All About Digestion, The Paleo NP Podcast Episode 17



Digestion basics


Gut pathogens and weight loss resistance

Gut healing and nutrition

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You’re listening to The Paleo NP Podcast - episode number 17.

Hey everyone, welcome back to another episode of the Paleo NP podcast. This week I wanted to talk about digestion, because it seems like I’ve been a broken record in talking about some of this stuff lately, and that usually means that it’s time to do a podcast episode about it! So, I just got back from a day trip, turned overnight trip thanks to the weather, to Kodiak, Alaska. Which is part of the reason this episode is coming out a day late. I had some catching up to do when I got home. And for those of you who aren’t familiar with Alaska, which is where I live, Kodiak is an island off the Southern coast of Alaska, and I just learned that it’s actually the second largest island in the United States (the largest is the Big Island of Hawaii). Anyway, I went there to do some consults with a friend and the weather was really bad, which is pretty normal there, and we got stuck overnight and then had a pretty scary flight home, made worse by the fact that I have a moderate fear of flying, but I’m home and alive, so that’s great. But while I was seeing patients on Monday, I did a lot of talking about digestion, so I wanted to do a podcast episode because I think it’s an important topic!

So we all eat food and are therefore familiar with digestion to a certain extent, but for a lot of people, what happens to their food after they chew and swallow it remains a bit of a mystery. And also, where things can go wrong and how to keep that from happening seems to be something that not a lot of people understand, so I thought it would be worth it to spend some time talking about those things. One of the most important things to know about your digestive tracts is that it serves as a barrier, and everything that is inside your digestive tract is actually on the outside of your body. And the job of this barrier is to determine what gets into your body and what stays on the outside. In general, we want nutrients to get in because that’s how you get fuel for your body and we want toxins and waste products to stay on the outside.  The other part of your digestive tracts job that isn’t directly related to its barrier function is to make sure that all the things that don’t get into your bloodstream are excreted in a timely manner because if stuff sits around for too long, those toxins and other waste products can damage your gut and cause increased intestinal permeability or what a lot of people know as “leaky gut.” And once your gut becomes leaky is when you start to have issues because it becomes hard for your gut to determine what should be let it and what should stay out. And you end up having things that should stay on the outside crossing into the bloodstream. Then your immune system attacks those things because they are seen as foreign invaders and this leads to increased inflammation and autoimmune disease.

Digestion basics

The process of digestion actually starts in your mouth. Chewing your food begins the process and then there are enzymes that are in your saliva that help start the process and those get released when you start chewing as well. So just inhaling your food and not doing a good job chewing it can really set you up for digestive issues because you are missing steps of the process right from the start. Chewing also helps to signal your body that food is coming further down the digestive tract and gets other digestive juices flowing, so missing that first step of just chewing your food is critically important to the whole process. We need to think of digestion as a top down process, so if things don’t happen properly at the top, they aren’t going to be fixed or happen properly further down either. So if you are missing a step anywhere in the process, so say for example stomach acid is not being secreted in the right amounts, then your digestion will be impaired no matter how well things are working farther down the process.

So after you chew and swallow your food it ends up in your stomach. Your stomach acid, which is hydrochloric acid, is primarily responsible for breaking down proteins and then for turning your food into a sludgey substance called chyme. Which is not very appetizing to think about, but it’s an important step in the process because your food needs to be broken down a certain amount before it can pass into your small intestines. And just a side note about stomach acid, one of the reasons a lot of people who haven’t eaten a lot of meat or who only eat fish and then start eating meat again, complain about digestive issues is related to stomach acid. People who have been vegetarians tend to have lower stomach acid than those who eat meat and if you go from not eating meat to eating meat without enough stomach acid, you are going to have some digestive upset. So I always recommend to people who are looking to increase their animal protein intake to start really slow and even start with meat cooked in the slow cooker (which essentially starts the digestive process) in order to get their body to start producing more stomach acid and avoid some of that digestive upset.

Another important thing to understand is that if you have enough stomach acid and the pH of the chyme is in the right range, that’s part of the signaling process for your pancreas to produce and secrete pancreatic enzymes. So if you have low stomach acid and the chyme doesn’t have the right pH when it passes into your small intestines, your pancreas never gets the signal to produce enzymes. This is one of the reasons why I’m becoming a big fan of using hydrochloric acid supplements instead of digestive enzymes in people who have digestive issues (so frequent burping after meals, excessive feelings of fullness, or bloating), because if you get the acid and pH right in the stomach, the pancreas will do its job and secrete the necessary enzymes. There are definitely times when your pancreas might not be keeping up either and that’s when digestive enzymes become helpful, but I always try and fix the problem at its root which is why I’m now leaning towards starting with HCL. So you may also be wondering why your stomach acid would be low, because we always hear about people with reflux or heartburn being put on things that block acid because too much acid is what’s causing the problem, which is really not the case at all. Low stomach acid is much more prevalent that high stomach acid. Probably anywhere from 30-50% of the people I work with have low stomach acid. And this would be caused by one of two things, so first would be suppression and the second would be inadequate production.

