Tiny Tenants, Big Impact – How the Microbiome Shapes Our Health

In this episode of the GBNO Show, Dr. Rob and Shannon welcome you to their new studio and podcast format, then explore the world of the microbiome, the trillions of microbes that live in and on your body. You will learn how your gut bacteria affect digestion, immune function, mental health, and weight management. We also explain why antibiotics and processed foods can disrupt your microbiome and describe practical diet and lifestyle changes you can make today to support a healthy gut.

• Full Episode Transcript
  https://heydrrob.com/episode-19-tiny-tenants-big-impact-how-the-microbiome-shapes-our-health/
• Further Reading: 
• The Human Microbiome Project (NIH) 
• “Gut–Brain Axis and Mental Health” (Journal of Clinical Nutrition) 
• EWG: 
  • Dirty Dozen: https://www.ewg.org/foodnews/dirty-dozen.php  
  • Clean 15: https://www.ewg.org/foodnews/clean-fifteen.php

Social:  

• Facebook: https://www.facebook.com/heydrrob/ 
• Instagram: https://www.instagram.com/heydrrob 
•  TikTok: https://www.tiktok.com/@heydrrob 
• YouTube: https://www.youtube.com/@heydrrob 

Intro Music:
“Got A Feelin’” (Album Version) by Albert Donaldi, used with permission.
Learn more at https://www.albertdonadi.com/
License document available upon request.

About the Hosts
Dr. Rob Jones 
25 years in chiropractic care specializing in spine, joint, and soft-tissue disorders. Expert in Active Release Therapy and functional rehabilitation to keep you moving pain-free.

Shannon Jones 
31 years as a clinical dietitian focused on obesity prevention, functional nutrition, and integrative medicine. She tailors nutrition strategies to prevent disease and support whole-body health.
Together, they bring over 50 years of combined clinical experience and share a passion for promoting foundational health so you c

Transcript

Episode 19: Tiny Tenants, Big Impact - How the Microbiome Shapes Our Health 

Introduction to the GBNO Show

Dr. Rob: Welcome to another episode of the GBNO Show, the Get Better Not Older Show. I am Dr. Rob Jones. This is my awesome wife, Shannon, the dietician.

Shannon: Hi.

Episode 19: The Microbiome

Dr. Rob: Hi. So, number 19—we are talking about, well, not just number 19—Episode 19. We’re talking about a very important and really one of the most talked-about things in the medical world right now, which is our “tiny tenants,” which you wrote in the title here, which I think is kind of cute, but it’s the microbiome. Okay? It’s the good bacteria that is all over the body. We’re going to get into that. But first—

Why Trust Us?

Dr. Rob: Why are you watching this? Between us—kind of older, but pretty fit people—we have over 50 years of combined experience. I’m your “outside in” guy, and Shannon is the—

Shannon: “inside out.”

Dr. Rob: Yes. So we’re going to help you move, feel, live better again, from the outside in and the inside out. So, again—trust us, because we kind of know some stuff. We’ve been around the block. So, anyways—

Understanding the Microbiome

Dr. Rob: Microbiome and all things related to it that we can fit in a short period of time here. We could make this a five-hour podcast and bore the hell out of everybody, but we’re going to keep it to clinical tidbits that we think are the most important things with relation to the microbiome. So why don’t you go ahead and describe what it is? Most people tend to know what it is because of the big push on probiotic supplementation and people learning about gut bacteria—good and bad. Go ahead and give the Cliff notes version on the highlights of what people need to know.

Shannon: Okay. Am I allowed to pause first?

Dr. Rob: I don’t know.

New Studio and Podcast Format

Shannon: Well, aren’t you going to say anything about our new digs?

Dr. Rob: Oh, yes. I—yeah, I kind of forgot about that. So we have a new GBNO symbol. Cool, right? Kind of professional.

Shannon: I know we’re special.

Dr. Rob: I know.

Shannon: And also one of the big changes—which this is going to be very tough for you—

Dr. Rob: Mm-hmm.

