What The Small Intestine Can Tell Us About Gut Health

KATHLEEN DAVIS: The gut microbiome is a super-important ecosystem of microbes that lives in each one of us. The strength of our gut microbiome impacts our overall health.

An underappreciated part of the gut microbiome is the small intestine. Most of the research into our microbiomes has revolved around the other end of the gastrointestinal tract. Think our colon and sampling, well, poop. But better understanding microbe disruptions in the small intestine may allow researchers to better understand disorders like IBS and celiac disease.

Joining me now to give us a crash course in the microbiome of the small intestine is my guest, Dr. Christopher Damman, Associate Professor of Gastroenterology at the University of Washington, based in Seattle. Welcome to Science Friday.

CHRISTOPHER DAMMAN: Wonderful to be on, Kathleen. Thanks so much for the invite.

KATHLEEN DAVIS: It’s great to have you. So let’s start off with just a quick anatomy refresher. So where is the small intestine located in the general gastrointestinal system?

CHRISTOPHER DAMMAN: So the small intestine is actually what connects the upper gut to the lower gut. So in other words, all the way from the stomach down to the colon, and there are several parts to it. There’s the very first part, which is the duodenum. That’s reachable with an upper endoscopy. And if you were to ever have one, that would be looked at.

After the duodenum, there’s the jejunum. That starts to get into the territory that’s very difficult to get to. And then the ileum– there’s the last part of the ileum called the terminal ileum that you can reach by colonoscopy at the very end of it. But a lot of the small intestine, because it is in a spot which is hard to get to, is relatively unexplored.

KATHLEEN DAVIS: So in layman’s terms, the small intestine comes right after the stomach?

CHRISTOPHER DAMMAN: Well put.

KATHLEEN DAVIS: So what role does the small intestine play in the gastrointestinal system?

CHRISTOPHER DAMMAN: So the small intestine plays a really important role in at least two elements of our body’s physiology. One is it helps us absorb our foods. So all the food that you eat, you start by chewing it. The saliva and the gastric juices help break it down. But that process of digestion is really completed in the small intestine. The small intestine then absorbs all of those broken-down nutrients. It can help build the cells in your body. So that’s one really important function.

Another is it actually has tons of immune cells in it. There’s actually a name for it called the Gut-Associated Lymphoid Tissue, or GALT. And that plays a really important role in helping the body distinguish between what is friendly and what is unfriendly in terms of antigens. So a lot of the foods that we eat, a lot of the good microbes in our gut are friendly, and the gut plays a role in helping tell the body that.

KATHLEEN DAVIS: How is the microbiome of the small intestine different from, say, the microbiome of the colon?

CHRISTOPHER DAMMAN: So the small intestine is really an almost completely different ecosystem from the large intestine. You could think of it maybe as disparate as a rainforest and a desert. And there’s certainly analogous organisms that are doing very similar things in the two different parts of the intestine. You could think of it maybe as a little ground vole versus a monkey in the rainforest. But the organisms, the species that are present there are actually quite different.

Now, as you get closer to the colon and the small intestine, those organisms start to transition a little bit, especially in the very last part of the ileum, the terminal ileum. And there, things start to look a little bit more like the colon. But the upper gut is very, very different.

KATHLEEN DAVIS: Can you give just a few examples of the microorganisms in the small intestines that are not maybe further down in this general GI tract?

CHRISTOPHER DAMMAN: Yeah, absolutely. So some of the organisms might actually sound a little bit scary or like pathogens. So strep species are very, very common. And we usually think of those in terms of strep throat, but there are healthy strep species too, namely Strep salivarius, and that gets its name because it’s present in saliva and actually present in the upper gut as well. There’s lactobacilli, and that would be familiar to people because those are often considered probiotics, and they’re present in yogurts. But then there’s lots of weird, exotic-sounding bugs as well that people wouldn’t recognize.

But what unifies these species is they tend to be a little bit more tolerant of oxygen than all of the anaerobes or the oxygen-fearing or sensitive bugs down in the colon.

KATHLEEN DAVIS: Are there disorders that are caused by a dysfunction of this microbiome in the small intestine?

CHRISTOPHER DAMMAN: Absolutely, and one of the biggest conditions that’s been associated with the upper intestine would be irritable bowel syndrome– and that was mentioned at the very beginning– and its cousin, overlapping cousin, small intestinal bacterial overgrowth. In both these conditions, there’s believed to be an imbalance in the microbes that are present in the upper gut, an imbalance that leads to an overzealous microbial population that breaks down fibers in places where it shouldn’t normally. And there’s some fibers that are more readily broken down, like the so-called FODMAPs. And folks that have these conditions, one of the ways that they often will help treat or address the disorder is by avoiding foods that have these types of fibers in them.

