Eating For Two: How Metabolism Establishes Interspecies Interactions in the Gut

Department of Bioengineering and Therapeutic Sciences and California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA.
Cell host & microbe (Impact Factor: 12.33). 10/2011; 10(4):336-47. DOI: 10.1016/j.chom.2011.10.002
Source: PubMed


In bacterial communities, "tight economic times" are the norm. Of the many challenges bacteria face in making a living, perhaps none are more important than generating energy, maintaining redox balance, and acquiring carbon and nitrogen to synthesize primary metabolites. The ability of bacteria to meet these challenges depends heavily on the rest of their community. Indeed, the most fundamental way in which bacteria communicate is by importing the substrates for metabolism and exporting metabolic end products. As an illustration of this principle, we will travel down a carbohydrate catabolic pathway common to many species of Bacteroides, highlighting the interspecies interactions established (often inevitably) at its key steps. We also discuss the metabolic considerations in maintaining the stability of host-associated microbial communities.

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    • "Processes such as host-microbe crosstalk, immune activation and inflammation, microbemicrobe signaling, microbial metabolism, and antimicrobial activity are all, by definition, bioactive in ecosystems such as the human gut (Holmes et al., 2012). Likewise, a wide range of molecules are candidate mediators of these processes, including small-molecule microbial products of primary metabolism (e.g., short-chain fatty acids [SCFAs]) as well as a diverse array of secondary metabolites including both secreted and cell surface peptides or sugars (Fischbach and Sonnenburg, 2011; Lopez et al., 2014). "
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    ABSTRACT: Human-associated microbes are the source of many bioactive microbial products (proteins and metabolites) that play key functions both in human host pathways and in microbe-microbe interactions. Culture-independent studies now provide an accelerated means of exploring novel bioactives in the human microbiome; however, intriguingly, a substantial fraction of the microbial metagenome cannot be mapped to annotated genes or isolate genomes and is thus of unknown function. Meta’omic approaches, including metagenomic sequencing, metatranscriptomics, metabolomics, and integration of multiple assay types, represent an opportunity to efficiently explore this large pool of potential therapeutics. In combination with appropriate follow-up validation, high-throughput culture-independent assays can be combined with computational approaches to identify and characterize novel and biologically interesting microbial products. Here we briefly review the state of microbial product identification and characterization and discuss possible next steps to catalog and leverage the large uncharted fraction of the microbial metagenome.
    Cell Metabolism 11/2014; 20(5):731-741. DOI:10.1016/j.cmet.2014.10.003 · 17.57 Impact Factor
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    • "Competition can be divided two broad categories: exploitative competition, which indirectly affects competitors by limiting the abundance of resources, and interference competition, which directly harms other strains and species through production of antimicrobial compounds (Mitri and Foster, 2013). In the gut, the stability of ecosystem is tightly maintained by various syntrophic links within a community (Fischbach and Sonnenburg, 2011). Microbial competitiveness of colonic microbiota is linked to the efficient exploitation of the limited nutrient (carbohydrate) supply (Louis et al., 2007; van den Broek et al., 2008; Derrien et al., 2008; Walter and Ley, 2011). "
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    ABSTRACT: Human commensal microbiota are an important determinant of health and disease of the host. Different human body sites harbour different bacterial microbiota, bacterial communities that maintain a stable balance. However, many of the factors influencing the stabilities of bacterial communities associated with humans remain unknown. In this study we identified putative bacteriocins produced by human commensal microbiota. Bacteriocins are peptides or proteins with antimicrobial activity that contribute to the stability and dynamics of microbial communities. We employed bioinformatic analyses to identify putative bacteriocin sequences in metagenomic sequences obtained from different human body sites. Prevailing bacterial taxa of the putative bacteriocins producers matched the most abundant organisms in each human body site. Remarkably, we found that samples from different body sites contain different density of putative bacteriocin genes, with the highest in samples from the vagina, the airway, and the oral cavity and the lowest in those from gut. Inherent differences of different body sites thus influence the density and types of bacteriocins produced by commensal bacteria. Our results suggest that bacteriocins play important roles to allow different bacteria to occupy several human body sites, and to establish a long-term commensal relationship with human hosts.
    Environmental Microbiology 10/2014; 17(6). DOI:10.1111/1462-2920.12662 · 6.20 Impact Factor
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    • "Once ingested, pectin is cleaved into constituent monosaccharides, including arabinose and xylose, in the large intestine [40]. They are subsequently fermented by microflora, yielding short chain fatty acids (SCFA), such as butyrate, propionate, and acetate [40,41]. The efficacy of pectin in exerting protection against ischemic injury might be mediated by SCFA generated because administration of butyrate by intraperitoneal injection prior to occlusion protected against myocardial injury in a rat model of ischemia/reperfusion [18]. "
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    ABSTRACT: BACKGROUND/OBJECTIVE Myocardial cell death due to occlusion of the coronary arteries leads to myocardial infarction, a subset of coronary heart disease (CHD). Dietary fiber is known to be associated with a reduced risk of CHD, the underlying mechanisms of which were suggested to delay the onset of occlusion by ameliorating risk factors. In this study, we tested a hypothesis that a beneficial role of dietary fiber could arise from protection of myocardial cells against ischemic injury, manifested after occlusion of the arteries. MATERIALS/METHODS Three days after rats were fed apple pectin (AP) (with 10, 40, 100, and 400 mg/kg/day), myocardial ischemic injury was induced by 30 min-ligation of the left anterior descending coronary artery, followed by 3 hr-reperfusion. The area at risk and infarct area were evaluated using Evans blue dye and 2,3,5-triphenyltetrazolium chloride (TTC) staining, respectively. DNA nicks reflecting the extent of myocardial apoptosis were assessed by TUNEL assay. Levels of cleaved caspase-3, Bcl-2, and Bax were assessed by immunohistochemistry. RESULTS Supplementation of AP (with 100 and 400 mg/kg/day) resulted in significantly attenuated infarct size (IS) (ratio of infarct area to area at risk) by 21.9 and 22.4%, respectively, in the AP-treated group, compared with that in the control group. This attenuation in IS showed correlation with improvement in biomarkers involved in the apoptotic cascades: reduction of apoptotic cells, inhibition of conversion of procaspase-3 to caspase-3, and increase of Bcl-2/Bax ratio, a determinant of cell fate. CONCLUSIONS The findings indicate that supplementation of AP results in amelioration of myocardial infarction by inhibition of apoptosis. Thus, the current study suggests that intake of dietary fiber reduces the risk of CHD, not only by blocking steps leading to occlusion, but also by protecting against ischemic injury caused by occlusion of the arteries.
    Nutrition research and practice 08/2014; 8(4):391-7. DOI:10.4162/nrp.2014.8.4.391 · 1.44 Impact Factor
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