Does Your Digestion Need a Tune-up?

digestionWell, does it?

We’re all going to be putting food in our bodies just about every day for the rest of our lives. Most of us will do it several times a day. We’ll chew it, send it down the esophagus into our stomach, and expose it to gastric juices and digestive enzymes. We’ll strip it of nutrients and send the excess down to the colon for dismissal, feeding resident gut bacteria along the way. The whole process should go smoothly. There shouldn’t be any pain or discomfort, bloating or constipation. Oh sure, nobody’s perfect, and there will be slow-downs or speed-ups from time to time, but in general a vital, fundamental process like digestion shouldn’t even register in our waking, conscious lives.

But sometimes it does.


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Symptoms of Digestion Problems

Sometimes digestion can be downright unpleasant, or even unproductive. The symptoms are familiar:

  • Bloating. Distended belly. Feeling overly full and unwieldy. Same weight but the pants don’t fit.
  • Excessive gas. No need to define it. You just know it when you see (hear) it.
  • Diarrhea. Acute (occasional) diarrhea that goes away immediately doesn’t indicate poor digestion, but protracted or chronic diarrhea is a warning sign.
  • Constipation. Same deal with constipation: acute normal, chronic not.
  • Stomach pain. Persistent gut pain should never be ignored.
  • Bleeding or pain on the toilet. Elimination should be painless.
  • Heartburn, or acid reflux. Although most people assume heartburn and acid reflux are caused by too much stomach acid, it’s actually the opposite: inadequate stomach acid is usually the culprit.

The Digestive Process: Troubleshooting Top to Bottom

To get to the bottom of these symptoms and hopefully fix them, let’s look at the actual process of digestion. We’ll go step by step down the line to identify and offer solutions for various issues that can arise at each.

What happens when you eat something?

The stops along the digestive route involve:

  1. Sensing and signaling
  2. Oral digestion, or chewing
  3. Mechanical digestion, in the stomach
  4. Duodenum digestion
  5. Small intestine digestion
  6. Colon digestion

Here’s how it works.


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Sensing and Signaling

You start digesting before you’ve even taken your first bite. Have you ever smelled burgers grilling, and you mouth started to water? Certain aromas can signal to your body that food is coming, and you begin to salivate and secrete digestive enzymes.

Even thinking about food can trigger a response.

Oral Digestion, or Chewing

Now, you’ve taken a bite.

First, you chew your food. Chewing is the first step in digestion. You physically break it up with your teeth into smaller pieces, increasing the surface area for digestive enzymes to access. Most of those enzymes appear later in the gut, but some appear in the saliva and start working immediately in the mouth during the chewing process.

Your taste buds communicate what you’re eating so that your body starts getting the right digestive juices flowing. For example, if you ate something sweet, you’ll make insulin. If you’re eating a fatty food, you’ll start secreting bile and enzymes.

Salivary amylase begins converting starch into sugar for easier digestion. Chew a potato for long enough and it’ll start tasting sweet.

Lingual lipase begins digesting the fats you eat. This is more important in babies, who express very high levels of lingual lipase in order to optimize their calorie intake from breastmilk. It still has an effect in adult fat digestion.

How to optimize oral digestion

Chew more: The longer you chew, the better you digest your food. In one study, healthy adults who chewed 50 times for each bite ended up eating fewer calories than those who chewed 15 times per bite, a strong indication of more efficient digestion and nutrient extraction.1 They were getting “more” out of their food simply by chewing it up more.

Heed your salivary amylase levels: How much salivary amylase you produce is determined by your genetics, with historically agricultural (and thus starch-consuming) populations tending to possess more copies of the salivary amylase gene than other populations. There’s no good way to test salivary amylase gene status because the commercial genetic analysis sites don’t cover it. You’d need a more specific (and expensive) test for that. Ancestry can be a rough proxy; try to match your carb intake with the carb intake (and thus amylase copies) of your recent ancestors. But whatever number of amylase copies you (might) carry, chewing more times per bite will increase the efficacy of the salivary amylase you do produce.

As for meat and other animal foods which salivary amylase doesn’t affect, chewing is still important because it breaks apart the fibers and makes the nutrients contained therein more accessible to protein-digesting enzymes (proteases) in the stomach.

Mechanical Digestion, in the Stomach

Leaving the mouth, the food travels down the esophagus on into the stomach, where hydrochloric acid and a protein-degrading enzyme called pepsin break the food down into a big semifluid mass of partially-digested food components, water, enzymes, and acid known as chyme. The stomach walls undulate (move up and down) and mix the chyme,

How to Optimize Stomach Digestion?

