Did you know that the microbiome is made up of 100 trillion cells of bacteria and yeast that line the mouth, skin and gut? Curious about the role they play in our health? Want to know how to make your bacteria work in your favor? Tune in to hear Ali and Becki go down the rabbit hole of the microbiome and discuss what happens in both a symbiotic (favorable) and dysbiotic (unfavorable) state. From mood stability to immune health to digestive function, the microbiome plays a critical role in expression of overall health or disease state. Learn to recognize the signs and symptoms of dysbiosis as well as what you can do to ensure a healthy and resilient gut population!

In this episode, Ali and Becki dig into the complex topic of the microbiome and address how dysbiosis or overgrowth of bacteria occurs in the first place as well as the multitude of symptoms and conditions an unhealthy biome can drive. Our neurotransmitters, immune system and digestion are regulated by our living bacteria in the gut which means that dysbiosis can impact many systems of the body and have seemingly unrelated symptoms. Learn about what to look for in a probiotic, when probiotics may not be enough and how you can reset your microbiome to work in your favor!


Also In This Episode:

Probiotic Challenge Step By Step:

Step 1: Grab a sewing tape, a notebook and a bottle of our Restore: Baseline Probiotic.

Step 2: Take your waist circumference measurement at your belly button for three days in a row from rise to rest and record.

Step 3: Start probiotic at 1 capsule at bed for 3 days. Continue to measure waist circumference at rise and at rest.

Step 4: Increase by 1 capsule capsule every 3 days until you meet 4 per night at day 10 of active probiotic challenge (not counting initial reads without probiotic)

Step 5: Try to continue at 4 per night for 3 days. Note changes in waist circumference as well as any changes in GI cramping, bowel movements, belching, or gas during challenge. Continue taking probiotic 1 at bed if well tolerated.

More resources and concepts discussed:


Welcome to the naturally nourished podcast, that delivers cutting edge food as medicine solutions for optimum health. Ali Miller is a nutrition expert sought out by the media and America’s top medical institutes for her revolutionary functional medicine interventions. From disease treatment to prevention, every episode will empower you with ways to put yourself back in control of your health. Please note, the topics discussed are for educational purposes only. Now welcome integrative dietitians Ali Miller and her co-host Becki Yoo.


A: Welcome to Episode 60 of the Naturally Nourished podcast on dysbiosis and the microbiome. This is Ali Miller here along with my co-host Becki Yoo.


B: Hey Guys.


A: And this topic is one that we have touched on in many episodes as the gut and the role gut bacteria are absolutely foundational to whole body health but today we really want to get into all things specific gut bacteria.


B: Yes and I can’t believe we don’t have an episode about this already we just see clinically that so, so, so, many seemingly unrelated conditions end up coming back to the microbiome.


A: Yes yes. From skin, mood, GI, all of the things. Hormones- all of the things.


B: Yep.


A: So before we get into this, let’s just give our listeners an update of what’s going on at the clinic.


A: Yeah so we are wrapping up the second to last month of the year, entering into December and I hope you all have a happy Thanksgiving holiday. I think we’re joining you the week just following and a lot of our clients are starting a big Beat the Bloat Cleanse which we launched this Monday so this episode is going live now and so you didn’t miss the mark, we are doing a Beat the Bloat Cleanse with discount off of our e-book so definitely check it out, and the idea is to really tighten back up on carbohydrate control and take this last month of the year to start to kind of streamline your wellness focus and keep you from falling off the rails so definitely a way to have discipline and focus and the beat the Bloat cleanse keeps you at 60g of carbohydrates per day, which really allows you to start to reset your microbiome which we’ll speak to more today about what that microbiome is and how it influences, but that’s  a big push in our clinic right now is out Beat The Bloat Cleanse that’s done hand-in-hand with that Beat the Bloat e-book and the Candida Cleanse and then there’s another grouping of people who are doing our 10 Day Detox so if they weren’t ready for the 6 week candida cleanse, and they’re a little nervous about sugar restriction over December, the 10 Day Detox has been an awesome jumpstart also to commit to at the end of this month going into early December to just kind of reset the body.


I recommend doing a nutritionally supported 10 day detox quarterly, so that means 4 times a year you guys, just like you change the oil in your car, you need to shift the fuel in your body and support the cleansing of your blood and support your liver and kidneys which are the two main organs that cleanse the blood and we- we definitely want to focus during this time of higher temptation to really harness in and honor and nourish our bodies so either one of those processes might be a good fit for you either with starting with our Detox e-book, which has the protocol for our 10 day detox, or with the Beat the Bloat e-book and you can either or see where you fit, and then start hitting the ground running.


B: Awesome and so if someone is considering cleanse, how would this work, Ali, with the holidays, let’s just be real.


