The trillions of microbes that inhabit your gut form complex interactions with each other and with their human host. An altered gut microbiota has been associated with a number of different diseases. Understanding the microbiome as an ecosystem can help identify means of restoring gut health and increase its resilience to future disturbances.
A few weeks ago, I attended Mayo Clinic’s Center for Individualizing Medicine Conference. Dr. David Relman, Professor of immunology and microbiology at Stanford, gave a fascinating lecture at about applying ecological theory to the microbiome. I had taken an ecology class in undergrad, and have studied the microbiome for over three years, yet I’d never applied my knowledge of ecology to thinking about the microbiome. Needless to say, I had a major shift in perspective!
A microbial rainforest
Imagine a rainforest. There are thousands of different species, all of which have their own specific “niche” in the forest. Some species interact with others to form complex networks that are mutually beneficial. Other species are predators, seeking out prey species. Still others are competing with members of their own species for limited resources.
What determines which species can thrive? The location, climate, available habitats, food sources, and community dynamics will all influence the overall composition of the community. If new species are introduced or a natural disaster occurs, the community composition will undoubtedly shift.
This is obvious in the case of a biological habitat like a rainforest. But the same thing is happening in your gut, right now. On a microscopic scale, thousands of microbial species are cooperating, competing, and fighting for their niche.
The gut as a community
We can think of the gut as a community of microbes – an ecosystem. It’s not a question of just one or two or three species; rather, it’s about how they are interacting and influencing complex, community-wide changes.
Moreover, it’s the habitat that determines what microbes can survive. This is why you don’t have the same microbes on your skin or your mouth as you do in your gut. The environment of the gut naturally selects for the microbes that thrive in that habitat.
So why don’t we all have the same gut microbiome? Several factors, including our genetics, diets, lifestyles, geographical location, and environmental exposures can all influence community dynamics by causing slight variations in the gut habitat from one person to the next. In fact, there is no one “healthy” microbiome, and even a single individual will show some change over time.1
Protecting or restoring the ecosystem
Think of yourself as a park ranger, responsible for maintaining the health of a rainforest. You’d probably keep a close eye on any invasive species. You’d also want to ensure the health of native species by making sure they had the foods and other resources they need to survive. You might even track the stability of the ecosystem over time. This is called conservation ecology.
If the forest is ravaged by a disturbance, you might help restore it by taking more drastic measures, such as providing certain nutrients to the ecosystem, removing invasive species, and reseeding it with native species. This is called restoration ecology. The restored ecosystem might not look exactly the same as it did before, but in many cases, it is healthy and can serve the same functions.
Now think of yourself as a park ranger for your gut ecosystem. If you have a relatively healthy gut microbiota, you’d want to continue to support the beneficial microbes with nutrients, and inhibit the growth of pathogenic microbes by limiting their food sources. In this way, you would increase the resilience of the ecosystem to any minor disturbances. Of course, you’d still want to avoid any major disturbances, like antibiotics or parasitic infections.
If you’re a park ranger of a gut ecosystem in need of repair, you’d first want to get as much information about the system as possible. What invasive species are present? What foods are these species relying on? Has the habitat been altered? How stable is this system? Later, I’ll discuss specific steps to repair a damaged gut ecosystem. But first, a quick lesson in community stability.
Peaks and valleys: multiple stable states
A community stability landscape can be a helpful way of visualizing the resilience of a community to disturbances. Take the figure below. Each ecosystem is displayed as a circle, and its position on the landscape is a depiction of how stable it is at any given time. The deeper the valley, and the steeper the walls around it, the more stable the community is. In other words, the community is more resilient to disturbance; you’d need a very strong disturbance to get out of that valley, and then you might be able to “fall” into another valley. The shallower the valley, the easier it is to perturb the system and achieve an alternative stable state.
(Adapted from Costello et al., 2012)2
Of course, the terrain that separates the valleys is varied and variable, and will depend on the individual. Additionally, these valleys can be associated with health or disease, and disturbances can be good or bad. If you take several courses of antibiotics, this could be a large enough disturbance to shift the community out of the “healthy” valley and allow the community to “fall” into a valley associated with disease.
