MICROBIOME MEDICINE FOR METABOLIC HEALTH WITH DR PAUL FROOMES (PART 2)
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Episode 300:
Show Notes
This episode is a continuation of a previous conversation with Dr Paul Froomes, brought on because of the depth and value of the discussion. Dr Mary Barson and Dr Paul dive deep into gut microbiome health, its relationship to metabolic disease, and practical steps for repair.
The Gut-Obesity-Dysbiosis Cycle
Poor diet — not the microbiome itself — is the root trigger of obesity and gut dysfunction. Once a poor diet creates gut dysbiosis, a vicious cycle kicks in: dysbiosis drives insulin resistance, increased hunger, and cravings, which perpetuates poor dietary choices. This cycle is at the core of why Real Life Medicine's metabolic health pillars — food, stress management, sleep, sunlight, movement, strength training, and social connection — are so foundational.
The Carnivore Diet: Short-Term Relief, Long-Term Risk
- Carnivore and very low-carb diets can temporarily relieve gut symptoms (bloating, distension, pain) by removing fermentable substrates that feed dysbiotic bacteria
- However, long-term carnivore diets starve the gut microbiome of fermentable fibers, reducing biodiversity and biomass, and decreasing butyrate production
- Reduced gut integrity raises the risk of TMAO production (from carnitine in meat), which is linked to coronary artery disease
- Dr Paul’s' approach: correct the dysbiosis first, then slowly reintroduce plant fibers to tolerance — "resilience and balance rather than restriction"
The Danger of Ultra-Processed Foods & Xenobiotics
Processed foods contain over 120 chemical additives (xenobiotics), some of which are known carcinogens or poisons permitted in micro-doses. These chemicals act like antiseptics — wiping out probiotic bacteria, damaging gut epithelial cells, and disrupting tight junctions in the gut lining. This allows toxins, partially digested food, and dysbiotic bacterial byproducts to leak into the bloodstream, driving systemic inflammation and insulin resistance. Dr Mary's powerful framing: we are participants in "a big scientific experiment conducted on us for decades without our consent".
Microbiome Testing Explained
Standard GP stool PCR tests are not sufficient for meaningful microbiome assessment. Dr Paul uses shotgun DNA sequencing on a fresh stool sample to identify:
- Pathogenic bacteria causing gut dysfunction
- Opportunistic pathogens in overgrowth
- Missing probiotic strains (e.g., Bifidobacterium, Lactobacillus)
- Yeasts, viruses, and parasites
This targeted approach allows precise probiotic restoration after treating the dysbiotic bacteria, often resolving symptoms patients have had for 10–20 years.
Lifestyle Factors That Shape the Microbiome
Beyond food, Dr Paul highlighted several key lifestyle factors:
- Chronic stress raises cortisol and alters gut permeability and motility
- Sleep is critical — the microbiome has its own diurnal (circadian) rhythm
- Nature exposure — walking in nature, swimming in the ocean — introduces beneficial environmental microbes
- Exercise improves gut motility and microbial biodiversity
- Pet ownership increases microbial biodiversity through shared microbes
As Dr Mary brilliantly noted: "A bushwalk can be a probiotic activity".
Practical First Steps for Gut Health
Dr Paul’s' recommended starting points for listeners struggling with IBS or functional gut issues:
- Rule out serious pathology first (colonoscopy if red flags like rectal bleeding, weight loss, or anaemia are present)
- Remove ultra-processed foods immediately
- Eat real food: grass-fed beef, line-caught fish, good fats (olive oil, avocado, coconut oil), and green leafy vegetables
- Gently introduce soluble fibers — start with leafy greens before progressing to beans and legumes
- Test your microbiome via shotgun sequencing for a targeted, structured recovery plan
Where to Find Dr Paul Froomes
- Website: themicrobiomeclinic.com.au
- Instagram: @dr.paulfroomes
- TikTok: @drpaulfroomes
Episode 300:
Transcript
Dr Mary Barson (0:04) Hello, my lovely friends. I am Dr Mary Barson.
Dr Lucy Burns (0:09) And I'm Dr Lucy Burns. We are doctors and weight management and metabolic health experts.
Both (0:16) And this is the Real Health and Weight Loss podcast!