A: Yeah so you know like I said, the 10 Day Detox is nine days without alcohol so that could be a really warranted beautiful thing, like I said, and maybe still get you a little bit more flexibility following those 10 days -the 9th and 10th days actually but technically we do allow pinot noir because it has the highest amount of resveratrol so something to consider would be 8 days without alcohol but a good way to kind of wring out the body if we’ve had a little bit of excess with the holidays and socializing and also kind of just, again, harnessing in on clean eating and single ingredient foods so I think it’s a very good time to do this. Also with the Beat the Bloat, like I mentioned, you do still get 60g of carbs so we do recommend avoiding refined sugars and we do recommend the whole protocol to be grain-free but you can still definitely do things like nut flour based cookies and nut butter based breads and such. You can still channel abundance and holidays flavor without going into too restrictive of a mode but it keeps you quite conscious which is a benefit during the holiday season versus just taking your hands off the wheel and that’s why a lot of people see a 5 up to upwards of 15 pound weight gain over the last 6 weeks of the year.


B: Wow. And then let’s talk a little bit about virtual keto because I know we have some spots already filling up.


A: Yes so if you’re a little gun shy on like “ok guys I love you but I’m not going to commit to anything until the 31st of December has closed” then the Virtual Ketosis Program may be an awesome fit for you and it doesn’t have to be exclusive, you could do the 10 Day Detox now, and then still jump into keto but our Virtual Ketosis Program starts that second Tuesday in January and spots are already filling up I think we only have about 40 spaces left and we do accommodate 100 spots in this program and this is a 12 week group you can learn more about it on AliMillerRD.com, under Books and Programs under Ketosis Class. And it is 12 weeks, there’s 6 live courses they’re all archived so you get to watch them, you get a spot in our private ketosis group you get customized materials, and the biggest emphasis of our keto program is it incorporates function integrative medicine so we talk about the influence of stress on the body we talk about the influence on gut bacteria, we talk about the role of carb cycling, the role of hormones, and how a very low carbohydrate high fat diet can be therapeutic to a multitude of disease factors and really provide you tools to maintain accountability throughout the process and this first group that’s completed the program we’ve seen phenomenal outcomes, I mean, what are some things that come to mind, Becki, that has been shared by participants? I know we’ve seen weight loss of upwards of 35-40 pounds from some participants over this 3 month period-

B: And definitely body composition shifts that-


A: Yep body composition shift, so body weight gain of lean muscle. We’ve seen hormonal influence changes we’ve seen a couple girls that had PCOS get pregnant which is super exciting during this process, we’ve seen people go off of diabetic medications, see improvements with their cardiovascular function and seen lowered cholesterol levels. All sorts of really, really cool things so I hope you guys will join us and snag your spot today and, yes, you don’t have to start until the 2nd week of January.


B: That gives a little bit of a buffer and it’s a perfect reset for setting your resolutions.


A: For sure and accountability is definitely key.


B: Yep. Alright and then last let’s just update folks about your book, the Anti-Anxiety Diet so how’s all of that going?


A: Oh yeah all of the things you guys. It’s going so amazing. I am about 20,000 words in, so that’s more than a third, close to half. And I have submitted most of my 30 recipes so I’ve been in my kitchen a lot more doing a lot of recipe testing as some of the fun things that I’ve updated that will be in this book. One is a cherry chia jam thumbprint cookie, which is amazing. Also, I have a hatch chili chicken soup, which uses hatch chilies and bone broth and pulled chicken and incorporates jicama for prebiotic fibers to fuel the gut microbiome and the whole book really takes on a premise of functional integrative medicine and how you can resolve anxiety from the root cause. It also talks about how anxiety is really an underdiagnosed condition in American culture and how there’s a lot of shame associated with it. There’s a lot of hype in our culture about being a multitasker and taking on many hats and juggling many balls and often we don’t honor the upper capacity or limitations of the mind and body. And so a lot of us go into this refractory burnout or panic or restlessness or worrisome mentality and I’m really excited to share this as a resource with all of you because I think it’s super comprehensive and it honors a much needed focus of mental health.


B: Awesome and I’m just excited about eating all of the recipes, you know? Beyond that I’m learning but I’m excited about photographing them and getting to test them out as well.


A: Yes.


B: So let’s get into today’s topic then on dysbiosis. Starting with the microbiome – so, Ali,i how do you explain the microbiome to listeners, and what it is, and, kind of, why it matters.


A: So there are 100 trillion, yes trillion, not billion, cells of bacteria and yeast that line our mucosal membranes starting in our mouth, lining our entire gut, and inside of our skin. And so the mucosal membranes and the collection of bacteria about 3-5 pounds of living bacteria, are known as our microbiome. And our microbiome has the ability to work with or against the host which would be your body that it lives in. And so there’s this concept of symbiosis when the bacteria or yeast and, probably for intent and purpose, I’m probably just going to use the word “bacteria” but throughout this episode if I say bacteria, it could also encompass yeast, ok?


