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Save the Microbes! Why We Need to Care for Our Tiny Critters

As humans, we’ve done a lot over the past several decades to help save endangered species and support the planet. From successes like getting giant pandas moved from "endangered" to "vulnerable" lists in 2016 to more local initiatives like communities turning their former fishing waters into a national park to encourage the growth of fish species, we have lot to be hopeful about.

From whales to wallabies, as a species we're usually quick to get on board with a campaign to save the creatures and environment around us (and rightfully so). But up until recently, we've overlooked one of the most important elements of our inner ecosystem: our bacteria.

We're planting a flag for this important cause: save the microbes!

OK, that might sound a little out of the box. After all, we've been taught to think of microbes
 as something to fight, that they're dirty, and maybe even dangerous. While it's true that some bacteria are harmful, most of them are actually incredibly beneficial to your body.

How Do Our Microbes Help Us?

You're completely covered with bacteria, inside and out. Before you start reaching for the hand sanitizer, though, remember that this is a great thing. The bacteria that make up your microbiome are partially responsible for everything from how well you sleep to your moods.1 And, these bacteria exist in a delicately balanced ecosystem. When the balance is about 85% beneficial microbes to 15% bad, everything is much more likely to work the way it should. (And we do mean everything: your immune system, stress levels, energy, weight management, skin, and nutrient absorption can all benefit, among other things.)

How can something that’s, well, microscopic, have such a huge impact on your health? Let’s take a look:

• Immunity: 80% of your immune system's cells live in your gastrointestinal tract, so it's no surprise that your gut microbiome supports your immunity. Good bacteria in the gut support your immune system in several different ways: they encourage a strong gut barrier, assist with protein synthesis (which is key for a proper immune response), and help the body produce the enzymes you need to stay healthy. Some microbes even produce antibodies that fight bad guy bacteria!2,3

• Digestion: The good bacteria in your gut not only help your body produce the enzymes it needs to break down foods for digestion—some bacteria even manufacture the enzymes themselves! For instance, L. reuteri produces lactase, the enzyme needed to break down dairy products.4

• Nutrient absorption: Beneficial bacteria in your digestive tract help your body properly absorb the nutrients from food by working with enzymes to break it down to the molecular level, so it becomes small enough for your body to absorb. They also support the health of your microvilli, the tiny, finger-like projections on the walls of your intestines that are key players in nutrient absorption.5

• Mood regulation: Gut bacteria are responsible for supporting the production or regulation of several important mood-related hormones and neurotransmitters, including serotonin (the "happy" hormone), GABA (which helps you stay calm), and oxytocin (the "cuddle" hormone). Beneficial microbes also help to support appropriate amounts of cortisol and adrenaline in your body, both of which are associated with stress.6,7

In light of all this, it's clear that microbes are one of the best allies we have in our quest for vibrant health. And yet, many elements in our modern culture threaten and outright destroy them—especially the misuse of antibiotics.

The Overuse of Antibiotics as Medicine and in Our Food Supply

Antibiotics kill bacteria indiscriminately, meaning that while they do wipe out the bad guys, they also destroy the good guys! This creates conditions where inhospitable bacteria can come in and recolonize before the good guys get going again.8 And this doesn't only affect you when you take medical antibiotics––many people are routinely exposed to antibiotics in food (often, without even knowing it). Did you know that the majority of antibiotics in the U.S. are consumed by livestock?

And we simply can’t talk about the overuse of antibiotics without bringing up the impending crisis of antibiotic resistance. While antibiotics are incredibly valuable when used appropriately, we've used them so indiscriminately over the past half a century that we've caused undesirable bacteria to evolve so that antibiotics are no longer effective against them. The consequences have the potential to be devastating: in fact, the World Health Organization states that antibiotic resistance is one of the biggest threats to both global health and food security in the world!