Dr Mary Barson (00:21) I am Dr Mary Barson. And today, I am joined by our very special guest, Dr Paul Froomes, gastroenterologist extraordinaire from Melbourne and expert in microbiome health and microbiome-based medicine. This podcast is a continuation from last week. So much goodness in here that we have decided to extend the conversation and keep going.
Dr Paul Froomes (00:57) The gut microbiome doesn't cause obesity, on its own. Poor diet is kind of what triggers it and starts it all off and keeps it going.
Dr Mary Barson (01:04) It sounds like it becomes a vicious cycle.
Dr Paul Froomes (01:06) Yeah, exactly.
Dr Mary Barson (01:07) The poor diet triggers the gut dysbiosis, the dysbiosis continues to trigger the insulin resistance, the increased hunger, the increased cravings. And so we are big proponents of metabolic health. And so at Real Life Medicine, our pillars of good metabolic health are the food, substance, stress management, sleep, sunlight, circadian rhythms, movement, strength training, social connection — all really just foundational lifestyle pillars that, when we can work on these and get them in a good balance, our bodies are going to be in a good balance as well.
Dr Paul Froomes (01:43) Absolutely.
Dr Mary Barson (01:44) Also, most of our clients, our beautiful people who do our courses, have got insulin resistance — it's very common. And so we also recommend reducing processed foods first, absolutely, but also keeping your sugar and starch intake lower while still feeding your gut microbiome with a good amount of natural fibers and plant-based foods. But being in this world, we do rub shoulders with the broader low-carb community. And in the low-carb community, there are pockets that are strong supporters of a carnivore diet. Real food, yes, which is good, not processed food, which is good, but also food that has got no plant fibers in it, essentially. And it seems that for many people who choose this diet, it often starts out as perhaps a bit of an elimination diet, perhaps people with autoimmune illnesses, they go this way and perhaps could be useful in the short term, but then there are people who choose this long-term. And what I fear is that there is a real dearth, like a real lack of understanding about what this could do to our gut microbiome long-term and to our health long-term. And I would love to get your input on that.
Dr Paul Froomes (03:05) We absolutely, it's an interesting discussion because I like you see a lot of that too, because when people come to me, they've usually seen a few GPs, naturopaths, they've seen multiple gastroenterologists and they've tried, they've done diet stacking. And in the end, they're either totally confused or they're on an elimination diet or they're on the carnivore diet. And that's the only thing that's given them some relief. Now, so you, like me, have seen many people that feel, actually, some of my gut symptoms, I'm getting some relief here on a carnivore diet. Essentially, as you said, it's a zero or very low carbohydrate diet. And it's understandable that it might improve some symptoms in the gut because essentially you're reducing all the potentially fermentable fibers or substrates. So bloating always improves on it and distention, pain, and therefore toxin production, because you're not feeding your microbiome, but you're also not feeding the dysbiotic bacteria. And yes, okay, so you can see some symptom relief. There's the occasional person I think is probably okay on that long-term, but that's probably genetic. They probably inherited some genes from early humans that literally lived. I mean, there are communities now where they just live on yak meat. They don't see a vegetable at all. But for the vast majority of humans, your microbiome is so important to physical, mental, and gut health that the carnivore diet is unfortunately kind of grossly missing something. And what that's missing is some fermentable fibers, because that is what is critical to biodiversity. So a rich population of good probiotic bacteria in the gut and biomass, meaning enough microbes in the gut to convey all these health benefits for immune function, nervous system function, muscle function, heart function, brain function. So what the key problem is, you know, already with the carnivore diet or these very, very low carb diets is that you're just not feeding a microbiome. You're going to have a weak microbiome. You're going to have less biodiversity, less biomass, which means less butyrate production, which is not going to be good for your long-term overall health. You're going to miss out on so many nutrients potentially that support intestinal mucosal integrity. And there's always a risk of the carnitine from meat that might be, if you've got dysbiosis, then produce this compound called TMAO, which has been shown to cause deposition of coronary fat or plaques, coronary artery disease. So I'm not a big proponent of the carnivore diet. It's okay to use it short term, but the key to getting people eating some plant-based fibers and healthy foods again is correcting their dysbiosis. I mean, our microbiome evolved alongside, you know, plant intake. You know, we would hunt and gather. And what we're, you know, we're gathering is carbohydrates, you know, tubers, leaves that we could eat because there weren't always ready protein sources. It took time to catch them. So completely removing fiber or fermentable prebiotics, we call them, really narrows down that gut ecosystem. And so you're going to miss out on a lot of health benefits. So for me, I would always, what I do with people with carnivore diet is correct their dysbiosis and then bring slowly, but surely bring back a more balanced diet by bringing the plant fibers back in according to their level of tolerance. But we can usually get everyone there.
