How Your Gut Bacteria Change With the Seasons

How Your Gut Bacteria Change With The Seasons

We often think of our ancestors as being more in touch with nature. And it's true––from using the solstices to mark certain times of the year to planting and harvesting according to specific changes in the weather, people in the past structured their lives more in tune with the rhythm of the seasons.

But recent research on the microbiomes of hunter-gatherers has shown that this connection with the seasons wasn't only grounded in external practices––it was biological, too.

A study of the gut microbiomes of the Hadza people of Tanzania showed that their gut populations vary seasonally, with certain types of microbes appearing during specific seasons, then dropping down to almost undetectable numbers in other seasons.1 Since the Hadza are one of the few remaining hunter-gatherer tribes, they can give us some of the clearest insights into what humanity’s gut health looked like for most of its history.

Why Is Seasonal Variation So Important?

The idea of change in the microbiome is nothing new; your gut microbiome is in constant flux. The unique mix of species found in your body changes according to what you eat, where you live, how much you exercise, how much contact you have with animals and other people, and even how much time you spend inside!2,3,4,5,6 But the recurring seasonal component is a new twist in microbial research, and scientists aren't entirely sure why it happens.

The prevailing thought is that this microbial shift has to do with the changes in what the Hadza eat during their two primary seasons. During the wet season, they tend to eat more berries, honey, and foraged foods, and their microbiomes reflect that, with species of bacteria that thrive on these types of food proliferating. During the dry season, though, their diet shifts more towards meat and those wet season bacteria drop dramatically, while bacteria related to meat consumption increase—making the microbial mixes much closer to those of people in industrialized societies.

The Possibility of Permanent Changes

Here's where it gets really interesting: In the Hadza, this pattern repeats year after year, with the bacteria counts reliably going up and down. However, the study also found that those bacteria that essentially disappear during the dry season in the Hadza also show up in very low numbers––or are entirely absent––in the microbiomes of those living in modern, Western societies.

When you combine this with research indicating that our gut microbiomes may have developed to change in response to temperature fluctuations, you get some fascinating implications.

Our bodies appear to have evolved to naturally adapt to seasonal changes—for instance, research shows that people who live in colder climates have different microbial compositions than those who live in warmer climates, and other studies show that exposure to cold changes the make-up of your microbiome in replicable, specific ways.7 While research is still ongoing, it looks like our bodies are meant to slow down and focus on fattening up in response to cold so that we can survive the winter. Exposure to cold can lead to shifts in your metabolism, your body tends to absorb calories faster, and your gut composition trends towards microbes that digest heavier, starchier foods better.8

Of course, this only applies if you're living a lifestyle that exposes you to seasonal change––and for many in the modern Western world, we experience much of the seasons by looking out the window. Spending time in climate-controlled buildings and eating a standard diet year round can confuse your body into thinking that the seasons aren't actually changing, which means that it doesn't transition completely into "spring mode."

And since research shows that changes in bacterial populations can become permanent over generations, the stakes become even more clear. While our ancestors' and the Hadza's microbiomes have the diet and lifestyle support they need to recover from season to season, many of our microbiomes don't, and the effects could be more serious than we thought.9

How You Can Seasonally Support Your Microbes

While the potential effects of microbial depletion are serious, things certainly aren't hopeless. You've got plenty of gut-friendly options for living more seasonally and supporting your microbiome year round, including:

1. Following seasonal light cues.

A healthy microbiome and good sleep go hand in hand. Your gut microbes help to produce or trigger the production of hormones related to sleep, including melatonin, which signals your body that it's time to sleep; serotonin, which helps you sleep deeply; and GABA, which makes you feel calm. This relationship works the other way too: even short-term sleep deprivation can throw your bacterial balance off, with studies showing that just two nights of sleep deprivation can cut the number of certain beneficial strains in half!10

You can help keep your microbiome and sleep cycles working properly by maintaining good sleep hygiene, supplementing with a premium probiotic like PRO-15, and looking to seasonal light cues.

Our bodies respond to changes in light––we're supposed to start winding down as the sun sets. This means that in pre-modern societies, people typically went to bed much earlier in the winter and stayed up later in the summer. However, using electric lights and spending a lot of time indoors throws this rhythm off, making your body think that daylight lasts for much longer than it actually does and causing your system to miss out on seasonal clues, like the sun setting earlier in the winter or later as we head into spring.

While it's probably not possible to totally change your schedule to go to bed with the sun, you can at least be aware of the shifts in light and try to follow your body's natural sleep rhythms a little more closely, so your bacterial good guys can maintain their Circadian rhythms and support high quality sleep. If nothing else, try to avoid using blue light screens after dinner: the light they emit can throw your Circadian rhythm off, leaving your body thinking it's daylight during the summer when it's actually after dark in winter!

2. Eating seasonally whenever you can.

As convenient as it may seem to have peaches in March, eating things out of season isn't the best option for your gut microbiome––which makes sense, given that we evolved eating seasonally. Foods forced to develop out of season contain lower levels of nutrients and higher levels of harmful substances like lectin, which damages the walls of your intestines and makes it easier for your gut microbiome to become unbalanced.11

What's more, unseasonal foods are commonly treated with pesticides or chemicals to speed up ripening, neither of which is good for your gut. So take a page from the Hadza playbook and try to change your diet in line with the seasons, emphasizing seasonal produce and local, organic food to protect your microbes and give them the support they need to really thrive.

3. Getting outside as much as possible.

Americans spend an average of 90% of their time indoors (usually in airtight buildings that don’t allow in fresh air), which is drastically different than how humans historically lived. We evolved to thrive in outdoor environments and adapt to the way they change season by season, and one of the ways that plays out is in the gut microbiome.