Other Threats to the Microbiome

Clearly the microbiome plays a crucial role in keeping us healthy. But for most of us, this balance is constantly under threat. Common, day-to-day activities in our modern Western lifestyles are really tough on good bacteria. The top threats to the microbiome and its microscopic inhabitants include:

• A low-fiber diet that's high in processed foods, dairy, sugar, and gluten. Dairy and sugar are two of your unfriendly bacteria's favorite foods, while gluten reduces the amount of certain types of important bacteria in your gut.9,10,11 What's more, most of us struggle to consume the daily recommended amount of 25 grams of fiber––which is particularly troubling when you consider that our ancestors got 50 to 100 grams of fiber a day!

• A sedentary lifestyle. Our current lifestyle––consisting largely of sitting––means that our microbiomes aren't nearly as diverse as they could be. Exercise is strongly connected with microbial diversity; studies show that regular, moderate movement increases the number of beneficial bacteria by up to 40%!

• Stress and too little sleep. Stress reduces the amount of blood flow to your gastrointestinal system and slows your digestion, which, over time, can reduce the diversity of your microbiome.12 And even just a few nights of getting too little sleep can drop the numbers of certain types of beneficial bacteria by a staggering 50%!13

• Pollution and environmental toxins. Americans spend 90% of their time indoors—a potentially serious problem given that most modern buildings are built in a way that encourages indoor air pollution. The result? You're exposed to a harmful microbial-toxin mix, which can damage your microbiome.14

• Overzealous cleaning. We've been taught that having a certain level of cleanliness is important for hygiene. And while it's true that some cleaning is necessary, we've gone really overboard with the whole hygiene idea. The way we clean now harms the microbiome, both through exposure to antibacterial cleansers and by removing good bacteria from our surroundings.15

Think Global, Act Microbial

When the microbiome is unbalanced or depleted, the consequences to health are potentially huge, both on an individual and global scale.

You see, your friendly flora don’t just affect you, they affect the people in your life, too. The vitality and wellness you can experience when your gut is in balance not only benefits your health and happiness, it allows you to contribute more to the world around you. And, consider this: you share your microbes with the people you're close to, which means that the healthier your microbiome is, the better influence you can have on the microbiomes of those near to you.16

And if you're a mother, you pass your microbiome directly to your child during the vaginal birth process, through breast milk, and via skin to skin contact. This "starter microbiome" sets your child up for a lifetime of better health, high cognitive functioning, and even a higher income potential.17,18 So while it may seem like passing on beneficial bacteria to your child is a family-specific benefit, the potential impact on global health (and healthcare costs), innovation, and the worldwide economy is incredible.

That's why we're doing our best to save the microbes. And we'd love for you to join us!

How to Save Your Mighty Microbes

You don't have to go on a march to save the microbes (although if you want to get that going, we're not going to stop you! In fact, we'd probably join in...) But you can nurture your own tiny critters in these ways too:

1. Watch what you eat, and pass on gut-friendly eating habits.

Your diet has a huge affect on your microbiome, so try to eat seasonal, local, and organic, whole food as often as you can. This means read labels and avoid additives, preservatives, emulsifiers, sugars, and all those fancy words you can’t pronounce; and instead focus on food that's wild caught, free range, and antibiotic-free.

By being more mindful of what you put into your body, you'll not only set yourself up for good gut health, you'll be able to model gut-friendly eating choices for others.19 Not sure where to start? We have a whole archive of gut-friendly recipes, plus a free cookbook for you!

2. De-stress, prioritize sleep, and move your body.

These three go hand in hand: by making it a point to manage your stress levels and practice good sleep habits, you help your body generate the energy it needs for effective exercise. Exercise in turn lowers your stress levels and helps you sleep well. One great way to support appropriate stress levels and good sleep is by reducing your screen time: studies show that spending more time on screens makes it hard to concentrate and can interrupt your sleep cycles. Similarly, exercising regularly can help encourage healthy sleep habits and reduce stress––all while supporting your microbiome.

3. Only take antibiotics when you absolutely need to.

As tempting as it may be to try to convince your doctor to give you antibiotics when you're not feeling well, it's really irresponsible (both in terms of your health and in terms of our health as a species). So stick to natural remedies when you can, and listen to your doctor's advice when they tell you that you can get back to feeling bright eyed and bushy-tailed without having to take antibiotics. If you are in a situation where they're necessary, make sure you give your microbiome extra love—studies show it can take a full year for it to bounce back after being exposed to antibiotics.20

4. Trade in your cleaning products for natural alternatives.

One of the easiest things you can do to protect your bacteria is to trade in your cleaning products for natural products, and ease up on the cleaning in general.

