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7 Interesting Signs Your Gut Bacteria is Out of Whack

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Having healthy gut bacteria is the key to overall well-being. When gut health is poor, the body, as a whole, suffers. This is why it is so important to know the common causes and signs of dysbiosis. In this article, we are talking about it all!

feeling sick due to gut bacteria imbalances

Reading Time: 12 minutes

I’ve said it before and I’ll say it again (because it’s really that important), gut health is the key to overall well-being. Your gut bacteria specifically is responsible for managing and maintaining various functions in the body. When gut bacteria is poor, the body, as a whole, suffers. As a result, you’re left with chronic, nagging health problems. And, until you start to look at the health of your microbiome, you’re unlikely to fully understand the root cause of your health issues.   


Did you know that we have an estimated 100 trillion microorganisms (microbes) residing in our gut? That alone should tell us it is worth focusing on! In a healthy gut, these microbes are diverse and mostly beneficial (good bacteria). Sometimes though, these microbes can be yeast and viruses (bad bacteria). The good gut bugs provide numerous health benefits to us, where an overgrowth of the bad gut bugs and pathogens can make us feel sick and create many imbalances over time. This ecosystem is known as our microbiome, and unfortunately when our microbiome is out of whack, imbalances and problems will arise. Most of us lack good diversity or have too many pathogens without enough beneficial microbes. This imbalance is known as dysbiosis. 

The diversity of microbes in the gut control just about everything in the body. They are responsible for functions such as: 

  • Inflammation levels
  • How we detox 
  • Our mood and behavior 
  • How we metabolize and breakdown our food 
  • Digesting and absorbing nutrients 
  • Protecting the lining of the digestive tract 
  • What foods we crave 
  • Our ability to fight germs and infections
  • How genes are expressed 
  • How hungry or full we feel 
  • Our weight 
  • Regulating neurotransmitters we make for our brain 
  • How well we can focus 
  • How tired we are

There are many root causes to dysbiosis. Many individuals have more than one cause and often present with a combination over a long period of time. Sometimes, dysbiosis has been going on for the person’s entire life before they experience the symptoms. Here are the most common causes of dysbiosis:

gut bacteria imbalances

A baby born vaginally is covered with beneficial bacteria through the birth canal that becomes the baby’s first exposure to microbes and develops the baby’s microbiome. When a baby is born via C-section, he or she misses this critical step and will often pick up the microbes around the environment (such as the hospital). Research continues to prove that babies born via C-section tend to have more signs of an imbalanced microbiome later in life. 

Formula vs. breastfeed

Research suggests the benefits to breastfeeding for the development of a healthy microbiome of the baby. This largely depends on the health of the mother. In some cases, a good formula with some beneficial microbes and probiotics can be a better option if the health of the mother is compromised. However the chance of developing dysbiosis is greater for those babies who are formula fed. 

GI Infections

This is often the most common cause of dysbiosis and can occur from food poisoning, traveler’s diarrhea, the stomach flu, parasites, and other illnesses that wipe out the good microbes in the digestive tract. Most people have a bout of food poisoning and get over it in a few days, however the body is unable to bounce back and recover from these infections. I am never surprised when I ask my clients when their conditions like IBS started and they mention it was after a bad food borne illness or after traveling somewhere and getting sick. 

Poor Diet

Usually the most common cause of dysbiosis is having a poor diet. Consuming excess processed foods, refined sugars, alcohol, junk food, inflammatory oils, and fast/fried foods can disrupt healthy microbes. Dysbiosis can also occur due to consuming a diet low in fiber, fruits, vegetables, and anti-inflammatory foods. 

Antibiotic Use

There’s a time and place for antibiotics and sometimes they are life-saving and necessary. Overuse of antibiotics though kills the beneficial bacteria in the same way they kill the bad bacteria. Wiping out all the good microbes can drastically alter the microbiome, even after only a few days of antibiotics. While the gut can fully recover on its own after a single use once in a blue moon, antibiotics are usually overused and prescribed too frequently when they are not always necessary. Studies show that children and adults using antibiotics frequently or long-term will most likely develop dysbiosis. 

