Article

The Application of Ecological Theory Toward an Understanding of the Human Microbiome

Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
Science (Impact Factor: 33.61). 06/2012; 336(6086):1255-62. DOI: 10.1126/science.1224203
Source: PubMed

ABSTRACT

The human-microbial ecosystem plays a variety of important roles in human health and disease. Each person can be viewed as an island-like "patch" of habitat occupied by microbial assemblages formed by the fundamental processes of community ecology: dispersal, local diversification, environmental selection, and ecological drift. Community assembly theory, and metacommunity theory in particular, provides a framework for understanding the ecological dynamics of the human microbiome, such as compositional variability within and between hosts. We explore three core scenarios of human microbiome assembly: development in infants, representing assembly in previously unoccupied habitats; recovery from antibiotics, representing assembly after disturbance; and invasion by pathogens, representing assembly in the context of invasive species. Judicious application of ecological theory may lead to improved strategies for restoring and maintaining the microbiota and the crucial health-associated ecosystem services that it provides.

Download full-text

Full-text

Available from: Keaton Stagaman
    • "In addition, stimulating a broader spectrum of microorganisms, either directly or via cross-feeding, could also promote greater diversity within the gut ecosystem. High levels of diversity are generally considered important for a functional gut ecosystem [56] . Several human gastrointestinal diseases are associated with reduced microbial diversity and gene richness [5 been reported to have an impact on the production of beneficial metabolites by gut microbes. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Purpose of review: A wide range of dietary carbohydrates, including prebiotic food ingredients, fermentable fibers, and milk oligosaccharides, are able to produce significant changes in the intestinal microbiota. These shifts in the microbial community are often characterized by increased levels of bifidobacteria and lactobacilli. More recent studies have revealed that species of Faecalibacterium, Akkermansia, and other less well studied members may also be enriched. We review the implications of these recent studies on future design of prebiotics and synbiotics to promote gastrointestinal health. Recent findings: Investigations assessing the clinical outcomes associated with dietary modification of the gut microbiota have shown systemic as well as specific health benefits. Both prebiotic oligosaccharides comprised of a linear arrangement of simple sugars, as well as fiber-rich foods containing complex carbohydrates, have been used in these trials. However, individual variability and nonresponding study participants can make the outcome of dietary interventions less predictable. In contrast, synergistic synbiotics containing prebiotics that specifically stimulate a cognate probiotic provide additional options for personalized gut therapies. Summary: This review describes recent research on how prebiotics and fermentable fibers can influence the gut microbiota and result in improvements to human health.
    No preview · Article · Feb 2016 · Current Opinion in Gastroenterology
  • Source
    • "Community ecology theory offers a framework to address questions related to the assembly and structure of communities (Koenig et al., 2011;Costello et al., 2012). While indicator speciesThe ISME Journal analysis pointed at the preferred inclusion of particular taxa in worm microbiotas, additional tools can be used to assess community assembly rules. "
    [Show abstract] [Hide abstract]
    ABSTRACT: It is now well accepted that the gut microbiota contributes to our health. However, what determines the microbiota composition is still unclear. Whereas it might be expected that the intestinal niche would be dominant in shaping the microbiota, studies in vertebrates have repeatedly demonstrated dominant effects of external factors such as host diet and environmental microbial diversity. Hypothesizing that genetic variation may interfere with discerning contributions of host factors, we turned to Caenorhabditis elegans as a new model, offering the ability to work with genetically homogenous populations. Deep sequencing of 16S rDNA was used to characterize the (previously unknown) worm gut microbiota as assembled from diverse produce-enriched soil environments under laboratory conditions. Comparisons of worm microbiotas with those in their soil environment revealed that worm microbiotas resembled each other even when assembled from different microbial environments, and enabled defining a shared core gut microbiota. Community analyses indicated that species assortment in the worm gut was non-random and that assembly rules differed from those in their soil habitat, pointing at the importance of competitive interactions between gut-residing taxa. The data presented fills a gap in C. elegans biology. Furthermore, our results demonstrate a dominant contribution of the host niche in shaping the gut microbiota.The ISME Journal advance online publication, 22 January 2016; doi:10.1038/ismej.2015.253.
    Preview · Article · Jan 2016 · The ISME Journal
  • Source
    • "In comparing the temporal dynamics of the oral microbiota in healthy and ECC children, we showed that plaque and saliva microbiota age of unrelated healthy children can explain over 50% of the variance in microbiota. The age-dependent changes observed could be caused by biological changes in tissues around the teeth during exfoliation of teeth (Crielaard et al., 2011), contact with external microbes (Kö nö nen, 2000), and/or development of immune systems (Costello et al., 2012), etc. Furthermore, the age-associated development of the healthy oral microbiota appears to be driven in part by changes in the relative abundance of taxa rather than the acquisition/loss of unique taxa with age, similar to the development of the skin microbiota at different ages (Song et al., 2013) but different from the gut microbiota at the age of 0–2 (Subramanian et al., 2014). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Microbiota–based prediction of chronic infections is promising yet not well-established. Early Childhood Caries (ECC) is the most common infection in children. Here we simultaneously tracked microbiota development at plaque and saliva in 50 four-year-old preschoolers for two years; children either stayed healthy, transitioned into cariogenesis or experienced caries exacerbation. Caries onset delayed microbiota development, which is otherwise correlated with aging in healthy children. Both plaque and saliva microbiota are more correlated with changes in ECC severity (dmfs) during onset than progression. By distinguishing between aging- and disease-associated taxa and exploiting the distinct microbiota dynamics between onset and progression, we developed a model, Microbial Indicators of Caries, to diagnose ECC from healthy samples with 70% accuracy and predict, with 81% accuracy, future ECC onsets for samples clinically perceived as healthy. Thus, caries onset in apparently healthy teeth can be predicted using microbiota, when appropriately de-trended for age.
    Full-text · Article · Sep 2015 · Cell Host & Microbe
Show more