Get your thiamine. Thiamine is a B-vitamin involved in hydrochloric acid production. If you want optimal stomach acidity—and you definitely do want it—you need to be replete in thiamine. The best source of thiamine is pork.

Watch the antacids. While heartburn meds can make a person feel better in an acute case of heartburn, they do so by inhibiting production of hydrochloric acid, which makes the stomach more alkaline and worsens your digestion in the long run. Pepsin cannot work without adequate acidity.

Try bitters. Post-meal bitters stimulate production of hydrochloric acid and assist many of the digestive organs, making the whole operation run more smoothly. But they must be bitter. Covering up the bitter flavor with something sweet mitigates the beneficial effect on digestion.

Get enough sodium. Low sodium levels reduce hydrochloric acid production. Make sure you’re salting your food to taste, as our moment-to-moment desire for salt is a good marker for sodium requirements. As long as you’re not eating packaged junk food, you won’t crave too much salt.

Try supplemental hydrochloric acid. A little betaine HCl, especially with protein meals, can really help if your acid production is too low. If you take betaine HCl and you feel a burn, you probably don’t need it.

Duodenum Digestion

Since the stomach is too acidic for amylase to work, the chyme migrates down to the duodenum, the first section of the small intestine immediately after the stomach where the pH is more alkaline. The pancreas produces protein-digesting enzymes as well as amylase and delivers them to the duodenum, where the full range of digestive enzymes can get to work liberating nutrients for absorption down the line. This is also where bile is introduced to assist in fat digestion.

Eat meals rather than graze. The human digestive system operates best when it encounters whole meals with plenty of time between subsequent meals, rather than a steady stream of incoming food. It even tries to enforce this; when a bolus of chyme enters the duodenum, the opening leading from the stomach to the duodenum tightens up to prevent more food from coming in. Overriding this with constant snacking will only impair your digestion and back things up.

Go for a walk. A short walk after eating speeds up the transition of food from the stomach through the duodenum into the small intestine. It “gets things moving,” in a good, beneficial way.

Small Intestine Digestion

After softening up in the duodenum, the chyme passes on into the small intestine where the bulk of nutrient absorption occurs. All along the intestinal walls lie villi — microscopic finger-like projections that increase the surface area of the intestinal lining and pluck nutrients from the passing slurry to be absorbed and assimilated. (You may have heard of villi in the context of gluten. Gluten can wipe out the villi in some people, leading to nutritional malabsorption.)

Optimize your serotonin. 95% of the serotonin in our body occurs in the gut; it’s one of the primary regulators of intestinal peristalsis — the muscular contractions that move and mix food through the digestive tract.2 I’ll have a much more in-depth post in the near future on this topic.

Fix leaky gut: Leaky gut isn’t just about allowing in pathogens and unwanted, allergenic food components into your bloodstream. It also impairs nutrient absorption and digestion in the small intestine. Go through this post and make sure you’re practicing excellent tight junction hygiene.

Pay attention to FODMAPs: Not everyone with digestive issues has to do this, but anyone who gets bloating, belly pain, excessive gas, and many of the other symptoms of poor digestion after eating should analyze their diet for FODMAPs and do an elimination trial. FODMAP foods include a wide range of fermentable fibers, sugars, vegetables, and fruits that have been shown to provoke uncontrollable and uncomfortable gut issues. These are often foods we consider to be healthy. Read the posts I’ve done on FODMAPs and follow the advice listed therein if you suspect you may have a problem with them.

You can also get tested for SIBO to see whether eliminating FODMAPs will benefit you.

Colonic Digestion

You don’t actually “digest” anything in the colon. Rather, you gather and expel the waste — mostly fiber — that’s left over from digestion. Some of that “waste” is food for the gut bacteria who live in your colon. So someone’s digesting the stuff, just not you.

Eat some prebiotic fiber. Ironically, sometimes you need to eat stuff you can’t digest in order to improve your digestion over the longterm. Fermentable, prebiotic fibers like inulin and resistant starch are some of the best-studied examples. They feed the (mostly) good gut bacteria, who in turn produce short chain fatty acids that power your colonic cells and improve your metabolic health.

