Trends in Ecology & Evolution
OpinionThe emerging medical ecology of the human gut microbiome
Section snippets
A new scientific connection: medicine meets ecological theory
The complex ecology of the human gut microbiome is of great medical importance, but researchers are only beginning to investigate its basic biology and to appreciate the challenges that it presents to medical science. The gut bacterial community has been implicated in a range of human health issues extending far beyond the gastrointestinal (GI) tract. Those issues that do directly involve the GI tract include inflammatory bowel disease [1], gastric ulcers [2], obesity and diabetes 3, 4, and
Sources of individual variation
Gut bacterial communities are highly variable among individuals, and apparently vary in ways that are important to health outcomes. Therefore, it is crucial to understand what determines the make-up and characteristics of individual gut microbiomes. The potential causes of individual variation that have received the most consideration can be classified into two categories, involving either local differences in the founding bacterial species that individuals are exposed to, or differing
Temporal variation within individuals
In the absence of any conspicuously varying external influences, human gut microbiomes show considerable temporal variation, both in the ileum [20] and colon [14]. Depending on the detail and the duration of observation, human gut microbiomes may appear stable, but similar to many others, these ecosystems are fundamentally dynamic, fluctuating such that only their average state is stable [14]. This is consistent with theory-based expectations of asymptotic dynamic stability, as opposed to
Long-term changes in gut microbiomes after transient perturbations
It is typical of complex dynamical systems, such as ecosystems, that perturbation may dislodge the system from its current basin of attraction, causing it to settle into an alternative stable state after the perturbation 18, 19. This type of behavior has been observed after perturbation of human gut microbiomes by a short course of antibiotics [14]. This observation has led to concerns that antibiotic treatment could accidentally cause an unexpected shift to an alternative stable state in a
Individualized responses to perturbation of gut microbiomes
In the standard paradigm of simple causation, a system can not be understood until experiments can be replicated and repeatable results produced. Thus, it is perplexing that different individuals responded differently to the same experimental treatment of perturbing their gut microbiome. A key consequence of multistability is that different instances of the same type of system, such as different individual gut microbiomes, may show very different responses to the same perturbation. Even within
Concluding remarks
Biologists have often been tasked with the difficult problem of managing complex ecosystem dynamics. Medical professionals have not been in the past, but that is rapidly changing. Because of the broad health importance of the human gut microbiome, all available conceptual tools must be used to understand and manage it. This is a pressing concern for public health as well as medicine. Beyond the issue of perturbing a single individual's microbiota, extensive antibiotic use, along with other
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Invasions of Host-Associated Microbiome Networks
2017, Advances in Ecological ResearchCitation Excerpt :We believe that ecological and evolutionary theory can be a unifying framework from which patterns and principles can emerge. There have been several attempts at synthesizing ecological methods and concepts to aid researchers studying the microbiome (e.g. reviews by Costello et al., 2012; Ley et al., 2006; Pepper and Rosenfeld, 2012). Here, our focus is more targeted.
Changes in human gut microbiota influenced by probiotic fermented milk ingestion
2015, Journal of Dairy ScienceCitation Excerpt :It was previously reported that a temporal core of 33 to 40 species that account only for 12% of the total OTU added up to >75% of the total sequences over a 1-yr period (Martínez et al., 2013). Various external influences such as diet change, geography, inflammation, stress, and physiological state could cause temporal variations within individuals (Pepper and Rosenfeld, 2012; Tremaroli and Backhed, 2012). Results from analysis of genus abundance also showed the relative abundance of probiotic strains during and after PFM ingestion.
Bioengineering the biosphere?
2015, Ecological ComplexityCitation Excerpt :In this context, it has been proposed that processes associated to invasion by pathogens can be understood in terms of standard invasion ecology. Treatments and recoveries from disturbance can actually be represented in terms of shifts among alternative states (Costello, 2012; Pepper and Rosenfeld, 2012). The human microbiome can thus be regarded as a large scale, multispecies ecosystem where both the effects of perturbations and potential recovery scenarios can be traced in detail.
Cyclic control equilibria for switched systems with applications to ecological systems
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