So suppression would be caused by things like acid suppressing or blocking medications, so TUMS or any of the proton pump inhibitor medications (or PPIs) that basically everyone seems to be on these days. And those would be medications like Prilosec. And these are so effective that they can suppress stomach acid to almost zero in some cases, which if you’ve paid attention to anything that I’ve said in the past 5 minutes you’ll understand that could be a huge problem and actually make a lot of digestive issues worse and not better. Because if you have zero stomach acid, how are you even going to digest your food? Your pancreas certainly won’t be releasing any enzymes in that case. And you will have trouble breaking down proteins, but stomach acid is also required to digest minerals like iron and vitamins like B12, so if you don’t have any stomach acid, you are well on your way to some serious vitamin and mineral deficiency (if you weren’t already there because B vitamin deficiency in general is pretty common). Stomach acid is also needed to help protect us from things like harmful bacteria, parasites, and yeast so you are also more likely to get an infection with low or no stomach acid

And if you actually read the labels on these medications, you’ll see that they are not supposed to be prescribed long term. I think they were only supposed to be used for 2 weeks or less, but now we have people who have been on them for over 20 years. I have a friend who was put on one in her 30s and basically told that she’d be on it forever or until her symptoms went away. But really, no one told her how to make that happen. Another really common cause of low stomach acid, especially in the older population, is H. pylori infection, which is what causes ulcers. And one of the way this bacteria survives is by suppressing stomach acid. And as I just mentioned stomach acid is one of the things that protects us from pathogens because they can’t survive in an acidic environment. And then another common cause of decreased stomach acid is chronic stress. In a situation where you have acute, or short lived stress, you’ll actually have an increase in stomach acid production, but over the long term, it actually decreases production. And this sort of all goes back and relates to the dysregulation of cortisol, which is a topic for another show entirely, but the easiest way to explain it is that you have two states for your nervous system - either sympathetic or parasympathetic and only one can be activated at a time.

So when you are in a chronic state of low level stress you are in a chronic sympathetic state, which means that your body is only prioritizing things that you need for survival, so it’s putting all of the available resources towards things that will allow you to fight for survival or run away. So things like making sure that your lungs and skeletal muscles have enough blood because those things will help you survive. And then at the same time resources are diverted from things that are not important to your immediate survival but are important for long term survival like reproductive organs, digestion, and tissue repair and regeneration (though there is some part of your fight or flight response that prepares your body for wound healing). So stomach acid production and gut health aren’t important when you are running away from a bear or getting read to fight to your death. Which means that your body doesn’t care if you are digesting the food that is already in your gut because it’s not important to your survival in that moment. And all this makes complete sense when you are actually running away from a bear (side note: you shouldn’t actually run away from a bear, but you get the gist of what I’m trying to say here). But if you’re sitting in traffic or in a meeting and having that same response, your life isn’t really in danger, but your body can’t tell the difference from a physiologic perspective and it has the same reaction. And from an evolutionary perspective, our bodies haven’t adapted to this chronic stress to react any differently yet.

This is also one of the reasons why it’s so important to chill out while you are eating. Rather than rushing around trying to shove your lunch in your mouth, or whatever, it’s important to make sure that your body can actually digest the food you are eating, and a lot of people don’t realize that their mental state and what they are doing while they are eating actually affects that. And as much as you don’t want to hear this - and I feel like a broken record when I talk about this, but it’s so important, but if you are having trouble healing or having symptoms that just won’t seem to go away, you need to look at how you are managing your stress. And I really don’t love the term stress management, but I prefer to suggest that people work on their resilience or how they react to stress because stress is a part of life, but how you handle it can have a huge impact on your health. When it comes to food and digestive issues, things like making sure you are sitting down while you are eating, chewing your food enough, maybe not watching TV at the same time, but just putting your entire attention on your food. And that can be surprisingly hard for people because it often means that you have to actually face your feelings instead of just zoning out in front of the TV with your dinner. And this gets into a whole different level here but it seems like a lot of times people are much more willing to take a pill or a supplement or even overhaul their diet than they are to face their feelings and address the underlying cause of something when it’s actually within them. I find that a lot of people would rather take a pill than address the relationship issue that’s making them stay at work for 14 hours a day because they’d rather be at work than at home.  


