Understanding Your Gut Microbiome

Understanding Your Gut Microbiome

Kara Jacobson

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If you’re here, you’ve probably heard the term microbiome before. You might even be familiar with the difference between your microbiome and your gut. If not, don’t sweat it! This stuff gets confusing! Check out our Introduction to the Microbiome for the basics. Then we’ll dive into the nitty gritty details of what exactly your microbiome does for your entire body.

Now let’s break it down!

What does the microbiome do?

Our microbiomes are responsible for 4 major functions that keep our body running and contribute to our overall health.

  1. Mining calories and nutrients from food you cannot digest or metabolize.
  2. Producing very important and impactful compounds that your body depends on for function.
  3. Breaking down things you don’t want or need.
  4. Keeping “bad” pathogens away.

Ready for a closer look? Here’s what those functions really mean.

  1. Mines calories and nutrients from food and metabolizes things you can’t.
    You probably already know that your digestive system breaks down the food you eat.
    Duh! But did you know that your digestive system relies heavily on the microbiome to do almost half of the work?1

    It’s been shown that guts with a high abundance of bacteria extract 50% more nutrition out of their diets than those with a low abundance.1,3,4 With millions of people taking vitamin supplements every day, perhaps we should take a closer look at the health of our microbiomes first—simply getting your gut back on track may remove the need to supplement at all. That’s what I call working smart!

    These bacteria don’t just mine for nutrients, they actually help you break down stuff you can’t.1,3,4 Ever eaten something that gave you heart burn, bloating, or indigestion? You’re not alone. In fact, millions of people report experiencing this kind of post meal discomfort every day. And some even take it a step further, declaring that they’re allergic or sensitive to something in their diet. What if I told you that some of this sensitivity and indigestion could be alleviated by nurturing a healthy microbiome? It’s true! The bacteria in your gut can help break down some of the top allergens and sensitivity-causing food components.1-7 Hello ice cream!

    (By the way there are billions of dollars being made in that industry alone - aka lactose intolerance, food allergy testing, etc. - but that’s a whole other post).

  2. Produces very important and impactful compounds that your body depends on for function.

    This is probably the space where we have the most research, so no one blog post is going to bring you up to speed. It would take 100 textbooks, there’s so much!

    Here’s what you need to know: upon eating prebiotics (found in fermented foods, fruits, veggies, and things with fiber), the microbiome produces VERY important compounds (called metabolites) that directly affect many aspects of your body and overall health.1-7 Let me make something clear – these metabolites are not some minor thing that sort of move the needle 1%. Rather, in many cases these metabolites are the body’s main driver for something important (aka your body can’t do it WITHOUT the microbiome’s help.) To make this more interesting, these compounds are hard to find in food so your body completely depends on this flora for their key work.

    I’ll give you one example of this, but know there are THOUSANDS more. Let’s talk about BUTYRATE. You’ve probably never consciously thought or cared about butyrate, but if you could tap into your liver or brain’s ego, it would be at the very top of their priority list.

    Butyrate is a short chain fatty acid that is highly connected to how you break down sugar, manage insulin, and regulate mood (the most studied is 50 different ways butyrate makes your brain release dopamine).6,7 In fact, diabetes, insulin resistance, and depression have ALL been significantly linked to low butyrate levels in the gut.1,2,6,7 Butyrate is “made” by very specific bacteria that eats a very specific type of prebiotic found in fermented foods, a variety of vegetables, and a few fruits. The moral of the story? If you care about your overall mood state and avoiding conditions like diabetes, you might want to care about what’s happening in your belly (and what you’re putting in your mouth).

    And it doesn’t stop there. These metabolites formed by your microbiome significantly drive the health and productivity of your inflammatory and immune system, your hormones, your mood, your skin, your metabolism, and your energy levels.1-3,6,7

  3. Keeping “bad” pathogens away
    Friendly bacteria in your gut can help identify the “bad” pathogens from the “good” bacteria and eradicate them before they make you sick.1,3,8,9 For this reason, probiotics are actually some of the top studied organisms by pharmaceutical companies, looking for the next “targeted” (vs broad spectrum) antibiotic.

    This battle between good and bad bacteria happens in your gut without you even knowing! Studies have shown that gut microbiomes with an abundance of bacteria can even reduce the effects of getting very sick from salmonella and e-coli, the 2 most common and awful sources of food poisoning in US.8-10 You know the coolest part? This inner battle isn’t even the only way your microbiome boosts your ability to protect against sickness. Don’t forget that the microbiome drives and influences immunity outside the gut, too, by impacting T and B cell counts. It’s like these critters are playing both offense and defense to keep you healthy from the inside out!

