MICROBIOME MEDICINE FOR METABOLIC HEALTH WITH DR PAUL FROOMES (PART 1)
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Episode 299:
Show Notes
In this fascinating first part of Episode 299, Dr Mary Barson sits down with Melbourne-based gastroenterologist Dr Paul Froomes — a Fellow of the Royal Australian College of Physicians with over 30 years’ experience — to unpack one of the most important and underappreciated topics in modern medicine: the gut microbiome. Dr Paul is the co-founder of the Microbiome Clinic, a practice dedicated to translating decades of microbiome research into practical, patient-centred care.
What sparked Dr Paul' microbiome journey
A dying patient with severe Clostridium difficile colitis was given a faecal transplant as a last resort — and walked out of hospital within days. That near-miracle inspired decades of research into how our gut bacteria shape our entire health.
What are "functional gut disorders"?
Conditions like IBS, functional bloating, and functional dyspepsia are often dismissed as "all in your head" — but Dr Paul explains they involve very real, measurable changes: altered gut motility, visceral hypersensitivity, immune activation, and gut-brain axis dysregulation.
The microbiome: your body's hidden metabolic organ
Trillions of bacteria in your gut do over 90% of the work of digestion, regulate immunity, produce nutrients, and balance your nervous system. When the balance tips from probiotic to dysbiotic, the consequences are far-reaching.
Diet is the #1 driver of microbiome health
Whole, real foods (think Mediterranean-style) feed probiotic bacteria; ultra-processed, high-sugar, chemical-laden foods starve the good bugs and feed the harmful ones. The SAD (Standard Australian/American Diet) is a microbiome disaster.
Dysbiosis drives almost everything
The downstream effects of an imbalanced microbiome include bloating, pain, constipation, diarrhoea, brain fog, fatigue, anxiety, depression, immune suppression, and even increased bowel cancer risk. Dr Paul describes gut axes connecting to every organ — brain, heart, liver, lungs, muscles and more.
The microbiome–metabolic health link
Dysbiotic bacteria extract more calories from food, promote insulin resistance, increase fat absorption, drive visceral fat accumulation, and even hijack appetite signals (via GLP-1 and PYY receptors) to make you crave sugar and overeat. A faecal transplant from an obese donor caused a woman to gain 37 kg — and she couldn't shift it three years later.
Butyrate: the metabolic superstar
This short-chain fatty acid, produced by probiotic bacteria, is central to metabolic health and weight regulation. No probiotics = no butyrate = worse metabolic outcomes.
⏭️ Watch Out for Part 2!
This conversation was so rich that Dr Mary called a strategic pause! Part 2 is coming next week, where the discussion continues with even more detail on microbiome-based medicine and practical strategies for improving your gut and metabolic health. Don't miss it! 🎧
Connect with Dr Paul
- Website: themicrobiomeclinic.com.au
- Instagram: @dr.paulfroomes
- TikTok: @drpaulfroomes
Episode 299:
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) Hello, lovely friend, and welcome to this episode of The Real Health and Weight Loss Podcast. I am Dr Mary Barson, and today I am very excited to be joined by a special guest, Dr Paul Froomes. Paul is a Melbourne-based gastroenterologist with more than 30 years' experience helping patients with complex digestive disorders. He trained at Melbourne Uni and is a Fellow of the Royal Australian College of Physicians. He has combined his advanced training in endoscopy and esophageal physiology along with his master's degree in liver disease at Melbourne University. He is highly credentialed. Throughout his career, Dr Froomes has focused on uncovering the root cause of conditions like irritable bowel syndrome, reflux, and inflammatory bowel disease, rather than simply managing the symptoms. He has published research, trained other doctors, and developed innovative treatments for the approaches grounded in microbiome science. He's also the co-founder of the Microbiome Clinic, which is a modern medical practice dedicated to translating all of the decades of microbiome research into practical, patient-centred care. Today he is passionate about raising awareness of how important our microbiome is and how useful microbiome-based medicine can be. We are delighted to have him with us. Thank you so much for joining us, Dr Paul Froomes. I would love it if you could tell our listeners a little bit more about you and what you do, and how you can help people particularly improve their gut health.