But a symbiotic state is when our gut bacteria are able to work with our body in favorable effects so we can actually see reduced inflammation, we can see improved digestive function, and beneficial regulation of our immune system, we can see increased nutrition absorption so from the foods we’re eating, probiotics or good gut bacteria help to break down food particles and enhance nutrition absorption as well as manufacture nutrients in the colon and then in a symbiotic state, we also produce a healthy balance of neurotransmitters including things like serotonin, and other natural mood stabilizers so pretty comprehensive, and you can see why this is important in the body. And then on the contrary, we can see dysbiosis and dysbiosis is the state against the or the opposite of symbiosis when bad or negative strains of bacteria take over, and we have imbalance in the body. So we can see some big things we associate with dysbiosis are GI distress so like gas, bloating, distention, belching, constipation, diarrhea. We can also see the opposing effects of the things that I noted in symbiosis so we can see increased inflammation we can see immune dysfunction, we can see imbalanced neurotransmitter production. We can see micronutrient deficiencies, or inability to absorb nutrients and also a delayed or lowered manufacturing of nutrients in the colon. So we definitely want to focus on getting our body into the most symbiotic state to support whole body health.


B: Ok so our bacteria make our neurotransmitters, they influence the immune system, and they drive digestive health so I think a lot of these concepts are already known about on the surface, but really when you take it down onto that deeper level it’s just so interesting and so incredible. So let’s talk a little bit about what short chain fatty acids are, how they’re connected to this microbiome talk, and what prebiotics are.


A: Yeah so short chain fatty acids are produced in the presence of prebiotics so they’re basically metabolic end products. We assess short chain fatty acids when we’re looking at a stool test as a functional medicine practitioner often the best snapshot of your microbiome is looking at stool because that is 90+% by weight, bacteria. And so short chain fatty acids are end products of metabolism that are manufactured in the presence of probiotics or good bacteria strains, and complemented by prebiotics and prebiotics are fermentable fibers or resistant starches. And so they’re basically like the fertilizer, if you will, to your probiotic and by the probacteria eating at the prebiotic fiber, production of short chain fatty acid is made. And short chain fatty acids include butyrate and organic acids. The butyrate is highly associated with protection against colon cancer so sometimes the higher the better, and we look at that as a marker of dysbiosis if butyrate is too low and then the organic acids made as forms of short chain fatty acids which include lactic and acetic acids, these play a role in lowering the pH of our intestines which help hand-in-hand which making less of an ability for pathogens or bad bacteria to grow.


So it’s kind of hand-in-hand. I few have beneficial short chain fatty acids, that is a sign of symbiosis and by having the short chain fatty acids, they create a defense mechanism against dysbiosis. So there’s a total chicken and egg relationship within this entire microbiome picture which is really cool and only further emphasized the importance of being in a symbiotic state because it perpetuates a symbiotic state throughout the body. So the short chain fatty acids play a role in regulating our bacteria state. They also have an influence on our sympathetic nervous system which is our body’s stress response so they actually can play a role with our release of serotonin on a mucosal level, which can help with relaxation and anti-anxiety effects and the short chain fatty acids have also been associated with influencing our memory and learning process so there’s some research studies that look at deficiencies of short chain fatty acids, not only with cancer, but also with early onset of dementia and Alzheimer’s.


B: So much here.


A: Yeah and so, again, it’s a chicken and egg; the short chain fatty acids make the feel good neurotransmitter release and then they also, in other mechanisms that are unknown still, influence our cognition, and our cognition is emphasized or optimized we’re probably experiencing less anxiety which means we need less serotonin and it’s the whole cool kind of cyclical things.


B: Awesome and so this story really starts off whether we’re going symbiotic or dysbiotic in our bacterial balance, it really starts off from the birth story.


A: Yes and that’s kind of what we talk about the initial thumbprint, if you will, of your microbiome and this starts with your birth and even there are some research studies that are looking at prenatal influences especially if the mother took antibiotics during pregnancy but we’re talking about the biggest thumbprint or influence is based on the birth through the vaginal canal and the breastfeeding and so if a baby is birthed through a cesarean section, it’s a much more sterilized influence on the body, the baby does not get exposed to the vaginal inoculation and also if baby is not breastfed, and what episode is that, Becki? Forgive me , was it 55? It was. 55 was on breastfeeding and, you guys, go on that if you missed it because we talk about all things that are in the breast milk and one of the big ones definitely are probiotics so you’re inoculating babe with breastfeeding and there are some probiotics that are added to formulas but definitely not in the same diversity or bioavailability in breast milk.


And also there’s something in breast milk called HMOs which are Human Milk Oligosaccharides and these fibers work very comparable to those prebiotic fibers which have beneficial defense against bad bacteria and also fuel good bacteria. So right away, from whether you were birthed through a  vaginal canal and/or breastfed we’re starting to inoculate the baby’s microbiome, if you will, and then also if there was exposure in utero or as an infant, or baby with antibiotics, we can see a higher correlation in a lot of studies on inflammatory bowel disease, IBS, obesity, and the influence of antibiotics in early childhood intervention.


B: So for those who are listening, we can’t really go back and change the past, but I’m sure many listeners can use this information in their households for their own children, but if we were born via cesarean section or not breastfed or given antibiotics for more than a year, what can we do now?