  4. Breaking down things you don’t want or need.

    Who loves heartburn? Just like hangovers, feelings of heartburn and indigestion are universally hated AND—you guessed it—can be mitigated with more diverse gut microflora.

Here’s how it works: Greasy meals or over-indulging can cause our bellies to produce extra acids to aid in digestion. While these acids DO help with breaking food down, they are also very powerful, so when they linger they cause our pH balance to get out of whack.1-3,9 This is when indigestion and heartburn occur (because the acids are so powerful). Guts with a high abundance of bacteria have been shown to not only help break down these hard-to-metabolize meals, they actually ALSO help break down our own bile and stomach acids post-duty.4-6,10 By reducing the time these acids interact with our lining, a healthy microbiome eliminates or significantly reduces upset stomach and indigestion after meals.1-3,10

Since we’re talking acids, I’d like to take a small tangent here and share the counterintuitive fact that JUST because something is acidic or alkaline when you ingest it does NOT mean it’s going to have that effect when it interacts with food and enters your body. For example, lemon juice vinegars and kombucha are all very acidic—yet they’ve repeatedly been associated with lower production of stomach acid when ingested and are therefore considered “alkalizing.” On the other side, there are alkaline foods (like chocolate, meat) that cause your body to produce more acid in order to digest them. All this to say is, people with chronic indigestion often report BENEFITS not worsening symptoms, when they drink things like lemon water apple cider vinegar or kombucha, despite their acidity.

With more than $1B spent on over-the-counter liquids to help with heartburn, indigestion and even hangovers every year, it’s a real wonder why people aren’t going to their gut as the first step and solution. Follow along for more tips, tricks, and to learn the science behind your gut and whole-body health.

Until next time, try doing ONE thing good for your gut. Fermented food? One more veggie/fruit? Some prebiotic soda? We promise, you won’t regret it. And don’t forget to #FOLLOWYOURGUT


  1. Eamonn M. M. Quigley, MD, FRCP, FACP, FACG, FRCPI, et al. Gut Bacteria in Health and Disease. Gastroenterol Hepatol (N Y). 2013 Sep; 9(9): 560–569.
  2. Guarner F, Malagelada JR. Gut flora in health and disease. Lancet. 2003;361(9356):512–519.
  3. Sekirov I, Russell SL, Antunes LC, Finlay BB. Gut microbiota in health and disease. Physiol Rev. 2010;90(3):859–904.
  4. Clemente JC, Ursell LK, Parfrey LW, Knight R. The impact of the gut micro-biota on human health: an integrative view. Cell. 2012;148(6):1258–1270.
  5. O’Hara AM, Shanahan F. The gut flora as a forgotten organ. EMBO Rep. 2006;7(7):688–693.
  6. Serena Sanna et al. Causal relationships among the gut microbiome, short-chain fatty acids and metabolic diseases. Nature genetics. 2019; 51, pages600–605.
  7. Mireia Valles-Colomer et al. The neuroactive potential of the human gut microbiota in quality of life and depression. Nature Microbiology. 2019; 4, pages623–632.
  8. Mutlu E.A., et al. Colonic microbiome is altered in alcoholism. Am. J. Physiol. Gastrointest. Liver Physiol. 2012;302:G966–G978.
  9. Lebeer S, Vanderleyden J, De Keersmaecker SC. Host interactions of probiotic bacterial surface molecules: comparison with commensals and pathogens. Nat Rev Microbiol. 2010;8(3):171–184.
  10. Lee YK, Mazmanian SK. Has the microbiota played a critical role in the evolution of the adaptive immune system? Science.2010;330(6012):1768–1773.
  11. O’Hara AM, Shanahan F. Gut microbiota: mining for therapeutic potential. Clin Gastroenterol Hepatol. 2007;5(3):274–284.

Today's blog is written by our very own Daina Trout, MS, MPH

Daina is not just our Co-Founder, she is also a nutritionist that has spent her adult life dedicated to finding and sharing health and wellness through food. With 2 masters' degrees in nutritional biochemistry and public health, Daina has called upon her education often while leading the way at Health-Ade - from how we make every batch of kombucha, to how we talk about gut health to consumers, to even how healthy our employee workplace is! She even writes a few blogs here and there. Happy reading! :)

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