Got Gut Health? Part 3: An Introduction to Dysbiosis

by | Feb 14, 2023 | Featured, Gut Health | 0 comments


Thirty years ago, if I told you that the bacteria in your body were partially responsible for the health and proper function of nearly every organ system, I’d probably have been laughed out of the room. However, research into the microbiome and dysbiosis has skyrocketed since that time, and the microbiome is well established to be either a source of health, or a source of potential inflammation and systemic dysfunction. 

The health of the gut microbiome is imperative for whole organism health. Dysbiosis has been implicated in numerous diseases from metabolic disease (insulin resistance, type 2 diabetes, etc) to autoimmune diseases to depression and other cognitive deficits. This post is going to dive into the basics of gut dysbiosis, which is defined by opportunistic, or bad bacteria overgrowth with decreased levels of commensal, or good bacteria. 


  • Framing the microbiome
  • What is dysbiosis?
  • Health effects of dysbiosis
  • Potential causes of dysbiosis
  • Potential solution

Framing the Microbiome

Many coaches and individuals reading this may know the importance of the gut and its microbes by now, it’s been significantly more mainstream within the past 3-4 years. You’ve probably heard of the gut-brain axis and know how important that is; negative alterations in the gut microbiome can result in brain fog, depression, anxiety, etc. 

In reality though, you can pick an organ and it most likely connects to the gut. There’s a gut-thyroid axis, gut-liver axis, gut-skin axis, even the gut-lung axis amongst others. Problems with digestion really do cause problems with the whole organism. 

Today we’re going to be talking about microbial dysbiosis, which is when we have some divergence in the microbiota from what we currently know as “healthy” (more on that later). It could be when good, or commensal bacteria decrease and opportunistic, pathogenic bacteria take hold. It could also just be overgrowths of good bacteria as well! 

The gut can be thought of as a large ecosystem. You can think of it almost like a rainforest. The rainforest is incredibly diverse; thousands and thousands of different species from the smallest insects to the largest animals. 

The thing with large ecosystems is that they depend on a precise balance. If one particular predator happens to over-produce, or even a new predatory species is introduced, you can have knock-on effects long down the chain. 

If one of the predators over-consumes something smaller on the foodchain, but that smaller species just happens to be very important for the overall ecology, then we can have the effect of killing off many species.

For example, theres a little rodent called an Agouti in the rainforest whose teeth are one of the only ones strong enough to break open certain seed pods, and therefore re-plant trees. If they were to go extinct or become over-hunted, then the population of many different trees would decrease. If these trees feed other animals, and those other animals feed other animals, then a lot of disruption occurs. 

The point here is that the gut microbiome is much like this. When certain species go out of balance, it can have large knock-on effects with other gut species, and many effects outside of the gut. 

What is Dysbiosis?

Simply put, bacterial dysbiosis is some sort of negative alteration of your gut’s microbial balance. This can be a reduction in overall microbial diversity; meaning the number of species within your gut significantly decreases. 

This can be a loss of beneficial bacterial species as well as a rise in deleterious ones. In practice, a dysbiotic microbiome usually has all of these traits. Decreases in diversity, lower beneficial bacteria, and higher pathogenic bacteria. 

Sometimes the bacteria aren’t even necessarily pathogenic; sometimes under normal circumstances and when they’re in balance, they’re commensal, but in other circumstances, when the balance is disturbed, they become deleterious. 

Think back to the rainforest analogy. A rainforest with 10-20 species instead of thousands means that keystone species are gone, causing many other species to go extinct. Trees are dying and not being replanted, and you have these 10-20 species romping around a dying area. Not a very healthy rainforest, right? 

Since the microbiome has been proposed to be a key modulator of human health, many researchers actually consider it to be an ‘essential organ’ of the human body. 

Potential Health Effects of Dysbiosis

Now that we’ve established what it is, let’s dive into the potential consequences of dysbiosis, starting with the local environment; the gut. 