Dr Paul Froomes (02:06) Right. Well, thank you very much for inviting me on the podcast, Mary. I always love talking about the microbiome and the gut. So as you've already mentioned, I'm a gastroenterologist, I guess. So I got interested in this whole field and developed what I do for people, which is optimise their health through their microbiome, because the microbiome is now considered to be probably one of the single most determinants of not just gut health, gut function, but also it's involved in the way physical disease develops and, of course, mental illness develops. And you can do a lot for someone's overall health by optimising their microbiome. And that's sort of fundamentally how I've evolved my career in gastroenterology. And so I guess I got triggered by the case of severe clostridium difficile enterocolitis I saw as a younger consultant as part of the team at a public hospital, where this patient was dying on inotropic support. And then one of the registrants rolled up, you know, this is like the day before we were pulling out, you know, we're going to turn him off, and produced a paper saying that faecal transplant cured the patient, or cured a number of patients, a case series in the States of people who were in exactly this situation, and produced a signed consent form from the wife to the meeting where all the consultants were, you know, the gastroenterologist, the infectious disease physicians, the ICU physicians, and we're all sort of looking at each other going, what is this? Well, I suppose, all right, we could do it, but, you know, just be aware you might die at the end of whatever this thing is, this faecal transplant. But so we did it down the nasodegenerative tube, and within 24 hours the bloody diarrhoea was just pouring out of the rectal tube. It just stopped. And then days later the patient's, you know, weaning off inotropes, kidneys working again, and then eventually they moved out of ICU to HDU and then walked out of the hospital. So that was a bit of a shock to the medical world in that hospital. And I thought, well, what have we just done? And when you look into it, it's really just a massive probiotic infusion essentially. And I thought if we can do that, then I need to get involved. So I got pretty interested in the microbiome from then on and spent decades reading about it, researching it, and then putting it into practice. And you probably know that gastroenterologists are not great with functional gut disorders. And now that we know that there is a clear cause, and that is obviously dysbiosis, then developing ways to treat that has been incredibly rewarding and incredibly helpful. So I just loved going into that field because of how effective it is.
Dr Mary Barson (04:51) Yes. I love that you said that. And for our listeners, could you explain what you mean by functional gut disorders?
Dr Paul Froomes (05:00) These are the orders, probably the biggest misunderstanding, I think, in gastroenterology is this grab bag of disorders called functional gut disorders. Now, most people think functional means nothing's wrong. It's like patients presenting with chronic gut symptoms. Classic ones are functional bloating, functional dyspepsia, irritable bowel, functional or slow transit constipation, functional diarrhea. There's literally probably 40 or 50 of these things now. And it just describes persistent gut symptoms that there's no structural disease that we can find. So they do all their screening tests, standard stool tests, blood work, celiac testing, colonoscopy, gastroscopy, CT scans, gallbladder function studies. And you just go, there's nothing. We can't find anything wrong here. So modern medicine struggles with those disorders and then just puts them in this basket of meaningless diagnosis called functional. And most gastroenterologists would think surgeons are functional. There's nothing really wrong. They're just stressed. They're just anxious. What I've found is that the commonest thing you'll see is IBS, irritable bowel.
Dr Mary Barson (06:14) Absolutely.
Dr Paul Froomes (06:15) It's not a structural disease, but it's not imaginary either. It's very real. And the physiological studies have shown that there is, in fact, actual disorder of function. So I don't think of functional meaning, nothing's wrong. You're just a bit anxious. It's in your head. You're a stress head. Go away. I've done your colonoscopy. Bye. Well, I think the research has shown that in irritable bowel syndrome, let's take that because most people understand what that is, there is altered motility. We call it visceral hypersensitivity. So the nervous system in the gut is hypersensitive. And so a bit of bloating or discomfort for someone who doesn't have one of these disorders wouldn't bother them. But in these people, it causes quite extreme discomfort and pain. That's the hypersensitivity component. There's also immune activation. So the immune system is overactive. And there's gut microbial imbalance, which we'll talk about. Fermentation instead of digestion. So there's gas production and extinction. And there's dysregulation of the gut-brain axis, which is what exaggerates these symptoms and, I guess, tends to make people think of them as, oh, it's all in your head.
Dr Mary Barson (07:29) And I see that a lot. Like they're extremely common.
Dr Paul Froomes (07:33) They are common.
Dr Mary Barson (07:34) Yes.
Dr Paul Froomes (07:35) And they're only getting more common. Yes. The very first case, you'll love this, the very first case of irritable bowel syndrome was written up in a Canadian medical journal. I can't remember how long ago, but early 19, mid-1900s. And it was two years after they set up the first three McDonald's restaurants. And it was a case in that sub, one of the suburbs where it had been built. And it was one of the main things this woman was eating. So that's probably the first case of food-induced dysbiosis, IBS.
Dr Mary Barson (08:10) I do love that.
Dr Paul Froomes (08:11) You would get that.
Dr Mary Barson (08:12) I absolutely get that. One of our main pillars in lifestyle medicine is real food, and it is so incredibly important. Can you tell us more about that food-induced dysbiosis? This is fascinating to me.