A: Yeah and even before that I just want to say because of course I had an emergency cesarean with Stella and you can also read, we’ll link on our show notes, my natural cesarean and how if you are faced with having to have a cesarean some of the things you can do include vaginal inoculation or seeding, which can definitely help to offset that sterility factor so there’s things that can be done even if that is your fate but, yes, like you said Becki, like “Ok am I screwed here I am 30 whatever and that was my fate, what happens with that thumbprint, how do I etch out that thumbprint or rework it for my benefit?” So we are realizing, we used to think that that thumbprint was kind of set in stone and you could make moderate fluctuations but that was kind of your fate. We are learning now in up-to-date research that lifestyle influencers including stress, oral medications, be them pharmaceutical or prescriptive or over-the-counter, and also diet and other lifestyle influences can definitely mold and drive microbiome expression, and can create significant variants. So these can actually overwrite that initial thumbprint, if you will.


So starting with stress, the first thing we think of with stress in that fight or flight mode, we can definitely have reduced saliva so less than about a quarter saliva is made and in our saliva is biofilms which play a big role with already that mucosal membrane, that microbiome capacity. And webs, if you will, or networks, of underlying mechanisms of bacteria in the saliva. The saliva also has antimicrobial properties or an ability to fight bad bacteria and that is of course helpful if we were to consume a pathogen like E.coli or salmonella in our food sources so when we reduce our saliva, we’re not getting as much of that beneficial balance or biofilm influence. Also, with reduced saliva means reduced enzymes which means we’re not breaking down our food particles as much so there’s more stagnation or fermentation especially if the bacteria is already as a baseline imbalances, you’re feeding more growth of that bad bacteria if you don’t have ample enzyme activity because the food kind of sits there and that’s where we can get that bloating or cramping or food baby, if you will.


Also we’ve seen secondary to saliva with enzymes and biofilms and all that stuff that the sympathetic fight or flight nervous system actually has the ability to sterilize our gut and can completely clean or flush out our lactobacillus. There were research studies that were done on rodents where they were looking at separating a baby mouse from the mama or putting them up to electroshock so some form of stress, a high stress environment and when they tested their guts, they were completely sterilized in lactobacillus and they’d had presence of lactobacillus prior to the reduced stressors. And also they had difference in secretory IgA, and secretory IgA is a significant marker of leaky gut so stress creates also more gut permeability and more reactivity to foods and chemical so how wild is that, like literally just your stress of your job could sterilize your gut, thrown off your gut microbiomes, and create food sensitivities?


B: That’s so crazy to think about. So what about influence of medications you mentioned?


A: Yeah so other medications could the- the first one, of course, antibiotics, right? So antibiotics are quite sterilizing and a lot of them are kind of atom bonds, if you will, that kind of plow out most of the bacteria in your gut and both the undesirable and the good bacteria and the issue is that a lot of the undesirable bacteria- it gets smart, it wants to live and so it becomes resilient or resistant to the antibiotics and they quickly rebound and they can rebound in more aggressive growth and this can lead to more dysbiosis than prior to antibiotic use. Especially this is concerning for people that are on long-term antibiotics for, like dermatological concerns, like acne and such.


This is really concerning because it has a huge sterilizing effect and can drive significant dysbiosis and even like kids that are dealing with chronic ear infections, odis media, tubes in the ears and are on antibiotic  multiple rounds throughout the year, this can create a lot of GI distress so definitely working with probiotics is super important piece of that puzzle. Another world beyond antibiotics is a buffers to our gut pH. So I mentioned that those short chain fatty acids reduce our stomach pH and a drop in pH of your stomach is actually creating more of an acidic environment, higher pH is actually more buffered and so we’re looking at an antacid creating a buffering effect and this could be something like an over-the-counter TUMS or Pepto-Bismol, or a PPI proton pump inhibitor like Nexium, protonics, omeprazole, pantoprazole, all of these drugs block our stomach acidity which can soothe the burn of heartburn or reflux temporarily but over time, that basic pH of the stomach sets up an environment for bad bacteria and yeast which only fuels the fire and can create more bloating, more distention, and can, in turn, create more reflux so definitely something that can add fuel to the fire if you will. I work with all of my clients to try to strategically wean, I do like to look at their scope to see if they have any risk of if they’ve had an endoscopy if they’ve had any esophageal wear and tear, or barrett’s esophagus, I always like to kind of soothe and cool before I wean them off of those drugs, but that’s definitely a goal is to get off of those medications which can have long term influence on the microbiome and micronutrient deficiencies.


And then there’s drugs that aren’t even related to the gut so, you know, beyond antibiotics and beyond the digestive PPIs and antacids, things like even birth control which we might not even connect, birth control has a huge influence in our estrobiome which is our estrogen digesting bacteria, crazy, we need  a whole episode on that, but our estrobiome has a huge correlation with our microbiome and that’s why we can see with the synthetic estrogen with birth control, dynamic influences on gut bacterial imbalance and that’s also why some people get yeast infections or flairs during ovulation or right after their period during different ebbs and flows of estrogen activity in their body.