Dr Mary Barson (06:49) Yes. Yes.
Dr Paul Froomes (06:50) So I agree it's resilience and it's balance rather than restriction.
Dr Mary Barson (06:56) Yep. And that resilience and that balance can be restored. So what I'm hearing here is you have, you've seen people that perhaps they had gut dysbiosis, they had symptoms, they weren't tolerating different foods, perhaps different plant foods, and they went carnivore, they got some relief, but then you helped improve their integrity, their gut resilience, their gut microbiome. And now they're back at a state where they can feed their probiome as well.
Dr Paul Froomes (07:25) Exactly right.
Dr Mary Barson (07:26) Yes. Yes. No, that sounds like a very, very, very balanced way to view it. I would like to just go back a little bit to, she called it, was it the xenobiotics, the toxins?
Dr Paul Froomes (07:41) Xenobiotics, which simply refers to the chemicals that have been allowed to be added to our food.
Dr Mary Barson (07:48) Could you elaborate more about xenobiotics and the dangers of a processed diet to everything, but specifically to our gut microbiome?
Dr Paul Froomes (07:56) Well, the problem is that these chemicals — and there's over 120 of them or plus now, some of which are known carcinogens, some known poisons that you would never dream of giving to a human to eat. But in micro doses, they do lots of wonderful things to food to make it have a great mouthfeel or emulsify it so that the ingredients don't separate out. And so taste, flavor enhancement. And the other key thing you get from these xenobiotics or chemicals is that you get flavor and preservation. So you can let it sit on a shelf literally for years. Shelf life, right? So these chemicals are dangerous because, well, they do a couple of things. Essentially they act like some sort of antiseptics or antibiotics. So they kill off probiotic bacteria. They can't tolerate them. Second is they can damage the epithelial cells of the gut and also damage what are called tight junctions. So your gut lining is only one cell thick, double layer of mucus and some secretory IgA in the middle. But these cells control what is allowed into your bloodstream. And they have these linkages between them called tight junctions. And when you eat certain chemicals like emulsifiers, it disrupts the barrier and then you get tight junction dysfunction or breakage, if you like. And the cells lining your gut, the gaps open up. And so then chemicals, partially digested foods, and also toxic metabolic byproducts of dysbiotic bacteria, they can get into your bloodstream. So this is where the inflammation and insulin resistance and disease process starts to get nasty. And it's driven a lot by these chemicals. So you're wiping out your microbiome diversity, you're wiping out your microbiome mass, you're damaging your gut lining, and then you're creating gut inflammation and then setting yourself up for disease. So I'm very, like you, a very big proponent of a chemical or preservative or xenobiotic processed food free diet. Natural eating is kind of what I call it.
Dr Mary Barson (10:07) Yes. It can be a difficult step for a lot of people, but it is one of the most powerful steps that you can take towards good health. Yes.
To divorce ourselves from this big scientific experiment that has been conducted on us for decades without our consent.
Dr Paul Froomes (10:23) Yeah. Yeah. We're one of the last countries to ban — only, what, 2025, we banned Paraquat, which is the most poisonous chemical on the planet.
Dr Mary Barson (10:33) Right.
Dr Paul Froomes (10:34) That was being used to kill bugs in farming.
Dr Mary Barson (10:38) But finding its way into our food system.
Dr Paul Froomes (10:40) Oh, yes.
Dr Mary Barson (10:41) Yeah. Yeah. Yeah. What advice would you give to people out there? So many of our listeners would be identifying with this. So many people have got irritable bowel and other functional gut disorders and may perhaps have felt a bit dismissed by the medical community in the past. What advice would you give to people listening who want to take steps to start repairing their microbiome and start repairing their health?