Increased Intestinal Permeability or “Leaky Gut” – If you want a deeper dive on leaky gut, refer to the earlier entries in this gut health blog series. In a nutshell, it’s when there is increased intestinal permeability, allowing in partially digested proteins and portions of bacteria cells, which can cause systemic inflammation. 

A healthy microbiome is very protective of the intestinal lining. For some examples, many species create short chain fatty acids (SCFA), which basically build up the mucus lining in the gut, protecting the intestinal cells underneath. SCFA’s also provide fuel for colonocytes, and have numerous systemic effects including beneficial effects on insulin sensitivity and appetite control. 

Bacteria also create post-biotics, or metabolites from processing dietary components, that protect the gut as well. For a few examples, polyphenols from fruits and vegetables get processed by bacteria into many diverse molecules which have been shown to protect against inflammation-induced intestinal permeability. 

Some species of healthy bacteria actually upregulate the genetic expression of proteins that are responsible for the tight junctions that hold our intestinal cells together, thereby preventing leaky gut. I think you can see what might happen if these species are lower or gone; we get increased intestinal permeability and therefore systemic inflammation.

IBS – We already half-way answered this with the first point, since increased intestinal permeability is also seen in most, if not all, cases of IBS, so we have that heavily contributing. Whenever we assess the microbiome of someone with IBS, we see that it’s heavily altered compared to a healthy microbiome, and this could be contributing to the symptoms associated; namely diarrhea/constipation, depression and brain fog, bloating and gas, and GERD and others.

SIBO – SIBO, by definition, is dysbiosis generally within the first half of the small intestine. The small intestine is normally lower in microbes in general compared to the large intestine, since we have many antimicrobial substances going through the small intestine, such as bile acids. The small intestine does most of the absorbing of nutrients, and the large intestine does most of the fermenting of fibers. However, if negative bacteria are allowed to take hold and overgrow, then we see a lot of the same symptoms that we do in IBS. 

Autoimmune Disease – This point connects the gut to the rest of the body. Within the gut, this can manifest as IBD, which is a good segway to autoimmune disease in general since IBD is autoimmune in nature.

IBD is an umbrella term that encompasses two diseases: Crohn’s and Ulcerative Colitis. Crohn’s can create lesions and destruction along any point of the digestive tract from mouth to colon, whereas ulcerative colitis creates tissue destruction in the colon. 

Autoimmune disease, as the name suggests, is when the immune system attacks the body’s own tissues. A healthy microbiome has significant roles in keeping the immune system healthy and self-tolerant, meaning it helps the immune system recognize the body’s own tissues as it’s own tissues and not a foreign invader. About 70% of the immune system is located in the gut, and your gut microbes actually have a role in training what type of immune cells will mature, and what kind of cytokines will be released. Indeed, dysbiosis has been implicated in many autoimmune diseases from Hashimoto’s to multiple sclerosis to Lupus.

Obesity, Insulin Resistance, and Metabolic Disease – People with obesity, insulin resistance, and metabolic disease have a characteristic dysbiotic profile compared to healthy individuals. Chronic hyperglycemia and hyperinsulinemia has been shown to cause dysbiosis as well as increased intestinal permeability, which can then exacerbate the systemic inflammation that’s already occurring. 

There is considerable evidence in mice and a decent amount of data in humans that it may be causative. If you take an obese mouse with insulin resistance, and transfer their microbiome to a lean germ-free mouse (this is a completely sterile mouse without a microbiome at all), the previously germ-free mouse will get obese and develop insulin resistance/type 2 diabetes. This has been replicated numerous times over the years. 

We have a ton of mechanistic data about how the microbiome can contribute to insulin resistance indirectly; systemic inflammation induces insulin resistance, LPS can travel through the portal vein to the liver and contribute to NAFLD, which induces liver insulin resistance, and there’s many more.

There are also a few published case reports of this happening in humans in the case of fecal transplants. Fecal transplants are done in western medicine to combat antibiotic resistant C. Diff, which can be exceedingly hard to get rid of. There are a few reports of those who got fecal transplants taking on many characteristics of the fecal donor.