Take probiotics. Certain probiotics have been shown to reduce bloating and belly pain, improve GI symptoms, improve IBS symptoms, reduce leaky gut, and reduce antibiotic-related diarrhea.34567 I created Primal Probiotics with precisely these probiotics to tip the balance in your favor.


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Digestion must be approached as a single unit. You don’t just pick one of these tips to try. You do them all, together, if they apply to you.

About the Author

Mark Sisson is the founder of Mark’s Daily Apple, godfather to the Primal food and lifestyle movement, and the New York Times bestselling author of The Keto Reset Diet. His latest book is Keto for Life, where he discusses how he combines the keto diet with a Primal lifestyle for optimal health and longevity. Mark is the author of numerous other books as well, including The Primal Blueprint, which was credited with turbocharging the growth of the primal/paleo movement back in 2009. After spending three decades researching and educating folks on why food is the key component to achieving and maintaining optimal wellness, Mark launched Primal Kitchen, a real-food company that creates Primal/paleo, keto, and Whole30-friendly kitchen staples.

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10 thoughts on “Does Your Digestion Need a Tune-up?”

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  1. “Constipation. Same deal with constipation: acute normal, chronic not.
    Stomach pain. Persistent gut pain should never be ignored.”

    Amen to that. I felt it but did nothing because I thought it was nothing; me just whining. Also, there was fatigue. Long story short, I ended up in the ER with e multiple day stay. It ended up being diverticulitis with a perforation. Almost needed emergency surgery that would have ended up with a colostomy bag. Aside from IBS and a gluten allergy, no real indicators, so be forewarned. Even just the constipation without the pain can be a big warning sign.

  2. Surprised there was no mention of the role of Helicobacter Pylori in digestive issues, especially as it relates to the duodenum. Changes things quite a bit so that some of the above information may have to be altered somewhat.

  3. The single biggest thing that improved my digestion was adding HOMEMADE fermented foods to my diet (even the good quality store bought ones did not do what the homemade ones do). I make my own krauts and fermented veggies, milk kefir, yogourt and kombucha and consume all of these foods daily. No bloating of any kind anymore and I can eat anything without digestive issues.

    1. Hello HA! Me, too!! Some friends of ours let us try their homemade sauerkraut, and I was AMAZED! It was crunchy and delicious, and nowhere near as acidic as the store stuff that they call sauerkraut. I started making our own. Ever since, my husband and I take turns making sauerkraut. We are never without it. It is a delicious addition to our salads and meats, and it has made us feel so much better!

    2. Thanks for this information. I’ve taken probiotics off and on for digestion issues but would prefer a more natural approach versus something that comes in a bottle from the healthfood store. I’ve also considered a FODMAPS diet but it’s very restrictive. I will try the homemade fermented foods.

  4. I appreciate this resource, thank you. My digestion has improved immensely since cutting out sugar and artificial sweeteners over a year ago (also was the last time I took any NSAIDS or antibiotics). I don’t get constipated anymore at all, but have been struggling with stomach pain probably most days for the last several months.

  5. But what, exactly, IS “bloating”? Which organ(s) are distended and WHY? Is it an inflamed stomach? Small intestine? Large intestine? Is it a certain type of bacterial growth out of control?

  6. Hi! I’d like to share something I stumbled upon that was the only thing that worked for debilitating digestive/IBS type symptoms: Yarrow (Achillea millefolium).

    About a year ago, I developed twin problems: Uterine cysts, along with severe digestive problems. It got to the point where I could only consume a handful of extremely bland foods and, even then, I often had severe, long-lasting pain. Without insurance or funds for treatment, I was guessing blind at what was wrong (and hoping it wasn’t cancer!), but what could I do? The only thing was to rely upon my lifelong study in herbal medicine.

    Having used Yarrow for its typical use, externally as a styptic, I decided to try it internally to treat excessive uterine bleeding. It’s not poisonous to consume, but is a POTENT BLOOD CLOTTER, so don’t risk taking it if that is a factor for you. ALWAYS discuss with your doctor! FYI I took 650mgs two times daily for a week. (It’s wise to limit medicinal herbs to one week; two max for some herbs. Another good approach is to take the herb for a week, take a week off, then take the herb for another week.)

    While the blood clotting worked, the Yarrow didn’t completely heal the cysts (although some burst and some came out; sorry about being graphic but sharing results is important). That was, by the way, painful!

    However, to my astonishment, my digestive problems completely vanished! It’s been five months, and I’ve had no further digestive pain or problems. I can eat any fruits, vegetables, or grains I like.