Similarly, if you’re in a “disease” stable state, the depth of the valley will determine the size of the disturbance necessary to shift the community back to a “healthy” stable state. For instance, some people might be in a shallow “disease” valley, and able to shift the community back to a “healthy” valley simply by improving their diet. Others might need targeted antibiotics, antimicrobials, or a restrictive diet to cause a massive disturbance and remove overgrown “invasive” species.
Computer modeling of microbial ecosystems provides clues
[Warning: this section is for the true microbiome/ecology geeks only – all others can skip to my recommendations in the following section.]
Researchers have already used complex computer modeling to predict several factors that influence microbial community stability.3
Competition: Interestingly, communities that have mostly competitive interactions are more stable, while those that are highly cooperative tend to be unstable. It’s thought that too much cooperation can create dependency, so if one species decreases in abundance, it can pull others down with it and derail the entire community.
Diversity: we typically think of a healthy microbiome as a diverse one, but at a certain point, increasing diversity tends to destabilize a community. However, competition can have a stabilizing effect that is dominant over, and may compensate for, the destabilizing effects of increased species numbers.
The immune system: during infection or gut dysbiosis, adaptive immunity can help by suppressing species that are highly abundant and causing harm. This density-dependent regulation is stabilizing to the community by preventing run-away positive-feedback loops.
Spatial structure: increased spatial structure, where growth of species is patchy and there is limited mixing, reduces the strength of interactions between species. This improves community stability.
Host feeding: many microbial species can thrive on nutrients provided by the host gut epithelium. Host feeding provides another carbon source for microbes and allows populations to grow until they are limited by the capacity of the host. This means more competition; thus, host feeding improves community stability.
How we can use this to push the microbiome from one stable state to another
Hopefully, you’ve now learned some basic ecology, and have a new perspective on the microbes inside you. Looking at the microbiome in this way can help us predict disease, confirm the return of health, and work to improve the resilience of our microbial communities to future disturbances. This is incredibly powerful and truly the future of microbiome medicine.
If you’re wondering how you might apply this information to your own gut ecosystem, here’s a few suggestions.
If you’re in a healthy state:
- Find out what microbes are there. This isn’t totally necessary for a healthy person, but it can be very interesting. It may also inform ways to further increase the health and resilience of your gut microbiota. See my suggested tests below.
- Increase your resilience to disturbance. Eat plenty of fiber and fermented foods, limit simple sugars, exercise, get plenty of sleep, and entrain your circadian rhythms. All of these are important for the health of the gut habitat and its microbes.
If you’re in a disease state:
- Find out what microbes are there and the state of the gut habitat. I have no affiliation with any of these companies, and all can be ordered direct-to-consumer.
- Comprehensive Stool Analysis with Parasitology (Doctor’s Data): provides the major bacterial groups present using culture-based methods, along with identification of parasites and several markers of digestion, absorption, inflammation that give an overall picture of the gut environment.
- 16S rRNA microbiome sequencing (UBiome): tells you which bacteria are present at the genus level. It is more sensitive and accurate than culture-based methods, but only tells you about bacteria and does not provide information about the gut environment.
- SIBO breath test: identifies whether bacterial overgrowth is present in the small intestine
- Urine organic acids test: can identify Clostridia or yeast overgrowth, nutrient deficiencies, and other metabolic imbalances
- Use narrow spectrum antibiotics or targeted antimicrobials to remove or knock-down pathogenic species
- Eliminate simple sugars that feed pathogenic bacteria
- Consider a short-term restrictive diet to starve specific types of pathogenic bacteria
- Restore the habitat: restore colonic pH and repair the mucosal lining
- Re-seed the gut with native species (think soil bacteria, not most probiotics you see in grocery stores)
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- Faith, J. J. et al. The long-term stability of the human gut microbiota. Science 341, 1237439 (2013).
- Costello, E. K., Stagaman, K., Dethlefsen, L., Bohannan, B. J. M. & Relman, D. A. The application of ecological theory toward an understanding of the human microbiome. Science 336, 1255–1262 (2012).
- Coyte, K. Z., Schluter, J. & Foster, K. R. The ecology of the microbiome: Networks, competition, and stability. Science 350, 663–666 (2015).