One woman, who was a lean marathon runner previously, gained significant amounts of weight and exhibited insulin resistance after her fecal transplant, and she claimed she did not change her diet or amount of exercise at all. This begs the question if it goes the other way around, and eventually we might start banking the poop of athletes and healthy individuals for use in trying to improve health. This certainly isn’t the case yet, so don’t jump the gun and go on a quest for Tom Brady’s poop. 

Hypertension and Cardiovascular Disease – If dysbiosis increases risk or can be potentially causative of obesity and metabolic disease, then it follows that it would affect cardiovascular disease. Metabolic disease and cardiovascular disease are intricately linked. The highly elevated triglycerides, small particle LDL, and inflammation seen in metabolic disease can initiate and progress atherosclerotic plaques, for example. 

Studies do show an altered microbiome in CVD much in the same profile as metabolic disease. The germ-free animal model has been used here too; when a rat with hypertension had its microbiome transplanted into a germ-free mouse, the previously germ-free mouse then developed hypertension as well. This was an animal study, so take it with a grain of salt as always, but given we have some human case reports on metabolic disease, it might be causative here as well. 

Others – I won’t go too in depth here, but just for a complete profile, dysbiotic microbiomes have been viewed in PCOS, cancer, Alzheimers, gout, osteoarthritis, liver disease, and others still.

Potential Causes of Dysbiosis

Many things across your lifespan affect your microbiome and can influence dysbiosis and it starts from the moment you’re born. 

Birth and Breastfeeding – Whether you had a vaginal birth or C-section birth influences how your microbiome develops and the core of what it will be in adulthood. Exposure to the microbiome of the vaginal canal contributes to cementing the microbiome of the baby. Subsequently, whether you were breastfed or formula fed matters – There are tons of prebiotics and microbes within breast milk that further establish and cement an infant’s microbiome. 

Hygiene Hypothesis – Growing up, the environment that the child is exposed to matters. Did they play outside alot, getting exposed to dirt, trees, etc? Were they around a lot of animals such as pets when they were younger? These types of activities can influence the microbiome in a positive manner as well. In fact, the observations that children that grew up on farms had significantly lower rates of allergies and autoimmune disease spurred what’s known as the “hygiene hypothesis”, which basically states that the level of sterility we live with today with less exposure to the elements and microbes fosters a less diverse and healthy microbiome and immune system.

Drugs – Many drugs influence the microbiome, and the number one culprit here is obviously antibiotics. Significant antibiotic use will 100% induce dysbiosis transiently in all cases. For some, it recovers rather quickly, but for many, these are lasting changes that can unfortunately take a long time and a lot of work to ameliorate. Other drugs that may contribute to dysbiosis include proton pump inhibitors, corticosteroids, NSAIDs, opioids, statins, and antipsychotics.

Lifestyle – Honestly, in nearly all cases of activities we know are bad for overall health, we see negative microbiome changes as well. This includes sleep deprivation, chronic stress, and a standard american diet. Diet is obviously going to be a large one, but maybe not in the most direct way you might think. Yes, a fiber-poor diet can starve certain microbes and allow others to take hold. Yes, processed foods can contribute to the overgrowth of bad bacteria. These would be direct modulations. But data suggests that if you change the health of the host, the microbiota changes, and vice versa; even cigarette smoking has been shown to induce a dysbiotic microbiome. 

Potential Solutions:

Going way in depth on gut health protocols is beyond the scope of this blog post, but if you look at the causes, you can reverse-engineer. 

You can’t exactly go back in time and change how you were born or if you were breast-fed, nor if you took doxycycline (antibiotic) for acne for years, like alot of people did. 

In general, we have 2 different tiers of interventions; the first tier being mastery of the basics. This would be keeping processed food intake minimal, making the majority of your consumption from whole foods, eating a diverse array of fiber-rich vegetables, getting adequate hydration and adequate exercise, getting a solid 8 hours of sleep per night, managing your stress, and taking walks after meals. 