Chronic Stress & Trauma

Stress is unavoidable but chronic stress that is ongoing for a long period of time can feed harmful microbes leading to dysbiosis (typically in the form of small intestinal bacterial overgrowth). Trauma can also lead to dysbiosis, even in the short term. This can be due to a car accident, move, break up, etc. Sometimes dysbiosis follows a good trauma, such as pregnancy and childbirth. Whenever the body goes through a sudden change, you are more likely to develop dysbiosis. 


We are surrounded by toxins. They are literally everywhere–in our food, soil, water, environment, home, cosmetics, personal hygiene products, cleaning supplies, and so on. This topic deserves an article of its own! Exposure to toxins can disrupt the good microbes in a similar way a gut infection would. 

Low stomach acid

Stomach acid is a weapon of defense against bad pathogens that are ingested. If we lack stomach acid (which most individuals do because of age, stress, and medication use), the pathogens grow in our gut since there isn’t enough stomach acid to kill them off. 

Zinc Deficiency 

Normally having dysbiosis will contribute to micronutrient deficiencies, however research shows that having a zinc deficiency alone can disrupt the diversity in the intestine. 25% of the population is deficient in zinc due to poor dietary intake and absorption, and this is one of the reasons it can alter the makeup of bacteria.


If your gut bacteria is out of whack and you are experiencing dysbiosis, there’s a good chance you feel it just about everywhere. Common symptoms appear like flashing red lights.

These are the more obvious signs that most people will correlate with gut bacteria imbalances:

  • Gas
  • Belching
  • Bloating or distention 
  • Diarrhea
  • Constipation
  • Stomach pain and cramps
  • Food sensitivities and intolerances 
  • Heartburn, reflux, gastroesophageal reflux disease (GERD)
  • Irritable bowel syndrome (IBS)
  • Small intestinal bacterial overgrowth (SIBO)
  • Inflammatory bowel disease: Crohn’s and Ulcerative colitis 
  • Celiac disease 

Other symptoms are more sneaky though. These not-so-obvious signs of gut imbalances disguise themselves as “normal” health conditions and escalate slowly over time making them difficult to notice. And even if they are more common to you, they are far from “normal.” The research proving an imbalance of gut bacteria affects illness is overwhelming. Just about every medical condition can be linked to the health of the microbiome. The following signs and symptoms are clues to discovering a potential imbalance in the gut that you should be looking out for. 

signs and symptoms of gut bacteria imbalance

The term “mental disorders” is all-encompassing. It can include mental struggles like memory loss, brain fog, irritability, mood swings, and anxiety. Yet, it also speaks to mental sickness, like depression, anxiety, addiction, and more. Neurotransmitters in our brain are constantly communicating with our gut and 90% of our serotonin receptors reside in the gut tissue which means that if the gut bacteria is out of balance and the gut lining is compromised, so is the communication to the brain. Leaky gut = leaky brain!

Metal imbalances linked to an imbalanced microbiome include: 

  • Memory problems 
  • Brain fog 
  • Depression
  • Anxiety disorder 
  • Alzheimer’s disease 
  • Attention deficit hyperactivity disorder (ADHD/ADD)
  • Autism 
  • Tantrums in children
  • Behavior problems in older kids or adults 

Nutritional deficiencies are extremely common due to stress, diet, lifestyle, low stomach acid, age, and medication use. If you are dealing with a gut imbalance, there is a high chance you’re deficient in several essential vitamins and minerals, including vitamin D, vitamin K, magnesium, iron, and vitamin B12. These deficiencies often cause additional physical symptoms, like fatigue, irritability, and constipation, which is why it’s important to get your micronutrient levels tested at least once a year by a functional practitioner (beyond just surface labs such as a CBC). 


Your skin is directly impacted by the health of your microbiome and inflammation on the inside will always result in inflammation on the outside. If you’ve ever struggled with skin issues, you know just how frustrating, embarrassing, and inconvenient they can be. Skin issues like eczema, acne, rosacea, and psoriasis are all inflammatory skin conditions that are directly correlated to the gut! In fact, there is a direct relationship between gut and skin health. If you’ve ever heard of leaky gut (AKA poor gut function), you should be aware that leaky skin is a common consequence. This is because the gut and skin are two innervated organs with crucial immune and neuroendocrine roles and are uniquely related in purpose and function. Both organs are essential to the maintenance of physiologic homeostasis. 