Dr Paul Froomes (08:26) Well, there's a number of causes of gut. So we think of your gut as essentially two components now. One is the structure, and that involves all the intestines, stomach, esophagus, small bowel, large bowel, gallbladder, pancreas. The second component of the gut now is called the microbiome. And the gut microbiome, for your listeners, refers to literally trillions upon trillions of bacteria that live in the gut. So that's what we're talking about. We're talking about this population of microbes that live in this lovely symbiotic relationship with humans. And they are not just there for looks. They're highly metabolically active, and they're doing basically 90% plus of the work of digestion, which is allowing nutrient absorption, motility function, nervous system balancing, immune system regulation. So the composition of these bugs needs to be what we call probiotic. The problem is that it often gets unbalanced, and it turns the opposite to dysbiotic, and that's when the problems occur. Now, this really depends on your food and lifestyle. So a whole food, mainly plant-based diet with good sources of protein and healthy fats, where you are not taking chemicals in, so you're eliminating highly processed foods, you're not taking regular antibiotics, you're actually not destroying your microbiome, but you're feeding it with a really healthy diet or a natural diet or a whole food diet, essentially the Mediterranean diet. You're going to simply nurture and foster the growth of good probiotic bacteria. So that means a healthy functioning gut. The opposite is true. If you start going down the standard American or standard Australian diet, the SAD diet, which is essentially really high in refined sugars, very, very high chemical load or xenobiotic load is what we call it, which is all the chemicals we put into processed food, and you're not eating enough fibre. So this is, as you can imagine, that's a very unhealthy diet. You're not feeding any probiotic bacteria. They basically die off. And dysbiotic bacteria, which are just sugar fermenters, take over the microbiome. So diet can keep your microbiome robust, healthy, biodiverse, and populated with probiotic bacteria, which means you are going to be super healthy, or it can be the exact opposite, promote dysbiosis and chronic ill health and dysfunction of the gut.
Dr Mary Barson (11:02) And is it true to say that what we eat is the main driver of the health of our microbiome ecosystem?
Dr Paul Froomes (11:09) Yeah, that would be a pretty accurate statement because these microbes eat, and it's not just us that eats. They consume something like 20 grams of carbohydrates, 10 grams of protein. They're entirely dependent upon what you feed them. And as we said, probiotic bacteria eat prebiotic fibres, and the bad bacteria eat sugar. So yes is the answer.
Dr Mary Barson (11:35) Yeah. I imagine this list is probably going to be exhaustively long, but in your expertise, could you give us a rundown of, like, what are some of the major consequences of having gut dysbiosis?
Dr Paul Froomes (11:49) Okay. Well, that's a long question to answer.
Dr Mary Barson (11:53) It is, yes.
Dr Paul Froomes (11:54) Let's just...
Dr Mary Barson (11:58) Everything would be an answer.
Dr Paul Froomes (12:00) Basically, the start is gut. So if you have dysbiosis of the gut, then, of course, you're going to affect, first of all, digestion. So you won't be able to break down food properly. So you'll have undigested food fermenting away in the gut. So that's going to cause irritation, pain, and nutritional depletion. Then there's excess gas production. So that's going to cause distention, belching, bloating, flatulence, wind, and pain, sometimes pain. Then there are things like toxin production. So dysbiotic bacteria produce probably the commonest one you will have heard of is LPS, endotoxin. But there are aldehydes, acetates, lactic acid, lactate. There's about... And gases, hydrogen sulfide, sulfur dioxide, methane, some of which are, you know, damage DNA and cells, also tight junctions. So they damage the gut. So you get gut damage as well on top of that. Then they trigger off pain receptors in the enteric nervous system. So that's when you get the pain in the nervous system, hypersensitivity. Then they send signals up the vagus nerve that are noxious. So the vagus nerve then activates the fight or flight response, so you get stress, anxiety. And then the next step from that is depression. So these are all consequences of a dysbiotic microbiome. Then there are certain bacteria that put you at increased risk of colonic polyps and bowel cancer. So there are other long-term dangers of having dysbiosis. But probably for most people, it's inducing all those symptoms in the gut: pain, bloating, distention, wind, flatulence, diarrhea, constipation, fluctuating on and off associated with the brain fog, the fatigue, the anxiety, the depression. They're sort of the main things that dysbiosis drives. And we know a lot about the metabolites they're producing that do that, that cause it, that induce the inflammation and the symptoms and the gas and the pain. But it's a double whammy because if you have dysbiosis, then you're also missing your probiotic. So you're no longer in a state of probiosis. So you're missing out on all the protein benefits of having a population of probiotic gut bacteria that are doing all the work of digestion, nutrient absorption, nutrient production for absorption, maintaining cellular integrity, your gut lining, maintaining normal gut nervous system function, immune function, so you become immunosuppressed. So dysbiosis has two sides to it. It's not just bad bacteria. It's the lack of probiotic bacteria. Now, that's just sticking to the gut and a bit of gut brain. But your listeners may not understand there is a gut microbiome link to every organ in the body. So there's a gut brain axis. We know about that. They've probably heard about that. But gut liver axis, gut heart axis, gut adrenal axis, gut muscle axis, gut eye axis, gut lung. Look, you could talk about every system.