Shannon: We’re going to try to really make these more 30-minute podcasts. Mm-hmm. Historically, we’ve run about an hour or so, and that’s going to be unique to these podcasts. We’re going to try to keep ’em shorter—

Dr. Rob: Yeah.

Shannon: —so people will actually listen to us.

Dr. Rob: Yeah. So let me translate that: “Rob, shut up. Stop talking. Stay on point.”

Shannon: “Dr. Rob, land the plane.”

Dr. Rob: Okay. Roll. Go. Okay.

Microbiome Basics

Shannon: So we have referred a lot to the microbiome in, well, continuously in almost all of our podcasts. I would say we’ve never really devoted an entire episode to it, but honestly—it could probably, as you say, be a five-part series. We are really doing very high level today. But the short and long of it is: your microbiome is trillions of microbes, bacteria, viruses, et cetera that live in your body, on your skin—every single organ in your body has these microbes. The biggest study came out around 2018; it was an NIH study. That’s where we started to realize: they used to think that there was nothing but brain matter in the brain. Now we know your brain has its own microbiome. So what is it? It’s these good and bad bacteria that live and populate these areas. As a matter of fact, we have so many bacteria we could cover the surface area of a tennis court, and we have more bacteria than cells in our body. That is hard for people to think. People typically associate “bad” with bacteria—this goes back to the days of Louis Pasteur. But honestly, it’s a balance of good and bad. You need both, and when it’s out of balance—which we call dysbiosis—that is where we start to see health concerns.

Impact of Microbiome on Health

Dr. Rob: Right. So recently—people follow us because we set examples—we changed our toothpaste completely.

What’s the name of the brand? Is it Hello?

Shannon: Mm-hmm.

Dr. Rob: Okay. Again, no affiliation with them, but that’s what we use. We changed it for many reasons: there are no chemicals, no fluoride—but there’s research coming out on how dysbiosis, or improper bacterial formation of the good bacteria in your mouth, can influence digestion, because digestion starts with salivary amylase in your mouth. It can affect bad breath, tooth health, tooth decay, et cetera. People brush their teeth and then rinse with Scope or whatever mouthwash they use, destroying the microbiome, wondering why their teeth break down and they get bad breath.

Shannon: And one thing you forgot— we had an entire episode on it—is why they may be hypertensive.

Dr. Rob: Oh, I forgot about that part.

Shannon: Yes.

Dr. Rob: Why don’t you reiterate?

Shannon: Well, basically you need to produce nitric oxide, and that starts in your mouth. What they’ve found is that by using mouthwash—and by using fluoride toothpaste—you’re wiping out the good bacteria in your mouth that create nitric oxide. That is a major problem for people.

Dr. Rob: So starting in the mouth. Now you go down into the gut, which most people—again, there’s microbiome on your hands, in your nose, ears, whatever—but mainly we’re going to talk about the gut today. “Gut” meaning large intestine. We don’t want a high amount of microbiome in the small intestine, because that gives you SIBO—small intestinal bacterial overgrowth—which can cause problems.

Shannon: Which definitely causes a problem.

Dr. Rob: Yeah. You read the symptom: “My gut is always upset, my stools are off, I’m irregular, I’m constipated, then I have the D, then I have diarrhea.” Your doctor says, “Oh, you have IBS—irritable bowel syndrome.” Instead of looking at your diet, they just hand you a pill. If you don’t feed it the right way, you’re going to get some symptom that leads to a syndrome or disorder. How do we correct it? Clean, healthy food.

Shannon: Right. I mean, back in the day—when I worked in the hospital—an IBS chart was like this high for a patient, just because it was constant problems. Why? Because everything begins in the gut. If you have what they call a leaky gut—which is honestly a major issue causing microbiome dysbiosis because of the food and our environment—you get eczema or acne or joint issues like rheumatoid arthritis. All the inflammation comes from leaky gut.