Now, this is a bit different if gut disease, multiple gut issues, and dysbiosis is already present. For example, you may actually have to avoid certain fibers, such as FODMAPS, in order to starve off some deleterious bacteria. 

Going in depth on how to resolve even the toughest of gut issues is exactly what we do inside of the Functional Nutrition and Metabolism Specialization, so please check that out if you’d like to learn more. 


  1. The microbes in your gut affect its health, and the health of your gut affects most other organs – the brain, the heart, the thyroid, the liver, and others.
  1. Dysbiosis is simply a deviation from what we understand as a healthy microbiome – Either significantly decreased diversity, or overgrowth of bad bacteria and loss of good ones, or all of the above.
  1. Dysbiosis has been observed in all gut conditions, obesity, autoimmune disease, depression and anxiety, hypertension and cardiovascular disease, insulin resistance and metabolic disease, and other diseases, and may actually be causative of some of these. 
  1. A healthy microbiome starts when you’re born – It’s influenced by vaginal vs. C-section birth, whether you were breastfed or formula fed, and whether you were exposed to dirt, animals, etc when you were younger. Then all things that affect the health of the host potentially affect the microbiome – Poor sleep, high stress, poor diet, sedentariness, and others.
  1. To keep your microbiome healthy, do the opposite of what I just said – Moderate stress, get good sleep, minimize processed foods, include a very wide variety of fibrous vegetables – the more variety the better, and just generally eat mostly whole foods.


Rui-Xue Ding et al. Revisit gut microbiota and its impact on human health and disease. Journal of Food and Drug Analysis. Volume 27, Issue 3, July 2019, Pages 623-631.

Katherine R. Amato, Marie-Claire Arrieta, Meghan B. Azad, Michael T. Bailey, Josiane L. Broussard, Carlijn E. Bruggeling, Erika C. Claud, Elizabeth K. Costello, Emily R. Davenport, Bas E. Dutilh, Holly A. Swain Ewald, Paul Ewald, Erin C. Hanlon, Wrenetha Julion, Ali Keshavarzian, Corinne F. Maurice, Gregory E. Miller, Geoffrey A. Preidis, Laure Segurel, Burton Singer, Sathish Subramanian, Liping Zhao, Christopher W. Kuzawa. The human gut microbiome and health inequities. Proceedings of the National Academy of Sciences Jun 2021, 118 (25) e2017947118; DOI: 10.1073/pnas.2017947118

Carding S, Verbeke K, Vipond DT, Corfe BM, Owen LJ. Dysbiosis of the gut microbiota in disease. Microb Ecol Health Dis. 2015 Feb 2;26:26191. doi: 10.3402/mehd.v26.26191. PMID: 25651997; PMCID: PMC4315779.

Wilkins, L.J., Monga, M. & Miller, A.W. Defining Dysbiosis for a Cluster of Chronic Diseases. Sci Rep 9, 12918 (2019).

Vijay, A., Valdes, A.M. Role of the gut microbiome in chronic diseases: a narrative review. Eur J Clin Nutr (2021).

Jason Martinez et al. Unhealthy Lifestyle and Gut Dysbiosis: A Better Understanding of the Effects of Poor Diet and Nicotine on the Intestinal Microbiome. Front. Endocrinol., 08 June 2021 |

Elena Scotti et al. Exploring the microbiome in health and disease: Implications for toxicology. Toxicology Research and Application. First Published December 10, 2017 Review Article.

Grace A. Ogunrinola, John O. Oyewale, Oyewumi O. Oshamika, Grace I. Olasehinde, “The Human Microbiome and Its Impacts on Health”, International Journal of Microbiology, vol. 2020, Article ID 8045646, 7 pages, 2020.

Chakaroun RM, Massier L, Kovacs P. Gut Microbiome, Intestinal Permeability, and Tissue Bacteria in Metabolic Disease: Perpetrators or Bystanders? Nutrients. 2020 Apr 14;12(4):1082. doi: 10.3390/nu12041082. PMID: 32295104; PMCID: PMC7230435.

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