Ok, so moving farther downstream in the digestive process. The chyme passes from your stomach into your small intestine where things like starches get broken down into smaller pieces called disaccharides and monosaccharides. Because in order for nutrients to be absorbed and used by your body for fuel they need to be in single molecule form and that’s what happens in your small intestines. There’s a lot that can go wrong in the small intestines. One of the most common things is that you just don’t get proper breakdown so rather than being in single molecule form, they are in bigger pieces and end up hanging around in your small intestine for much longer than they should. And when that happens they become food for pathogenic (or “bad”) bacteria which is already in your gut. There are over 500 species of bacteria in your gut and some of them are beneficial and some of them aren’t, and just like anywhere else in nature, the balance is really important. But as long as the good outweighs the bad, you usually don’t have an issue. But what happens when those food particles don’t get broken down in the right way is that they feed the bad bacteria and then you end up with an overgrowth of bad bacteria and something that’s called SIBO or Small Intestinal Bacterial Overgrowth. There isn’t usually all that much bacteria in your small intestine except for at the very end of it, most of the bacteria is in your colon. But in cases of SIBO, you get more bacteria in your small intestines and those bacteria make gas through fermentation when they eat the food that’s hanging out in your small intestine instead of being digested and passing through.

So this causes things like gas and bloating and can even cause changes in stool frequency or consistency. And I know a lot of people think that the stomach is where all the action happens in our digestive system, but your small intestines are really where the magic happens. They have the big job of absorbing all the nutrients from your food and it’s unfortunately where a lot of issues occur. And something that I want everyone to understand, because this is what makes dealing with some of these things so difficult is that these processes and the problems that can occur with them are often more cyclical than linear. So for the gut, if your stomach acid is low then you aren’t digesting your food well in your stomach. Then you also aren’t producing pancreatic enzymes because the signal isn’t there (due to the low stomach acid) and then you aren’t breaking down the food in your small intestines well and it sits around and gets fermented by the bad bacteria which causes gas and digestive distress. This can go on further to cause inflammation, which makes you more susceptible to bacterial or other gut infections. So, say you get a gut infection which further affects your ability to break down food and causes more inflammation and makes your gut leaky. Leaky gut causes your body to have an autoimmune response which continues to promote inflammation in your gut making it even worse at digesting food.

So this cycle just continues to feed itself (pardon the pun, apparently I’m channeling my grandma who loved a good pun) and it becomes hard to know exactly where to start fixing it. So with SIBO, the lactulose mannitol test is kind of the standard for testing. So if you establish that you have SIBO then your options for treatment would be to either kill the bacteria with an antibiotic or botanicals or you starve them out, which is the premise of the GAPS diet. And something that I’ve come across a lot lately with my clients and patients is FODMAP intolerance, which I think is probably related to SIBO, but that is hard to say because a lot of people aren’t interested in paying for the testing for SIBO, but since FODMAPs are a class of fermentable carbohydrate, people who have SIBO are generally intolerant to FODMAPs. And it seems like maybe you could just eliminate the FODMAPs and be good, but the problem is that things like onions and garlic are FODMAPs, so if you were always avoiding them, you could pretty much never go out to eat or buy any sort of packaged food because onions and garlic are everywhere. But it’s things like this where it becomes important to try and figure out the underlying cause of things rather than coming at it from the top down. So deal with the underlying infection that hasn’t been detected yet, or leaky gut, or the stress that’s causing your gut to be overly sensitive, or whatever the underlying cause is and eventually you can start adding some of the foods that are problematic back in. And often the best approach is really to dial in your diet to the best of your ability and make sure that you’ve addressed the lifestyle and stress partso the equation, and if those things don’t give you the results you are looking for, then it might be time to get some testing done.

Gut pathogens and weight loss resistance

So if you aren’t responding to a gut healing protocol, and by not responding, I mean that your symptoms aren’t improving, after about 30 days, then that’s a strong case for something like an opportunistic infection. And the bacteria that cause these infections are a normal part of your digestive tract and they don’t cause any issues as long as they are balanced out with good bacteria as we talked about a bit ago. Another problem could be bacteria that don’t even belong in the gut at all and those can get in through the food you eat. And we also have parasites. And there are some parasites that depending on who you talk to, there’s a different take on them, so some doctor’s feel like they are a normal part of the digestive tract, and there are others who will tell you that they definitely cause problems. But I think the bigger picture here is important because in someone with a healthy gut and a good balance of the good bacteria, these types of things may not cause any issues at all, so it’s not a problem. But then if you have someone who has a problem with the balance of their gut flora and they have a lot of stress in their life then the same thing that doesn’t bother the person with the healthy gut can cause a lot of symptoms in someone else.