B: So wild and I’m sure so many listeners have been on birth control in the past, or are still on it for 10 years ongoing so that’s certainly something to consider.


A: Yeah and even beyond medical drugs, medical intervention like radiation, surgeries that are sterilizing so like, you know, me having a caseation if someone had a gallbladder removal, if someone’s had radiation from cancer treatment, that all can kind of sterilize gut bacteria so we really want to work on rebounding as quickly as possible with comprehensive bacterial balance.


B: Awesome and then let’s talk a little bit about diet and how that can have a role in influencing the symbiotic or dysbiotic bacteria.


A: Yeah so excessive sugar and refined carbohydrates feed bacteria and yeast. So one first line of defense is going low glycemic and then another thing even is jumping into a ketogenic state which would kind of really wring out that excessive use of glucose as fuel when we’re using ketones as fuel, ketones are made from our body’s fat stores and these have much more of a neutralizing effect on our microbiome so this allows us in turn, especially hand-on-hand with a gut protocol or therapeutic supplements to basically not only starve off, but kill off the dysbiotic bacteria and in a different way than we would with an antibiotic, raising natural antifungals and antibacterials, they’re more selective, they’re not as much of an atom hit so they more work to kind of play the field  versus dissolving the field, if you will.


So restricting excessive sugar is the first line of defense and then actually also what is concerning is a  diet that’s too low in fiber because you don’t get those prebiotic fibers. So I’ve seen in clients that go keto if they’re too focused on just their numbers of keto and not getting enough fiber with our program and not getting 2-3 cups of leafy greens every single day throughout the protocol, and then even during most days somewhere between ½ to 2 cups of nonstarchy vegetables so getting things like brussels sprouts and broccoli, and cabbage, these prebiotic sulfur fibers help to beneficially influence the microbiome. If we’re only doing hard boiled eggs, meats, and fats were actually going to not have as much of a symbiotic state which can throw off whole body health so diet is important to get ample fiber but yet low glycemic or even ketogenic so very low carb with ample fiber, and the last thing that I mentioned just in food and lifestyle is to be mindful of your drinking, but of course excessive alcohol can be sterilizing, but even water, chlorine and sodium fluoride can be two of the most sterilizing influences, that’s why they’re added to our city drinking water, right? To kill off bacteria in the water and they can kill off the bacteria in your guts so really important to look at good quality, filtered water we do a home delivery service of glass globes of water that we drink exclusively and I have my water bottle as a security blanket, I bring it into every restaurant and it’s just kind of my big thing and a big commitment to my health.


B: Awesome and then is adding probiotics, will that be enough to get ahead of these influences  or is there something else that we need to do?


A: So yeah, like I said, if you’ve had sterilizing influences, like especially during and post antibiotic treatment I always recommend doubling your probiotics for that same equal amounts of days and getting both a comprehensive probiotic as well as a good 50/50 blend so that would mean in the formulas that I carry on AliMillerRD.com the Spectrum Probiotic and then one of the either Targeted Strength or Baseline depending on really your bacterial need, but you really have to think of the gut as a garden bed so just adding seed if our garden bed is cement, if it’s totally sterilized and doesn’t have any soil, just adding seed doesn’t mean that a garden’s going to grow, right? So, or like throwing seeds on aluminum or metal, nothing’s going to happen so it can be a great start to add in probiotics and I recommend everyone takes probiotics but you also need to make sure that you either have a low growth of bad bacteria or you might need to plow the garden bed. Like I mentioned, if you have dysbiosis before the good bacteria is accepted and that’s an important thing to think about if that garden bed is filled with weeds, just throwing seeds those seeds are going to be strangling the growth of the beneficial flowers, if you will. So that’s not going to help if you want to do a cleanse before you could proliferate the good bacteria. Again, adding soil to the garden which would be these prebiotics fibers in your vegetables and nonstarchy fiber vegetables are going to be nuts and seeds fibers and such are going to be the fertilizer and the soil that’s going to keep it all viable. So it’s all important but probiotics are definitely huge piece.


B: Awesome and I love that analogy of the garden bed, I think it just makes so much sense for clients when they hear that. So let’s get into, before we go into particular strains, or favorite formulas, let’s just talk about that probiotic challenge that you see in clinic.


