The application of ecological theory towards an understanding of the human microbiome

By E. Costello, Keaton Stagaman, Les Dethlefsen, B. Bohannan, David A. Relman. Science, 2012

1,331 citations recorded by the source corpus.

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.

Subfields: Biological Psychiatry, Infectious Diseases, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/fe0c4b6bc63a02b6dabd81b094465cffe1264cff

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Citations in the corpus

Human genetics shape the gut microbiome. (2014, neutral): “The gut microbiome is environmentally acquired from birth (Costello et al., 2012;Walter andLey, 2011), therefore itmay functionas anenvironmental factor that interactswith host genetics to shape phenotype, as well as a genetically determined attribute that is shaped by, and interacts with, the host ”
The composition and stability of the vaginal microbiota of normal pregnant women is different from that of non-pregnant women (2014, background): “Stability and resilience of ecosystems are now recognized to be important in understanding the fitness of the community, as well as the response to perturbations [56,214-220].”
Host lifestyle affects human microbiota on daily timescales (2014, background): “It has been hypothesized that new microbial community states are reached when disturbances either change gut environmental parameters, altering the presence or absence of equilibrium points on a state landscape, or when they alter gut microbiota themselves, shifting communities between fixed equilib”
Antibiotic-Induced Changes in the Intestinal Microbiota and Disease. (2016, background): “All three mechanisms have been implicated in the transfer of ARGs (Figure 3) [97,110].”
Ten questions concerning the microbiomes of buildings (2016, background): “Humans can acquire some components of their own 492 microbiome from their surroundings [147] and are continuously exposed to the indoor 493”
Diet dominates host genotype in shaping the murine gut microbiota (2014, background): “74 Cell Host & Microbe 17, 72–84, January 14, 2015 a2015 Elsevier I dicts that the gut microbiota may be able to tolerate more subtle dietary interventions (Costello et al., 2012).”
Habitat degradation impacts black howler monkey (Alouatta pigra) gastrointestinal microbiomes (2013, background): “Reductions in GI microbiome diversity may reduce microbial functional groups, making the microbiome less efficient, less resistant to disturbance and more susceptible to pathogenic invasion (Rosenfeld, 2002; Costello et al., 2012).”
Conducting a Microbiome Study (2014, background): “Human Studies Commonly Applied Exclusion Criteria In human studies, antibiotics, diet, body mass index, age, pregnancy, and ethnicity all have been reported in the literature to have varying degrees of influence on themicrobiota composition of the gut and of other body sites (Costello et al., 2012).”