Leaky Gut Explained

Dr. Rob: Okay, I’ll explain leaky gut really quick. When you take in food, in the small intestine—the first part is the duodenum—you have these little projections called microvilli. That’s where food particles, when broken down, are absorbed. They meet the circulatory system; nutrients go into your blood, distributing to your cells for energy, vitamins, minerals, etc. In between those microvilli are little gaps. If your gut is unhealthy, the mucosa is inflamed and cracked—think of chapped lips—you get cracks. Then food particles slip through into your general system, not in the circulation. Your body says, “Holy crap, that is something foreign. I need to attack it.” It’s not like a virus where you know how to attack it; instead, you send a massive immune response. You attack that little food particle, then guess what? You’re ramping up total immune function. Now the immune system is confused: “I don’t know what to do; there’s so much inflammation, let’s attack the skin.” Suddenly you have eczema (skin disorder of unknown origin) or acne, or rheumatoid arthritis, all because of leaky gut. That’s what leaky gut means.

Shannon: Autoimmune diseases. We could do an entire podcast on leaky gut. The takeaway is once your gut is compromised—once those tight junctions are compromised—it’s not just local. It’s a systemic reaction: “Everybody, all systems go, we have an intruder!” This leads to autoimmune diseases because it’s an immune response to leaky gut. Dysbiosis starts there: bad and good bacteria out of balance, and health issues follow.

Microbiome and Mental Health

Shannon: Another big one is mental health—that whole gut-brain connection. Now they’re tying anxiety, depression, etc., to bacteria. We see more autoimmune disease and mental health issues. Why? You take a step back: “What’s happening?” Our food source is one culprit: we no longer eat real, nourishing food for our bacteria; they’re starving. It’s like a tropical rainforest without water: can’t survive. To feed the rainforest (our microbiome), we must eat real fruits, vegetables, legumes (beans, chickpeas, etc.), real plant foods. But we’re spraying everything with glyphosate. If you’re not eating organic, you’re getting pesticide on everything, breaking down your gut barrier, causing issues. Our food system is the problem; now bacteria are to blame. So what do we do? Protect the microbiome.

Dr. Rob: Can I rewind one sec? I love real-life examples. Years ago, I had a patient who was a psychology professor. He told me about studies where they took depressed rats and nondepressed rats, swapped their microbiome (poop), and the rats’ symptoms flipped: depressed became nondepressed; nondepressed became depressed—with no change in behavior, environment, or food. Just microbiome.

Shannon: This is a real deal: it’s called a fecal transplant. They treat disease this way. Especially extreme dysbiosis—we’re talking C. difficile, which is hard to eradicate. Fecal transplant helps. Even for weight loss: obese rats get microbiome from a thin rat, and the thin rat becomes obese. We’ve talked about digestion and metabolism, immune system, mental health, weight. What about the brain? They used to think the brain had no microbiome; now they know it does.

Dr. Rob: Right. Again, the gut-brain axis controls everything. You mentioned patients with skin issues—rosacea, acne—what you did for them with stool analysis?

Introduction to GI-Map and Gut Health

Shannon: Okay. When I assess patients—who come to me for disease prevention or weight loss—I look metabolically. If they complain about thyroid or Hashimoto’s, eczema, rashes, etc., my brain says we need to see what’s going on in your gut.

Recently our own daughter called, “I’m going to a dermatologist.” I said, “Okay, you’re wasting your time; you probably just need a GI-Map and see what’s happening in your gut.” She went to a dermatologist. He said, “We don’t know what this is—try this topical.” It did nothing. We did the GI-Map, fixed her gut, and her skin cleared up.

Dr. Rob: So what’s a GI-Map?

Shannon: You get to poop in a box. There’s no way around it: you provide a stool sample. It’s a snapshot of what’s in your gut that day. We look at colonies: if someone has skin issues, we find overgrowth of Strep and Staph. We also look at other colonies: “Oh, they have no Akkermansia; that’s why they’re resistant to weight loss.” You can associate different bacteria colonies with how they manifest in your health: “Overgrowth here, not enough there,” and treat accordingly.

Dr. Rob: It’s like labs: doctor orders a CBC, lipids, blood sugar, liver enzymes, thyroid. They look at numbers: 15–30, 100–300, etc. It’s the same: but instead of cholesterol numbers, they measure colonies of good and bad bacteria. Too much bad (Strep, Staph) manifests as infections—those can be deadly. So that’s what I was going to say before you rudely interrupted me.