A: Yeah so, for you listeners, this is an awesome thing to try so I recommend starting with a 50/50 blend of lacto and bifido and the reason is, a lot of these sexy probiotics are very wide spectrum so a lot of these soil-based organisms and a lot of the like viacell and multi multi strains, yes, they can be beneficial but it’s very diverse, it’s like wild flowers and the most well researched strains of bacteria are lactobacilis and bifido and so if we’re talking about now known if we’re in a state of dysbiosis we want to first inoculate, or set up camp, of the two most well researched strains so I recommend starting with our Baseline Probiotic which is our Rebuild Baseline Probiotic, and this is a 50/50 blend of lacto and bifido cultures so it’s a good blend of those 2 well researched formulas and it’s 15 billion CFUs so 15 billion is a pretty moderate amount, it’s aggressive it’s definitely higher than your Align and some of the over-the-counter ones, but 15 billion is a good baseline that’s why it’s called Baseline. So you start with 1 at bed for 3 nights and you then increase by 1 in 3 day increments. So days 1, 2, 3 you would take 1 capsule of the Restore Baseline Probiotic, then on days 4,5, and 6, you would take 2 capsules; 7, 8, 9 you would take 3 capsules and so at day 10-12 you would be on 4 capsules and that would bring you up to 60 billion (15 billion per capsule) colony forming units and what you want to assess is each day, you may take waist measurements by taking measurements at your belly button to see variances of bloating or distention from rise to rest to rise. And definitely chart those down or write those down, check for bloating or distention, belching, flatulence, changes in bowel movements, shifts in energy, dermatological flairs, and if things improve with the increase of the probiotic, then I’d recommend shifting to my Targeted Strength Formula for 2-3 months. This is a 60 billion colony forming unit per capsule so instead of taking 4 at bed, you’d take 1 at bed. It’s going to give you kind a heavy hit to inoculate the biome for 2-3 months and then you could go back to the Baseline Formula.


B: And then what happens if there is intolerance where we have some of those negative symptoms?


A: Yeah so if you start your probiotic and you get loose stools or you get constipation as you go up the scaling, or you get more bloating or fermentation, then definitely we want to look at doing a bacterial cleanse. If your dysbiosis symptoms are significant and you’re resonating with maybe you’re on anti-anxiety medications or and antidepressants and you’re dealing with diarrhea and constipation chronically and you’re dealing with a food baby, you may want to do more of a direct GPS approach to your body with a stool sample. So you might go into doing an advanced stool assessment which you could look at under my Clinic tab on the Alimillerrd website and click on Labs and you could read about our GI tests, and the stool tests and that’s something you can do and in that panel, we would get resistance of reactivity scores so we would know what natural antimicrobial and antifungal formulas would be the most effective, but I would even recommend before you invest $300+ into that panel, that the best place to start would be with the Candida Cleanse Bundle. So this incorporates 4 different formulas and although it’s called a Candida Cleanse Cundle, it can be so much more multifactorial because it has a lot of agents that would work for dysbiotic bacteria and even agents that could work on parasite activity. So the first formula in there is called GI Cleanup and GI Cleanup is a particular form of a probiotic that has macrophage properties or basically what it does is eats away at bacterial, it’s called- it’s got pro phageinfleunce so it can actually eat away at bacteria die-off and create space in that garden bed so this is kind of like the start of that plow or the cleanup in that garden bed.


And then the other compound in there is called Burberin Boost and Burberin Boost- Burberin is an antibacterial, antifungal and anti – I think I said antimicrobial, antifungal property and it also a little bit of supporting compounds for liver and can even, it’s been shown in research, burberin is one of my go-tos to lowering hemoglobin A1c of regulating your blood sugar levels. So really great for whole body health. Definitely can support the liver, which helps the detox process during the cleansing but it does have the antimicrobial and antifungal influences as well so that’s actually for your first agent for your kind of weed killer, if you will. Then the other weed killer in your artillery of this bundle is CandiActive and CandiActiv, although named more specific to acetate candida, it has compounds that are good for bacteria, yeast, and parasite as well, driving with oregano and thyme oil.

And it works with apoptosis or basically bacterial cellular suicide so it brings oxygen and these potent essential oil plant-based compounds, and tannins into kill off bacteria, yeast, and even parasite activity. And then the last player in this bundle is called Ultimate Detox and this is taken to help the body in the removal of the die-off and so if you’re just kind of plowing the garden bed, and you’re not getting, you’re not removing the weeds and they’re just kind of composting, they might reseed and might grow back so we want to remove the die-off. Also we can get an influence where the root isn’t pulled out of the bad bacteria or the Ultimate Detox helps us to get into what’s called biofilms are basically these underlying mechanism of bacteria, and that way we’re really getting at the full piece of the bad bacteria to clean them up completely.


B: Yeah and let’s just share with listeners, I know that sometimes in a cleanse, things can get way worse before they get better, this is referred to as a herxheimer reaction so let’s just talk about what this is and how we can support the body best through this.


A: Yes so with Herxheimer reaction often that is, and that’s very common with functional medicine, is we’re kind of pushing the body against the way it had been functioning and the body can work in a commensal relationship with bad bacteria or even parasite, and we see this in archaic studies on more kind of Paleolithic studies on the human microbiome and so we do want to still cleanse and create as much symbiotic environment but there can be a decline during a cleansing property and this is often because there are endotoxins, which are basically internal toxins that are released by microbes when they are dying or being killed off. So as we’re bring in the Burberin Boost and the CandiActive these players are a giant, like the weed killer and there’s  a little bit of fight back from the bacteria or there’s the die-off influence which can create kind of like a pre-flu aching ,it can create fatigue, it can create a little bit of a dull headache, it can create dermatological flaring, and so we really want to support our body’s detox processes which is why we’ve added that Ultimate Detox into that Candida Cleanse Bundle.