Another thing to try: hand wash dishes instead of using the dishwasher. Studies show that doing this exposes you to lots of beneficial microbes, which diversifies your microbiome and teaches your immune system to respond appropriately to stimuli, instead of overreacting to every little thing.21

5. Spend time with animals.

You might have had one of the best probiotic sources hanging out in your home the whole time: your pets! Pets are a great source of bacteria, since they tend to roll around in the dirt outside, then track it (and the bacteria it contains) back inside. Once it's in your living space, you become exposed to it and you diversify your microbiome without even trying. Plus, spending time with pets has all kinds of other health benefits, like decreased stress and improved immunity in children!22

6. Open your windows.

You really can't get much simpler than just opening a window. But even this seemingly-small action can have a big impact on your bacterial friends. Since buildings are designed to be as air-tight as possible, bacteria can't get in or out easily. This means that the "bacterial soup" of old bacteria and the unsavory substances they can emit tends to stagnate inside, leading to a proliferation of inhospitable bacteria––and the negative effects they have on our health! All of this can be remedied by simply opening the windows when you can to let the outside in.

7. Support your microbial populations with probiotics and prebiotics.

Give your inner microbial ecosystem the love it deserves by bringing a mix of probiotics and prebiotics on board. (In case you were wondering, probiotics are beneficial bacteria, and prebiotics are the indigestible fibers that feed them.) Since our modern Western lifestyle makes it really hard to get enough of either one, supplementing with a premium probiotic like PRO-15 and a food-based, organic prebiotic powder helps introduce a host of friendly flora to your gut, along with the perfect nutrition those little good guys need to thrive.

Modern life has been good to us in many ways, but it’s done a number on our microbes and we’re all paying the price. In fact, the average American adult has about 1,200 species of bacteria in their gut—this is a full third less than that of the Amerindians from the Amazonas of Venezuela, an indigenous group living a much more primitive, traditional lifestyle.

Thankfully, with the last 10 years of research, we now know better. The healthier our microbiomes are, the healthier we are, and the healthier the planet is as a whole. So do your best to save the microbes by making conscious lifestyle choices. If we start taking care of them the way they take care of us, we'll all benefit.


1. Hao, W.L., Lee, Y.K. (2004). Microflora of the gastrointestinal tract: a review. Methods in Molecular Biology, 268, 491-502.

2. Lievin, V. Peiffer, I. Hudault, S. Rochat, F. Brassart, D., Neeser, J. and A Servin, A. (2000). Bifidobacterium Strains from Resident Infant Human Gastrointestinal Microflora Exert Antimicrobial Activity. Gut 47(5). doi: 10.1136/gut.47.5.646

3. Pierre, P. (2009). Immunity and the Regulation of Protein Synthesis: Surprising Connections. Current Opinion in Immunology 21(1). doi: 10.1016/j.coi.2009.03.003.

4. Ojetti, V., Gigante, G., Gabrielli, M., Ainora, M.E., Mannocci, A., Lauritano, E..C, Gasbarrini, G., Gasbarrini, A.(2010). The effect of oral supplementation with Lactobacillus reuteri or tilactase in lactose intolerant patients: randomized trial. European Review for Medical and Pharmacological Sciences, 14(3), 163-170.

5. Shen, T.Y., Qin, H.L., Gao Z.G., Fan, X.B., Hang, X.M., Jiang, Y.Q. (2006) Influences of Enteral Nutrition Combined with Probiotics on Gut Microflora and Barrier Function of Rats with Abdominal Infection. World Journal of Gastroenterology 12(27).

6. Bravo, J. A., Forsythe, P., Chew, M. V., Escaravage, E., Savignac, H. M., Dinan, T. G., . . . Cryan, J. F. (2011). Ingestion of Lactobacillus strain regulates emotional behavior and central GABA receptor expression in a mouse via the vagus nerve. Proceedings of the National Academy of Sciences, 108(38), 16050-16055.

