“Great”, you’re thinking, “I’m covered in little germs microbes and they live on me in their special habitats, icky, but so what?” These microbes may provide specific benefits, such as the nutritional examples mentioned earlier. However, perhaps one of the biggest services these microbes have is simply taking up space! “Niche filling” or “colonization resistance” is an important and essential ecosystem service. In any habitat, there are places to live and nutrients to feed upon. An example is my attempt at gardening. Each spring we clean out the garden and plant seeds and seedlings. Most years we put down weed cloth around the seedlings. My organic gardening teacher recommended planting clover as a cover crop. Both are doing the same thing – filling an available habitat to prevent weeds from colonizing and competing with the plants that we hope to harvest later. This past summer I got busy and didn’t get the weed cloth down. UGH. The weeds overtook the garden this year and we only got a few tomatoes and peppers. The squash, beans, and broccoli were overrun. Bummer – lesson reinforced.

Similarly, your microbial ecosystem needs to stay intact, filled, and in balance. Aristotle once said “Nature abhors a vacuum”. When there is a space and nutrients where an organism can live some critter will move in there. This is especially true in disturbed areas like at the edge of a forest or roadside or after clear-cutting or a tree fall. Your body is the same way. Disturb your native microbiome and those habitats open up for new and potentially pathogenic microbial colonizers. However, there are different types of disturbance, some that are more damaging and more likely to result in disruption (or dysbiosis) of the human microbial ecosystem.

Changing seasons, shifting nutrients

At, and perhaps before, birth you are seeded with microbes from your mother [1]. Those initial “seed” microbes multiply to fill the available habitats and keep out pathogens. In the gut, different types of bacteria will dominate depending on the nutrients the person feeds upon and can change over time with changing diets. Those microbes that can feed on plant fibers, such as cellulose, will increase in number when you eat a salad. Eat a steak and baked potato with melted cheese and sour cream and a different set of bacteria will increase in your microbiome. One recent study had 10 volunteers drastically change their diet between being plant-based (grains, legumes, fruits and vegetables) to animal-based (meat, eggs, and cheese).

Figure 7c. Levels of bacteria (using 16S rRNA) and fungi (using ITS) associated with the animal-based diet are plotted over the plant- and animal-based diet arms. Lactococcus lactis, Pediococcus acidilactici and Staphylococcus-associated reads all show significantly increased abundance on the animal-based diet (P < 0.05, Wilcoxon signed-rank test). For fungi, significant increases in Penicillium-related fungi were observed, along with significant decreases in the concentration of Debaryomyces and a Candida sp. (P < 0.05, Wilcoxon signed-rank test). g=genus, s=species. David, L. A., et al. 2014. Diet rapidly and reproducibly alters the human gut microbiome. Nature 505:559-563.

Although the participants only fed on the different diets for 5 days, most participant’s microbiomes shifted when the diet changed! [2] The speed and degree of the changes in the microbial communities was impressive.

The mac-n-cheese influence

These diet induced fluctuations are one example of disturbance or changes in the environment in which the microbes live. As the nutrients change, so do the types of bacteria that can feed upon those food stuffs. As a science mom obsessed with microbes, it’s been hard watching my oldest daughter’s diet change. When Jac began eating solid foods, she ate a wonderful balance of diverse fruits, vegetables, spices, grains, meats, and dairy products. At 4, her list of acceptable foods began to shrink. Two years later she’s focused primarily on meat, cheese, and milk with apples, carrots, and broccoli thrown in here and there. There are a few other fruits she eats sometimes and, hmm should you consider all the ketchup she slathers on real food a vegetable? Overall, her current diet is a shadow of the healthy diversity it once was. It’s some consolation to me that perhaps those plant-fiber loving bacteria are kept going by those few fruits and veggies or are simply waiting for the time for her appetite to expand again. She loves animals, so I appeal to the “zookeeper” in her. I tell her to “feed her good bacteria” the food they need! (This is what happens when you talk about beneficial microbes too much around your kids). Sometimes it works.

Other studies of modern hunter-gatherer populations suggest that these diet induced changes in the microbiome are normal [3]. Such fluctuations may have helped our ancestors feed on a diversity of foods and perhaps even to expand into temperate regions where the seasons and thus different foods available change.

Scurf and other mouth stuff

Another example of normal disturbances of the microbiome occurs when you brush your teeth. The plaque covering your teeth is secreted by bacteria as they are attaching and forming cities of bacteria, called biofilms. (See this post for the first scientific description of tooth “scurf”.) The mechanical act of brushing and flossing removes a portion of the bacterial community. Remaining members recolonize the tooth’s surface, especially when nutrients they can feed upon are present [4]. Again, it’s the presence and abilities of native members of the oral microbiome who colonize the mouth, removing places for potential pathogens to live and feed. Whenever I think of this “niche filling” benefit that our healthy microbiome provides, I think of Dr. Seuss’s poem about nutches and nitches.

Anne and baby Emily’s rendering ala Crayola of nutches and niches in the gut.




So take care of your zoo of microbial pals. When those nutches colonize your niches they are helping YOU out by keeping out potential pathogens. With these natural disturbances of the microbiome, a subset of the normal microbiome members and healthy diversity can remain. From this subset of cells, the healthy microbiome can regrow and rebound given time and the proper conditions. In contrast, the next post covers disturbances that are catastrophic to the native microbiome from which healthy recovery is more difficult.


  1. Dominguez-Bello, M. G., E. K. Costello, M. Contreras, M. Magris, G. Hidalgo, N. Fierer, and R. Knight. 2010. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proceedings of the National Academy of Sciences 107:11971-11975.
  2. David, L. A., C. F. Maurice, R. N. Carmody, D. B. Gootenberg, J. E. Button, B. E. Wolfe, A. V. Ling, A. S. Devlin, Y. Varma, M. A. Fischbach, et al. 2014. Diet rapidly and reproducibly alters the human gut microbiome. Nature 505:559-563.
  3. Schnorr, S. L., M. Candela, S. Rampelli, M. Centanni, C. Consolandi, G. Basaglia, S. Turroni, E. Biagi, C. Peano, M. Severgnini, et al. 2014. Gut microbiome of the Hadza hunter-gatherers. Nat Commun 5.
  4. Zaura, E., E. A. Nicu, B. P. Krom, and B. J. Keijser. 2014. Acquiring and maintaining a normal oral microbiome: current perspective. Front Cell Infect Microbiol 4:85.



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