We used to have it as an option and we just felt like “ok there’s too many people who are emailing us about having these die-off side effects” and since we’ve incorporated that without making an option and just making it a part of the protocol, that has extremely subsided so having the Ultimate Detox in your cleanse helps significantly so there’s 2 phases of detoxification. There’s day 1 which is activation of toxins in the release process and making them water soluble and then phase 2 is the excretion of encapsulation, supporting those toxins to be eliminated through the waste products of the body. So we want to support phase 1 with antioxidants, and during this protocol you’re going to be, as I mentioned, lower carbohydrate so antioxidants can come in low carb forms like green tea, and in pomegranate seed which are also great form a fiber, and in polyphenols that are in cacao, like raw cacao powder, and in turmeric and ginger so those are great antioxidants and then high sulfur compounds in the diet from our cruciferous vegetables like our cauliflower, Brussels sprouts, cabbage, kale, all those thing help in that phase 2 detox support and that all hand-in-hand is supported by fiber and ample fluid. So when we’re looking at fiber we want to get at least 35 grams a day and then having at least 2-3 liters for fluid per day to help to move and create bowel motility and also support the liver and kidneys that fluid is going to have to cleanse the blood and reduce that solute load to hit those detox glands.


B: And then I’m also thinking about other ways we could support our detox. Let’s talk about some other foods and some other ways to support that detox process.


A: Yeah so another one I’m thinking of that would work hand-in-hand with the antioxidants, the blog on our turmeric shooter so the Turmeric Lemonade I think we called it, you could do that the keto version keeping the honey out, so definitely make sure that you would eliminate the honey in that recipe so we’re going more for the high hit of lemon to stimulate bile flow from the liver and also getting that turmeric as the antioxidant, anti-inflammatory, and also turmeric itself helps the liver and apple cider vinegar flush is something that could be incorporated halfway through your cleanse.


I like to keep all probiotics actually out during the first three weeks of a 6 week cleanse so that we’re really just focusing on that plowing influence of the body and then following on the proliferation or rebuild during the second half of that cleanse and then we follow 6 week cleanse within at least 4 week focus bacterial rebuild and that’s with our Bacterial Rebuild Bundle and the Probiotic Bundle, that’s all available in our Beat the Bloat e-book so definitely a good deal for those of you that think this dysbiosis might be you. And then add some salt baths and massages are huge, as well as oil pulling. Oil pulling helps to prevent the bacteria from translocating into the oral cavity or ear, nose, and throat so when you’re doing a cleanse definitely extremely focused on oil pulling with the coconut oil, and epsom salt helps the detox process and also some of the aches that can occur with the die-offs.


B: I’m also thinking sauna would be a good tool.


A: For sure anything that would upregulate that cleanse and we have a blog called Coping with a Candida Cleanse that we will put in the show notes so you all can read a little bit more about what that herxheimer reaction looks like and how you can support your system and, of course, we’ll also put links to that Beat the Bloat e-book which talks about the whole process as well.


B: Awesome, so it’s really important to understand that pushing through is necessary to getting the full effects of that cleanse. So I do want to wrap up here by, before we summarize of listeners, let’s just really really briefly talk about the gut as the second brain of the body.


A: I love how you give me a double release. So ok, really, really briefly because I think that especially with my writing of the Anti-Anxiety Diet, I could do an entire episode on the second brain of the body and it’s a whole chapter devoted on this element but I will try to be brief. So the gut is intertwined with neurons and second only to the brain, ok? Over 500 neurons in the gut, and we also manufacture over 30 neurotransmitters in the gut, most of them working in the same way that they do in the brain so, in fact, we’re talking about over 90% of our serotonin and also the storage and production of the serotonin is in the gut so we’re talking about your feel good anti-anxiety landing gear, mood stabilizer, antidepressant serotonin, we’re talking about 50% of our dopamine which is that reward-seeking bliss, so can you use how dysbiosis can drive food cravings, right?


So serotonin, dopamine, and GABA, all of these play a huge role with fermentation and good bacteria balance. And we call the gut the ENS, or enteric nervous system, internal basically nervous system in the digestive area and it’s a primary division of our autonomic nervous system so our autonomic nervous system plays a role on the function of the body that is regulatory so it controls our heartrate, it controls our digestion, it controls our respiratory rate, sexual arousal, it is a primary driver of that sympathetic nervous system or fight or flight mode, and so when we’re talking about this ENS, both because it manufactures those neurotransmitters and holds a lot of them and then has over 500 neurons, this is really the second brain of the body and it controls so many of these regulatory functions. And it can work in connection with the central nervous system so the brain and the brainstem, right?