Shannon: I was just adding a random, “Did you know?” about MRSA.

Dr. Rob: Well, a patient can pick up MRSA in a hospital—Methicillin-resistant Staph aureus—and need high-powered IV antibiotics, wiping out everything. But to solve the problem—clean, healthy food; organic fruits and vegetables; healthy meats; healthy fats—it’s not hard. The problem over the last 50 years is food is so monetized that less than 1% of a grocery store is healthy. Even in the “produce” section: if it’s not organic, an apple or lettuce has been sprayed with glyphosate, Roundup. That enters your body, destroys your gut microbiome, adding carcinogens. So it’s eating organic.

Shannon: The sad thing is that’s how it is in the U.S. It’s not like that in the rest of the world—but food manufacturing here is so subsidized. (We won’t get political.) Now that we know about microbiome, we must avoid antibiotics when possible—they’re like an atomic bomb on your microbiome. If you ever were on antibiotics, everything’s wiped out. You don’t just take one probiotic and hope everything’s cured. You have to feed the bacteria what they need. A lot can be done without antibiotics: oregano oil can wipe out certain bacterial infections. We rush to antibiotics for a sniffle; if it’s a virus, antibiotics do nothing. If you have a bacterial infection, there are natural remedies. We’ve gotten too quick to prescribe antibiotics.

Dr. Rob: That’s why we have MRSA, and why pharmaceutical companies keep creating more powerful antibiotics—people get infections that Bactrim can’t resolve; they need specialized antibiotics.

Solutions for a Healthy Microbiome

Shannon: So what can we do to create that “tropical forest” of a microbiome, nurture it, and keep it? We’ve talked about it already, but yes: eat fresh fruits and vegetables—ideally organic. If it’s got pesticide, it causes problems. The Environmental Working Group (EWG) tests pesticides in adults’ and children’s urine and publishes the “Dirty Dozen” and “Clean Fifteen.” Shop organic for the Dirty Dozen; the Clean Fifteen have negligible pesticide in the produce. We’ll put those links in the show notes. You have to feed bacteria what they need.

Also, make sure your probiotic is a live-culture, third-party–tested brand—what you buy is what you get. Then there are prebiotics, postbiotics, butyrate, and fermentation. Butyrate is a short-chain fatty acid from fermenting fruits and vegetables. To keep microbiome alive, feed it healthy organic produce. Another big tip: timing of eating. If you stop eating by 7 or 8 p.m. and fast at least 11 hours, overnight, the lining of your large intestine (mucosa) sloughs off. Bacteria eat that slough, keeping the lining smooth and slippery. If you eat late, bacteria stay active overnight, you miss that slough-and-feed cycle, and your gut becomes dry, sticky, and inflamed.

Dr. Rob: Plus you need good sleep: if you don’t sleep well, you don’t get that benefit.

Shannon: Stress is also hard on the microbiome. Our Get Better Not Older lifestyle is truly about diet, sleep, stress management—shameless plug for our protocol.

Dr. Rob: So when you were a kid, get dirty—play in the mud, be around animals. Sterile microbiome doesn’t do you any good. Limit processed foods: read ingredients. Many protein bars or shakes have sucralose at the end—an artificial sweetener that creates dysbiosis. Stay away from sucralose and aspartame; use stevia, honey, maple syrup, or monk fruit. You must exercise, get outside, eat real food, sleep, and manage stress.

Final Tips

Dr. Rob: We’re close on time. Last tips: as a kid, get dirty—mud, animals. Eat organic, avoid artificial sweeteners, fast overnight, get sleep, manage stress, exercise, and live holistically.

Shannon: And try not to take antibiotics if you don’t have to.

Outro

Dr. Rob: So for Ms. Shannon, our awesome dietician who’s going to help you get better, not older, from the inside out—

Shannon: (inside out)

Dr. Rob: I’m Dr. Rob Jones, helping you get better, not older, from the outside in. Until next time—GBNO: get better, not older.