7. Tillisch, K., Labus, J., Kilpatrick, L., Jiang, Z., Stains, J., Ebrat, B., . . . Mayer, E. A. (2013). Consumption of Fermented Milk Product With Probiotic Modulates Brain Activity. Gastroenterology, 144(7).

8. Möhle, L., Mattei, D., Heimesaat, M., Bereswill, S., Fischer, A., Alutis, M., . . . Wolf, S. (2016). Ly6Chi Monocytes Provide a Link between Antibiotic-Induced Changes in Gut Microbiota and Adult Hippocampal Neurogenesis. Cell Reports, 15(9), 1945-1956.

9. 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.

10. Bonder M.J., Tigchelaar E.F., Cai X., Trynka G., Cenit M.C., Hrdlickova B., Zhong H., . . . Vatanen T., Gevers D., Wijmenga C., Wang Y. and Zhernakova A. (2016). The Influence of a Short-Term Gluten-Free Diet on the Human Gut Microbiome. Genome Medicine, 8(45). doi: 10.1186/s13073-016-0295-y

11. Magnusson, K., Hauck, L., Jeffrey, B., Elias, V., Humphrey, A., Nath, R., . . . Bermudez, L. (2015). Relationships between diet-related changes in the gut microbiome and cognitive flexibility. Neuroscience, 300, 128-140.

12. Bailey, M. T., Dowd, S. E., Galley, J. D., Hufnagle, A. R., Allen, R. G., & Lyte, M. (2011). Exposure to a social stressor alters the structure of the intestinal microbiota: Implications for stressor-induced immunomodulation. Brain, Behavior, and Immunity, 25(3), 397-407. doi:10.1016/j.bbi.2010.10.023

13. 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

14. Kembel, S.W., Jones, E., Kline, K., Northcutt, D., Stenson, J. . . . Green, J.L. (2012). Architectural Design Influences the Diversity and Structure of the Built Environment Microbiome. The ISME Journal 6. doi:10.1038

15. Arrieta, M., Stiemsma, L. T., Dimitriu, P. A., Thorson, L., Russell, S., Yurist-Doutsch, S., . . . Finlay, B. B. (2015). Early infancy microbial and metabolic alterations affect risk of childhood asthma. Science Translational Medicine, 7(307). doi:10.1126/scitranslmed.aab2271

16. Lax, S., Smith, D., Hampton-Marcell, J., Owens, S.M. . . . Gilbert, J.A. (2014). Longitudinal Analysis of Microbial Interaction between Humans and the Indoor Environment. Science 345(6200). doi: 10.1126/science.1254529

17. Rollins, N.C., Bhandari, N. Hajeebhoy, N. Horton, S. . . . Victora, C.G. (2016). Why Invest, and What it Will Take to Improve Breastfeeding Practices? The Lancet 387(10017). doi: 10.1016/S0140-6736(15)01044-2

18. Cesar G Victora, C.G., Bahl, R. Barros, A.J.D., França, G.V.A. . . . Rollins, N.C. (2016). Breastfeeding in the 21st Century: Epidemiology, Mechanisms, and Lifelong Effect. The Lancet 387(10017). doi: 10.1016/S0140-6736(15)01024-7

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

20. Zaura, E., Brandt, B. W., Mattos, M. J., Buijs, M. J., Caspers, M. P., Rashid, M., . . . Crielaard, W. (2015). Same Exposure but Two Radically Different Responses to Antibiotics: Resilience of the Salivary Microbiome versus Long-Term Microbial Shifts in Feces. MBio, 6(6). doi:10.1128/mbio.01693-15

21. Virant, F. S. (2015). Allergy in Children in Hand Versus Machine Dishwashing. Pediatrics, 136(Supplement).

22. Fall, T., Lundholm, C., Örtqvist, A. K., Fall, K., Fang, F., Hedhammar, Å, . . . Almqvist, C. (2015). Early Exposure to Dogs and Farm Animals and the Risk of Childhood Asthma. JAMA Pediatrics, 169(11).


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.

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