Dr Paul Froomes (11:10) Well, so you, like me, obviously see a lot of people struggling with gut problems like bloating, pain, altered bowel habit, food intolerances, brain fog. It literally drives them crazy. And they're, as you said, often dismissed. I find most patients have been dismissed and their symptoms not validated, and they're just told they're stress heads. "Go on a FODMAP diet and go away." But look, sensible first steps would be to make sure there's nothing serious wrong. So exclude your red flags. You know, if you've got weight loss, rectal bleeding, anemia, go get your colonoscopy, your scopes done — exclude anything nasty. So you've got to go through that process. I think that's very important. You're not going to miss Crohn's, ulcerative colitis, cancers, ulcers, et cetera, et cetera. Structurally, make sure you are okay. Then the first step is just to simplify the diet: remove ultra-processed foods, start eating some plant-based foods, grass-fed beef, line-caught fish, good protein sources, get good fat sources into you. So things like medium-chain triglycerides, coconut oil, pure olive oil, avocado, et cetera, et cetera. And gently introduce soluble fibers. So don't go for the really heavy fiber-rich and soluble fiber-type foods, all the beans and legumes. Necessarily first start off gentle by just bringing it in. So eat a bit more of the green leafies and just bring a bit of fiber gently into your diet. But then the next step would be, okay, well, that's just a good sensible thing to start with. But then I'd probably say, right, let's go assess your stool pattern. So let's go and test your microbiome and just see where you're at. We can then diagnose your dysbiosis so that we can start making more, using intervention to change you in a more structured and significant way so that you become asymptomatic. You don't have these symptoms anymore. In fact, what you've had for 10, 20 years is gone. That's very exciting to go into that space.
Dr Mary Barson (13:21) Yes, absolutely. Could you tell us more about that microbiome testing? Because I'm sure many of our listeners would be interested about what's a good way to go about it, because I'm sure there are some bad ways as well.
Dr Paul Froomes (13:33) Well, look, for my purposes, I try to keep it simple. I've designed a microbiome mapping test that suits my purposes because I'm interested in the bacteria and knowing what they've got. I want to know what the bacteria are that are causing the problem and which probiotics are missing. So essentially, it's a microbiome stool test done on a fresh stool sample and it's sent into the laboratory where they use high-throughput or shotgun sequencing DNA technology, which basically gives you a nice readout of pathogenic bacteria. So that's bacteria that are clearly linked to gut dysfunction, symptoms, and illness. Then there's what are called opportunistic pathogens. So these are sort of in between. They're not pathogens, but they're bacteria that, if they get into an overgrowth situation, then you've got dysbiosis. So these are bacteria just waiting to cause trouble. Then we look at yeasts, viruses, parasites, and then we look at a large number of probiotics to see what you're missing. So that allows me to target, okay, there's your culprit bacteria and there's your missing probiotics. The names of the bacteria are not that relevant to your patients. They will never have heard of them, but they're helpful for us because we can deduce quite a bit about which particular bacteria causes which symptom, which is likely to cause diarrhea, which is likely to cause constipation, which toxin is made by which bacteria. So it's helpful for the clinician in explaining the symptoms away and then targeting those. Then you know, okay, just how intensively or what you need to do in terms of probiotic restoration following treating or eradicating the dysbiotic bacteria. So there's a lot of different stool tests out there. The normal stool PCR, which is the one that your GP will give you — by most GPs will start with — is not enough. You need to go and sequence the microbiome and get a readout of all the species that are available to look at. No stool microbiome test is fully complete because there's probably 400–600 different species, but no one does that. But you can certainly look at the ones that make up the majority of the microbiome. Honestly, it's useful. It helps when you target them — you get a better result. So that's how I look at it. I use a particular lab at the moment, but that may change depending on what comes out in the future. But I keep it simple because patients: what does that mean? Prevotella copra — what's that? I just say, you explain it as bad bacteria that make toxins that cause the damage and the symptoms and stop your gut functioning. And you're missing the probiotics. Some patients have heard of Bifidobacterium or Lactobacillus. You can mention those and tell them these are what are going to make everything work properly. If we can biohack it, and you have a probiotic microbiome, your gut works normally again. And they're absolutely staggered at hearing that usually. And then when you do it, it's even more exciting.
Dr Mary Barson (16:50) Yes, for everyone. And I love that your emphasis is on their understanding and not making you feel smart. That's very good.