Then there are things like yeast overgrowth, which yeast is also a normal part of your digestive tract, but just as with everything else, the good bacteria keeps the yeast in check. So when there isn’t enough good bacteria, the yest can overgrow. And if any of these are present, no matter what you are eating or what supplements you are taking, if you have an infection in your gut, things aren’t going to work right. And in this case, digestive discomfort is one of the symptoms you would experience if you had this sort of infection, but unfortunately, it’s not always that easy and straightforward. Because the inflammation that’s caused by these things becomes widespread, you can have symptoms that don’t seem at all related to your gut, but are, in fact caused by a gut infection. One of the most common ways for this to manifest is with skin issues so things like psoriasis and eczema, which have an autoimmune component, but are really connected to leaky gut. I think something like 40% of people with leaky gut don’t actually have any digestive symptoms, and it’s really important to understand that. Because I see a lot of people who when I tell them that they have leaky gut are like, “but I don’t have any stomach issues.” But then when we treat them for leaky gut, their symptoms get better. There’s also a lot of literature and research on depression and how it might actually be inflammatory in nature, and that it’s definitely connected with your gut health. So for example, any time you have inflammation the gut releases these inflammatory mediators called cytokines into your blood. These travel into your brain and suppress the activity in your frontal cortex, which is what happens in depression.

Then in terms of weight loss and weight loss resistance, cortisol is involved. So you have a gut infection that causes inflammation which activates your stress response (and you release cortisol), and really this could happen with any type of infection or illness, which is where you get into that ugly cycle again. But inflammation itself is actually linked to weight gain and the metabolic issues that are seen in metabolic syndrome, which if you want to know more about that you can listen to the episode all about metabolic syndrome and insulin resistance. There are studies that have shown that inflammation in the gut and inflammatory cytokines can suppress activity in your hypothalamus which plays a big role in weight regulation. So if your hypothalamus isn’t working properly it throws off your body’s ability to regulate your weight. In order to fix this, you have to identify what’s going on. And this is where stool testing comes in. So there are different tests available depending on who you work with, but this is really the most accurate way to determine what is going on. And then the treatment would depend on what type of organism you are dealing with. And if you have multiple infections, that makes the situation more complicated and I definitely don’t recommend self-treating in most of these cases because you can really get into some dangerous territory, especially when you are dealing with more than one type of infection.

Gut healing and nutrition

So, if you are into managing this on your own, then if you do a 30-day gut healing protocol and you see not change at all, then I would definitely suggest getting some testing to see what’s happening. If you do a 30 day protocol and you do see some improvement, but you aren’t back to where you want to be, then I would say stick with it for another 30 day or even 60 days and then see where you’re at. But if you ever reach a point where your improvement has plateaued and you still aren’t where you want to be, then I’d get help. If the issue is just diet-related, then it should improve pretty quickly. And when I say gut healing protocol I’m referring to something like a strict Paleo diet or something like the Whole30. Or even a GAPS approach would work or a Paleo elimination where you remove eggs and nightshades, but whatever you are doing you need to make sure that you are eating bone broth because that is so important for gut healing. You also want to make sure that you are getting fermented foods and of course as we already talked about you NEED to address your stress. A couple of other things to keep in mind when it comes to gut healing is that you want to make sure that you are chewing your food enough as we already talked about as well as making sure that you are relaxed and not eating in a rush. In general eating more seafood, vegetables, fermented foods, organ meats, and bone broth helps to improve your gut health. You can use lemon juice, apple cider vinegar, or betaine HCL to support your stomach acid production (if you use HCL, I’d strongly suggest working with a practitioner who can guide you with this), and definitely don’t go drinking straight apple cider vinegar because that can sometimes be just as problematic. I’d also advise working with a practitioner on these issue either way because they can help you figure out what to do next when something doesn’t work, or how to troubleshoot some of these issues.

That’s all I’ve got for you this week. If you are loving the show or just enjoyed this week’s episode, I would love it if you would head to iTunes or the Podcast app on your phone and leave a rating or a review. I have gotten a few messages from people who have tried to leave reviews but they don’t seem to be showing up, but it sounds like it’s an issue with iTunes, so if you’ve tried to leave a review and couldn’t, I still appreciate you! Also, if you have a question that you would like me to answer, feel free to send me an email, leave a comment on a blog post, or come find me on Instagram and ask me all of your questions. You’ll be able to find show notes for this episode at See you next week!