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: 12.18). 09/2013; 67(1):459-75. DOI: 10.1146/annurev-micro-092412-155642
Source: PubMed


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.

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    • "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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    ABSTRACT: The microbial mechanisms and key metabolites that shape the composition of the human gut microbiota are largely unknown, impeding efforts to manipulate dysbiotic microbial communities toward stability and health. Vitamins, which by definition are not synthesized in sufficient quantities by the host and can mediate funda- mental biological processes in microbes, represent an attractive target for reshaping microbial communities. Here, we discuss how vitamin B12 (cobalamin) impacts diverse host-microbe symbioses. Although cobalamin is synthesized by some human gut microbes, it is a precious resource in the gut and is likely not provisioned to the host in significant quantities. However, this vitamin may make an unrecognized contribution in shaping the structure and function of human gut microbial communities.
    No preview · Article · Nov 2014 · Cell Metabolism
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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.
    Full-text · Article · Jun 2014 · PLoS ONE
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    ABSTRACT: Complex host-gut microbiota interaction is involved in the formation of a unique ecosystem in our body, the “gut ecosystem”. In order to understand the complex gut ecosystem, we propose integrated multi-omics approach, where multiple layers of unbiased cyclopedic analyses such as genomics, transcriptomics and metabolomics are combined. Applying this approach, we have revealed the mechanism that gut microbiota-derived acetate, a short-chain fatty acid, protects mice from enterohemorrhagic Escherichia coli O157-infectious death. We have also shown that butyrate produced by gut microbiota such as order Clostridiales promotes differentiation of regulatory T cells from naïve T cells in colonic lamina propria, through epigenetic modification. Epigenetic modification by butyrate also acts on colonic macrophages to confer anti-inflammatory phenotype by rendering them hyporesponsive to Toll-like receptor signaling. Short-chain fatty acids also signal via their G protein-coupled receptors. For example, it has been suggested that gut microbiota-derived short-chain fatty acids absorbed in the blood play a role in regulation of systemic inflammation by inducing apoptosis of neutrophils as well as chemotaxis of regulatory T cells.
    Preview · Article · Jan 2014 · Japanese Journal of Clinical Immunology
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