Or it can can work- actually we’ve seen in up-to-date research, really crazy independent to or in response to our sympathetic nervous system or fight or flight mode. So the Vagus nerve which is what goes to the nerve stem all the way down to the colon is our largest nerve which plays a big role in that sympathetic relaxed rest and digest or the sympathetic stressed fight or flight and this is kind of the highway of information that carries the signals of brain to gut as well as signals from the microbiome so here’s where it gets really crazy. So the microbiome we’ve seen actually can upregulate and respond based on pathogens or bad bacteria influence, and also, as I mentioned, the microbiome can be sterilized by stress response so there is this two way signaling of the vagus nerve or that information highway of our brain, and our gut, based on the microbiome and so if we have pathogens or bad bacteria release, our gut will actually tell our brain that we need more epinephrine or adrenaline or stress response and that is often carrying more pathogenic activity which then also sterilizes our serotonin which then doesn’t allow us that relaxation rebound from stress response and it’s just this like chronic chicken and egg relationship of fight or flight mode and so really wild. I’ve seen clinically when doing a bacterial cleanse it’s extremely important to watch the serotonin state, potentially some people benefit from use of something like 5 HTP or a precursor with serotonin building blocks, or L-threonine on higher doses to regulate neurotransmitters because we can actually see vasovagal influence like fainting, or blood pressure changes, or dynamic panic attacks or anxiety because of that sterilization influence and that gut role with our neurotransmitters.


B: That is so wild and crazy. So really optimizing our microbiome supports not only our digestive and immune health which we’ve talked about, but also this optimal neurotransmitter production and mood stability.


A: Totally and so, like I said, I have an entire chapter in the Antianxiety Diet on this concept because social stress and anxiety drives excessive output of our catecholamine stress responding neurotransmitters which includes you know, our epinephrine, like I mentioned, and dopamine, and norepinephrine and that has been trended in research to influence the growth of bad bacteria and then that bad bacteria or sterilization from stress drives down the serotonin so now we’re experiencing more anxiety, more stress response, without the landing gear to help our mind and the body then start to have the physiological influence of elevated blood pressure, increased weight gain from excessive cortisol and all of the cascade influence of inflammation.


B: Right and then does dysbiosis even impact down to the level of something like BDNF?


A: Yeah so I’ve actually seen there’s the influence of the microbiome on our neurotransmitters in that second brain in the body and then the last thing I’ll say, because you told me to be brief Becki is, cause that’s the whole thing, right? Our brand derived neurotrophic factor so this is something we’re really researching in brain trauma, in cognition, dementia, Alzheimer’s, and we’re seeing that the BDNF when it drops in the hippocampus of the brain, depression and anxiety is seen in higher rates, and so there’s actually new drugs that are starting to target the BDNF in the hippocampus and we’ve actually seen with stress response and microbiome influence, they’ve done desterilized gut studies where they’ve actually added probiotics to a sterilized gut and they saw that the BDNF increased in the hippocampus in the brain, and that actually reduced anxiety and depression and enhanced the production in turn of serotonin so adding a lactobacillus supplement actually had an influence on this antiaging brain property, which also again connects this gut as the second brain of the body. So probiotics not only have a neurotransmitter influence, they have a brain restorative influence as well.


B: That’s totally wild and I think we could do a whole other episode, like you said, on the gut brain connection I’m sure we will in the future. So I can’t wait to learn more about all of these things, but for now for today’s episode on dysbiosis we’ve covered the foundation information, what it is, how dysbiosis occurs, how you can assess and what you can do about it and why this all matters as the most important piece.

A: Yes and so I hope you all food for thought – the first thing I would challenge all of you listeners to start with that 50/50 blend of the lacto and bifido probiotics. Try if you can’t find one my Baseline Probiotic and we’ll put a link in the show notes and we’ll also write out that probiotcis challenge in our show notes and you can find the show notes as a reminder on AliMillerRD.com under the podcast tab and then click on the episodes and that’s where you’ll see all of the show notes and so try that probiotic challenge as a litmus to yourself and then if you don’t get a bad reaction, you could just keep with that and the playing field and keep probiotic-rich foods in the mix. I know we didn’t talk a lot about those days but I know we have tons of resource in other episodes and speak a lot to those so you could keep just as a baseline that baseline probiotic and probiotic food and fiber, and be all steam ahead, or if you have dysbiotic intolerance or decline, or some of these symptoms we’re talking about, definitely look deeper into that Beat the Bloat and the Cleanse and how you can plow the fields and have a beautiful, optimized, microbiome garden bed with only petunias and roses. So thanks guys for listening and as always, please share this podcast with friends and family that you feel could benefit and if you liked the episode please head over to ITunes, just take a couple minutes of your person times to honor Becki and my time to put this content and knowledge out for you guys by sharing it on your social media and/or giving us a 5 star review on ITunes which helps us to be visible in the food as medicine scope so others can learn as well.


Thank you for listening to the Naturally Nourished Podcast. Visit our blog at Alimillerrd.com for recipes, wellness tips, and food as medicine meal plans. Connect with Ali at Becki at AliMillerRD on InstaGram or Twitter and Facebook. Until next time, stay nourished and be well.

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