KATHLEEN DAVIS: OK, can you remind me what a FODMAP is?

CHRISTOPHER DAMMAN: [LAUGHS] Yeah, so it’s an acronym. Let me see if I can remember it. So it’s, let me see, Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyols.

KATHLEEN DAVIS: OK, I see why we have the acronym. How much do scientists actually know about the microbiome of the upper gut versus the lower gut? Is there a discrepancy in what we know?

CHRISTOPHER DAMMAN: Absolutely. So we’ve really focused on the low-hanging fruit, so to speak, and that’s the stool that we flush down the toilet every morning and every evening. It’s easy to get, and otherwise it just goes to waste. But researchers love it because they can understand what’s happening in the gut. It’s a nice proxy for the whole gut.

But there is really a limited amount of research looking at the upper gut, for the reasons that we’re talking about. It’s just very difficult to get to. And the upper gut may be disproportionately involved in things like digestion and our immune system. So it’s really a bit of an unexplored frontier still in gastroenterology.

KATHLEEN DAVIS: Why are the small intestines harder to study than the colon? I mean, is this just a general problem of it’s a lot easier to study poop coming out of us versus getting into our guts to study?

CHRISTOPHER DAMMAN: Absolutely. So the two biggest ways that we’ve had for studying the small intestine, up until very recently, have been an upper endoscopy– and that’s something that you’d have if you had heartburn that wasn’t controlled by medication that decreases acid in the stomach– and these very unusual anatomical situations where people have had surgery on their intestines, and there’s a little portal or ileostomy where the small intestine actually empties through the abdominal wall into an ileostomy bag.

KATHLEEN DAVIS: There has been quite a bit of research about how ultra-processed food alters the gut microbiome. Is this the same for the small intestines?

CHRISTOPHER DAMMAN: There’s very little research that’s connected the small-intestine microbiome to ultra-processed foods. Certainly there are connections there to the lower gut and stool and colonic microbes, but I think this is a very fruitful area for research.

And hypothetically, the nature of ultra-processed foods is the balance of the whole foods is disrupted. They’re concentrated for sugars, for fats, and a lot of the fibers and other nutrients, so-called phytochemicals that are present in plants like polyphenols, are removed. And both fibers and polyphenols probably play an important role in shaping not just the colon bugs but the bugs that are in the small intestine. But I think future research, this is a very ripe area for discovery.

KATHLEEN DAVIS: So we’ve talked about how hard it is to actually study the small intestines. Is there an opportunity for new technology to advance this research?

CHRISTOPHER DAMMAN: 100%, and there’s actually some new technology that’s come out in recent years. And for a while now, we’ve had clinical tools that just take pictures of the small intestine, and they help diagnose things like little blood vessels that can bleed and lead to anemia in people. But very recently, there are at least a couple new technologies or classes of technologies that allow us to look at the small intestine, not just by looking at it but also sampling, taking bits of the juices that are present there so that we can look at the microbes and all of the metabolites that they’re producing.

And one of those is a little pill that has a trap door and a compartment, and it’s triggered to open up for different pHs along the gut tract so it can sample different parts of the small intestine. That’s going to be a game changer moving forward using that technology in the context of different diet studies so we can understand how the small intestine is being impacted too.

But there’s another technology which, unlike an upper endoscopy, which is about the size of my pinky in diameter, very, very thin filament, almost the size of an angel-hair pasta that goes through the nose and is minimally invasive, doesn’t require sedating medications, and provides a portal to the small intestine. So I think the combination of these technologies will be pivotal for understanding, charting, characterizing the small intestine.

KATHLEEN DAVIS: So in addition to being a researcher, you also are a physician. You see patients. How close are we to a time where a patient can walk in your door and you can give them a targeted treatment based on the microbiome of their small intestines?

CHRISTOPHER DAMMAN: So I love this idea, and there’s been a lot of talk of personalized medicine and personalized nutrition and being able to characterize the microbiome and say, this is a prescription for food specifically tailored to you. There’s actually some companies that are making forays into this, early forays, largely around blood glucose control and diabetes.

But the reality of this is in general practice, we’re probably a little ways off still of this becoming a reality. And I’d say in the meantime, it really goes back to very simple adages of eating a whole-food diet and the advice that you’ve received from your doctor from the beginning, which is to eat nuts, seeds, beans, fruits, vegetables, whole grains, things that are present in well-studied diets like the Mediterranean diet or the DASH diet.

KATHLEEN DAVIS: That’s about all the time that we have for now. I’d like to thank my guest, Dr. Christopher Damman, associate professor of gastroenterology at the University of Washington. He’s based in Seattle. Thanks so much for joining us today.

CHRISTOPHER DAMMAN: It’s been a pleasure. Thank you, Kathleen.

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