven the explosion of microbial genome and community profiling projects, and the loss-of-function and gain-of-function strategies long employed in model organisms are now being extended to microbial genes, species, and communities from the human gut. These developments promise to deepen our understanding of human gut host-microbiota relationships and are readily applicable to other host-associated and free-living microbial communities.

    • "In fact, Pasteur proposed in 1885 that animals would not be viable without their associated microbes (Gordon and Pesti, 1971). Although the establishment of germfree mice, rats, and other mammals 60 years later disproved this bold hypothesis, gnotobiotic (known life) studies comparing germfree and conventional animals have revealed a tremendous and wide-ranging impact of resident microbes on host development , metabolism, immune responses, and behavior (Dantas et al., 2013; Diaz Heijtz et al., 2011; Faith et al., 2010; Goodman and Gordon, 2010; Smith et al., 2007). These experiments quickly indicated that one fundamental service of the gut microbiota is production of vitamins for the host. "
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    Cell Metabolism 11/2014; 20(5). DOI:10.1016/j.cmet.2014.10.002 · 16.75 Impact Factor
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    • "Several factors, including pathogen-driven inflammatory responses occurring in the gut could explain some of these disagreements [29]–[34]. However, there is a need to establish well-controlled model systems in order to improve our understanding of the specific host derived factors that affect bacterial conjugation [35]. In this study we establish such an in vitro experimental system using intestinal epithelial cells in co-culture with clinical E. coli isolates able to donate and receive an ESBL (extended spectrum beta-lactamase) plasmid. "
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    ABSTRACT: Bacterial conjugation in the human gut microbiota is believed to play a major role in the dissemination of antibiotic resistance genes and virulence plasmids. However, the modulation of bacterial conjugation by the human host remains poorly understood and there is a need for controlled systems to study this process. We established an in vitro co-culture system to study the interaction between human intestinal cells and bacteria. We show that the conjugation efficiency of a plasmid encoding an extended spectrum beta-lactamase is reduced when clinical isolates of Escherichia coli are co-cultured with human intestinal cells. We show that filtered media from co-cultures contain a factor that reduces conjugation efficiency. Protease treatment of the filtered media eliminates this inhibition of conjugation. This data suggests that a peptide or protein based factor is secreted on the apical side of the intestinal cells exposed to bacteria leading to a two-fold reduction in conjugation efficiency. These results show that human gut epithelial cells can modulate bacterial conjugation and may have relevance to gene exchange in the gut.
    PLoS ONE 06/2014; 9(6):e100739. DOI:10.1371/journal.pone.0100739 · 3.23 Impact Factor
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    ABSTRACT: Background: Skin is our first line of defense against pathogenic microorganisms and the intimate contact between the epidermis and microbes has been well known. Purposes: Microbes that cause infection are associated with inflammatory dermatoses and exacerbate wound healing. It is therefore of vital importance to understand the intricacies of skin-microbiota interactions. However, until recently our knowledge and understanding was limited by being unable to deal with uncultivatable microorganisms, which constitute a large majority. Basic procedures: Recent advances in DNA sequencing methodologies, analysis tools and affordability led to major breakthroughs in defining the cutaneous microbiome. Main findings: We now know that four phyla, Actinobacteria, Firmicytes, Proteobacteria and Bacteroidetes, constitute preponderance of skin bacteria, while Malassezia dominates the fungal microbiome. We know that there are some 300 different bacteria inhabiting our skin. We also know that there is remarkable interpersonal variation, that the microbiota change over time, that different body sites harbor specific microbial arrays and that microbiota characteristically change in skin diseases. Principal conclusions: The recent advances led to appreciation that microbes are, for the most part, our allies, useful and protective, and that with increased understanding we will be able to harness our cutaneous friends to maintain and promote our health.
    Journal of Dermatological Science 05/2014; 75(2). DOI:10.1016/j.jdermsci.2014.05.001 · 3.34 Impact Factor
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