Dr Mary Barson (15:06) Totally, yes.
Dr Paul Froomes (15:07) But it is linked to everything. So gut dysbiosis is probably one of the main drivers of every single degenerative disease of ageing there is, plus a whole lot of other problems that people suffer. And they've even linked the microbiome to pretty much all the immune diseases now. So it's a very important area of health that is largely overlooked, in my opinion.
Dr Mary Barson (15:34) Yes. That is very interesting and extremely important to hear. I would like to focus a little bit more, zero in more about metabolic health, obesity, weight gain, diabetes, hyperinsulinemia, and to get your expertise on the link between gut dysbiosis and these more metabolic conditions because that is something that our listeners are particularly interested about.
Dr Paul Froomes (16:00) Right, right. Okay. So, well, people got really interested in this aspect of the microbiome when there was a mother in Rhode Island who developed nasty C. diff colitis resistant to vancomycin, which is the antibiotic we use to treat it. And so she was offered a fecal transplant as the only solution. But back then you could only use a first-degree relative. The only first-degree relative she had was an obese daughter. So now everyone is saying, oh, no, not a good idea. And Bec Gessner just said, well, what do you mean? There's no link between the microbiome and obesity. People said, well, actually, this was probably 25 years ago, there are animal models. So if you do a fecal transplant from an obese human into a germ-free lean rat, the rat rapidly becomes obese. So we're thinking, okay, that's interesting. Maybe there's something to this. We now know there's an obesogenic microbiome. There's also a diabesogenic microbiome. So essentially what happened was she got her daughter's microbiome, she put on over the next year 37 kilos, and three years later she still hadn't lost it, couldn't lose it. So that got everyone thinking in this space, what is this link between the gut bacteria and obesity or weight gain or metabolic health? So what we now know is that your gut microbiome is kind of almost like it's like a metabolic organ. As I mentioned, these bacteria are very busy. They don't just sit there. They're metabolically very active. And so that influences weight regulation now through a number of mechanisms. So these bacteria usually act through signal molecules on various receptors to influence metabolic health. So the first thing they do is dysbiotic gut bacteria will increase what we call energy harvest from food. So you can eat the same meal as an identical twin, but if one of them's got dysbiosis, they will extract and absorb more calories from the same meal than a lean person. And that's because these microbes are involved in doing that, breaking them down and releasing more calories. They'll alter short-chain fatty acid production and these little things related to metabolic health. And particularly it'll affect insulin signaling. These bacteria can literally promote insulin resistance, which is highly inflammatory, and that's the basis of metabolic health being good or bad. They can alter biometabolism and therefore fat absorption to be increased. They produce altered permeability inflammation. Inflammation's involved in insulin resistance and weight gain. The other thing is they make little signal molecules that bind, so that affect your appetite. So they can make you crave carbohydrates or sugars or overeat, and that's through alterations in, as everyone knows, the GLP-1 receptor and also another receptor, PYY. So they're literally altering and regulating your appetite to increase dysbiotic bacteria. So you're just eating more as well as absorbing more calories and starting to become insulin resistant. And then the other problem is you lose your microbial diversity when you've got dysbiosis. Remember we mentioned you lose all your probiotics and you're getting endotoxemia, you're getting increased gut permeability, inflammation, insulin resistance, and then bang, you start to get visceral fat accumulation. And so that is a big problem. And butyrate, which is one of those short-chain fatty acids I mentioned before, is very important and central to metabolic health. And so if you haven't got the probiotics, you don't make the butyrate. And so if you change it in butyrate, you can correlate increases in butyrate production with weight loss and improved metabolic health. So you need to correct the dysbiosis, you need to bring the probiotics back. But diet's a big part of that too.
Dr Mary Barson (20:03) Dr Paul Froomes, I am absolutely loving this conversation. I think that, though, we'll have to have a little break here, and we will continue on with the rest of this beautiful information next week, going to make this podcast a two-parter. This conversation is so fascinating and so important that I want to keep going into more detail. So we will continue next week.
Dr Lucy Burns (20:36) 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.