Dr Paul Froomes (16:57) Yeah, you don't want to confuse your patients. They're confused enough already.
Dr Mary Barson (17:01) Yes.
Dr Paul Froomes (17:02) By searching the internet themselves, getting different diets from different people and being told it's all in their head, they're usually very confused and pretty disappointed.
Dr Mary Barson (17:13) Yes. Confused and disillusioned. Yes.
Dr Paul Froomes (17:16) Their journey thus far.
Dr Mary Barson (17:17) Yes. So we have talked about food as one of the most significant ways that you can shift your gut microbiome for good or for bad. What other factors are important?
Dr Paul Froomes (17:32) So in a general way, lifestyle is very important. Chronic stress, which we call distress — because there's eustress, which is enough to get you going and get you doing things. But when you're exposed to too much stress, excess stress, chronic stress, cortisol releasing peptides up, cortisol's up, adrenaline's up, that's been proven to alter the gut microbiome as well as gut permeability and motility. So in terms of lifestyle, yes, diet, but then stress — managing that and learning to do things in your life that balance or counteract stress. So you list all your stresses on one side and list all the fun things on the other side that balance it out. And usually everyone's stress list is three times longer than their nurturing list. So getting that right is a big help. Sleep, as you mentioned, is terribly important for metabolism and also for your gut microbiome, which also has a diurnal rhythm. So sleep-wake cycle, getting that balance, is very important for your microbiome. Also getting out into nature. There are microbes everywhere in nature. So getting out into the ocean, for example, it's literally teeming with microbes. Getting out and going for a walk in nature — just plants are shedding microbes, the soil's shedding microbes, all of which we're supposed to pick up. We have contact with other people. We're essentially human are surrounded. It's not just internal in the gut where the microbiome is, but it's in the mouth, the skin, eyes, everywhere. We're kind of surrounded by a cloud of microbes. It's about probably 50 centimetres in diameter, but varies in people's richness. So you will share microbes with other people and hopefully some good ones, but unfortunately in the West, it's often bad ones. But that's another way of nurturing your microbiome. Having a pet — as you've probably heard — you will share microbes with your pet, and people with pets have increased biodiversity compared to people who don't. So there are kind of a few lifestyle things — getting out and exercising. Exercising improves motility and biodiversity as well. So there's diet mixed with a whole lot of other lifestyle things that all play a role in both human health, but also in gut microbial medicine and biodiversity.
Dr Mary Barson (19:57) I love that. A bushwalk can be a probiotic activity.
Dr Paul Froomes (20:01) That is — absolutely it can.
Dr Mary Barson (20:02) Fabulous. I love that so much.
Dr Paul Froomes (20:06) And swimming in the ocean.
Dr Mary Barson (20:07) Yes. I love that too. So good. Thank you so much, Dr Paul Froomes. This has been a fascinating conversation and I am sure a really, really helpful one as well for our listeners. If our listeners wanted to find you and find out more about you, where could they go?
Dr Paul Froomes (20:27) So two places they can find me. We have a website called the microbiomeclinic.com.au, and that's where people can literally book in and book a video console. There's also, if people want to come and see me in person, there's drpaulfroomes.com.au. And also you can just follow the Instagram link at the Microbiome Clinic.
Dr Mary Barson (20:50) Fantastic. And we'll have all of those links in our show notes.
Dr Paul Froomes (20:52) And get a few little takeaways each day.
Dr Mary Barson (20:53) Yes. Excellent. Which is where I had already known you as a fabulous gastroenterologist. I'd heard of you, but it was seeing one of your Instagram posts that particularly piqued our interest as wanting to get you on as a guest.
Dr Paul Froomes (21:08) Oh, great. Well, it's great to be on.
Dr Mary Barson (21:10) Thank you so much. I really appreciate it. Your knowledge and expertise is so extremely helpful, and thank you for your great work. I think I'd love to have you as a guest again in the not-too-distant future.
Dr Paul Froomes (21:22) Well, thank you very much for having me on. It's been a pleasure.
Dr Lucy Burns (21:27) The information shared on the Real Health and Weight Loss Podcast, including show notes and links, provides general information only. It is not a substitute, nor is it intended to provide individualised medical advice, diagnosis or treatment, nor can it be construed as such. Please consult your doctor for any medical concerns.