Spending time in nature increases your microbial diversity, both by exposing you to all kinds of different bacteria and by lowering your stress levels. (When you're stressed, your body slows down digestion to the point that only bacteria that can cope with a slow food transit time survive. This lowers the diversity of your microbiome, which makes it much more likely for it to become unbalanced.)

If you tend to spend certain seasons (like spring!) indoors because you're worried about pollen, consider this: spending time outside trains your immune system to react appropriately to stimuli, so getting outdoors in non-pollen seasons could help give you the microbe-rich environment you need to calm overactive immune responses.12

4. Giving your microbes year-round support with prebiotic fiber.

One of the best things you can do to enhance your seasonal microbe care is to make sure you're giving your microbes enough prebiotic fiber all year long. While our ancestors consumed between 50 and 100 grams of fiber a day (and had fantastically diverse microbiomes as a result!), most of us only get about 10-15 grams.13 Prebiotic fiber specifically feeds the beneficial species that tend to struggle or even disappear in the face of modern Western stressors, including those at risk of permanently disappearing. So try to get as much of it in your diet as you can, and consider supplementing with a premium prebiotic powder to make sure you're giving your good guys the support they deserve.

As the seasons show us, change is a constant, whether that's something as simple as a change in the weather or something as profound as a shift in the way we live our lives. But as humans, we're incredibly adaptable, and now that research has made it clear just how important our microbial friends are, taking measures to protect and support them is an obvious next step. So try to change with the seasons, at least a little bit––once you start, you'll find it surprising how fast it feels like your new normal!


1. Smits, S.A., Leach, J.L., Sonnenburg, E.D., Gonzalez, C.G. . . . Sonnenburg, J.L. (2017). Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania Science, 357(6353), 802-806 doi: 10.1126/science.aan4834

2. David, L. A., Maurice, C. F., Carmody, R. N., Gootenberg, D. B., Button, J. E., Wolfe, B. E., . . . Turnbaugh, P. J. (2013). Diet rapidly and reproducibly alters the human gut microbiome. Nature, 505(7484), 559-563.

3. Ege, M.J., Melanie Mayer, M., Normand, A.C., . . . Mutius, E. (2011). Exposure to Environmental Microorganisms and Childhood Asthma. The New England Journal of Medicine, 364, 701-709 doi: 10.1056/NEJMoa1007302

4. Clarke, S. F., Murphy, E. F., O'Sullivan, O., Lucey, A. J., Humphreys, M., Hogan, A., … Cotter, P. D. (2014). Exercise and Associated Dietary Extremes Impact on Gut Microbial Diversity. Gut, 63(12), 1913-1920. doi:10.1136/gutjnl-2013-306541

5. Fujimura, K.E., Johnson, C.C., Ownby, D.R., Cox, M.J. . . . Lynch, S.V. (2010). Man's Best Friend? The Effect of Pet Ownership on House Dust Microbial Communities. The Journal of Allergy and Clinical Immunology, 126(2), 410-2, 412.e1-3 doi: 10.1016/j.jaci.2010.05.042

6. Kort, R., Caspers, M., van de Graaf, A., van Egmond, W., Keijser, B., & Roeselers, G. (2014). Shaping the oral microbiota through intimate kissing. Microbiome, 41.

7. Suzuki, T.A., Worobey, M. (2014). Geographical Variation of Human Gut Microbial Composition. Biology Letters, 10(2). doi: 10.1098/rsbl.2013.1037

8. Chevalier, C., Stojanovic, O. Colin, D.J., Zamboni, N. Hapfelmeier, S., Trajkovski, M. (2015). Gut Microbiota Orchestrates Energy Homeostasis During Cold. Cell, 163, 1360–1374. doi: 10.1016/j.cell.2015.11.004

9. Erica D. Sonnenburg, E.D., Smits, S.A., Tikhonov, M. . . . Sonnenburg, J. L. (2016) Diet-induced Extinctions in the Gut Microbiota Compound Over Generations. Nature, 529, 212-5doi: 10.1038/nature16504

10. Benedict, C., Vogel, H., Jonas, W., Woting, A., Blaut, M., Schürmann, A., & Cedernaes, J. (2016). Gut microbiota and glucometabolic alterations in response to recurrent partial sleep deprivation in normal-weight young individuals. Molecular Metabolism, 5(12), 1175-1186. doi:10.1016/j.molmet.2016.10.003

11. Gundry, S. R. 2017. The Plant Paradox: The Hidden Dangers in "Healthy" Foods That Cause Disease and Weight Gain. New York, NY: Harper Wave.

12. Abreu, N. A., Nagalingam, N. A., Song, Y., Roediger, F. C., Pletcher, S. D., Goldberg, A. N., & Lynch, S. V. (2012). Sinus Microbiome Diversity Depletion and Corynebacterium tuberculostearicum Enrichment Mediates Rhinosinusitis. Science Translational Medicine, 4(151). doi: 10.1126/scitranslmed.3003783.

13. Brownawell, A. M., Caers, W., Gibson, G. R., Kendall, C. W., Lewis, K. D., Ringel, Y., & Slavin, J. L. (2012). Prebiotics and the Health Benefits of Fiber: Current Regulatory Status, Future Research, and Goals. Journal of Nutrition,142(5), 962-974. doi:10.3945/jn.112.158147


Rachel Allen is a writer at Hyperbiotics who's absolutely obsessed with learning about how our bodies work. She's fascinated by the latest research on bacteria and the role they play in health, and loves to help others learn about how probiotics can help the body get back in balance. For more ideas on how you can benefit from the power of probiotics and live healthier days, be sure to subscribe to our newsletter. To learn more about how a healthy microbiome can enrich your life, subscribe to our newsletter.