Active autoimmunity is THE tell-tale sign of gut dysfunction and the place you must start. After all, the majority of the immune system is located in the gut! When the bacteria in the microbiome is compromised, meaning there’s not enough good bacteria or theirs some “bad bacteria” in places we don’t want it, the  immune system often follows suit. In the case of autoimmunity, the immune system kicks into high gear and treats itself like a foreign invader or pathogen. If you want to reduce your symptoms of an autoimmune condition or even reverse it completely (which is possible!), you must address bacteria imbalances and heal your gut. 

Autoimmune conditions linked to an imbalanced gut include: 

  • Crohn’s disease 
  • Celiac disease 
  • Multiple Sclerosis 
  • Rheumatoid arthritis 
  • Lupus 
  • Diabetes (Type 1 and 2)
  • Hypothyroidism 
  • Hashimotos 
  • Grave’s disease 

Raise your hand if you feel groggy and lethargic all day long.  If so, you could be dealing with a classic case of chronic fatigue. Chronic fatigue is never a diagnosis on it’s own and always has a deeper root to it. Before I found out about my gut imbalance and autoimmune conditions, I was misdiagnosed with chronic fatigue just because I was chronically tired all the time but nobody was able to figure out WHY. This is often the #1 complaint I hear from clients when we first start working together. 

Being tired all the time is not normal and is usually a really good indicator your body has an imbalance somewhere, and that somewhere is almost always the gut. When the bacteria is out of balance due to a combination of gut infections, stress, lifestyle, diet, and/or intestinal permeability, nutrients aren’t transported to the mucosal cell membranes in the tissues and therefore, can’t make their way to the areas of the body that need them. Nutrients give us our energy and life so if we are eating even healthy foods but lacking the nutrients from them because they are “leaking” through the tight junction gaps along the intestine, we become exhausted. If you’re experiencing fatigue that is unbearable and you struggle to get through the day, then it’s time to take a deep dive into your gut function and identify the root cause of your sleepy body. 


Yo-yo weight loss and stubborn weight gain often indicate poor gut health. When the gut contains high levels of pathogenic bacteria and low levels of healthy bacteria, maintaining a healthy weight can be a real struggle- even when you’re doing all the “right” things due to increased inflammation. Difficulty losing weight, being overweight or obese, or even having a hard time gaining weight are all not so obvious signs your gut bacteria is out of whack. 


Craving sugar morning, noon, and night isn’t just because you have a sweet tooth. As you’ve probably guessed, constant sugar cravings point right to the gut. When your gut bacteria is healthy and you’re receiving optimal levels of nutrients, cravings typically disappear, or at the very least, decrease. In fact, many gut infections such as SIBO and candida albicans can actually make you feel hungry all the time. In addition, remember when we talked about mental health? Our neurotransmitters also control our hunger cues and cravings, so if these key neurotransmitters aren’t signaling the way they should due to gut imbalances–you are more likely to feel uncontrollable hunger and sugar cravings throughout the day. 


Yes, there’s more! Studies have also linked an imbalanced microbiome to less obvious symptoms and diseases such as: 

  • Headaches and migraines 
  • Bad breath
  • Frequent colds and illness 
  • Hormonal imbalances such as polycystic ovary syndrome (PCOS), endometriosis, premenstrual syndrome (PMS)
  • Asthma 
  • Allergies 
  • Fibromyalgia 
  • Cancer 
  • Heart disease 

Depending on how long you have been suffering with dysbiosis, it is likely some level of leaky gut (or intestinal permeability) is present. Leaky gut occurs when the lining of the gut is compromised leading to more food sensitivities, gut infections (since they can easily pass through the gut barrier), nutrient deficiencies, dysfunctions in the blood brain barrier, and inflammation. When you develop more food sensitivities and get infections overtime, your immune system will be in a constant state of inflammatory response. Imagine eating healthy foods every day that your immune system is reacting to? It just creates a vicious cycle. 

Inflammation is your immune system response to any threat, infection, or injury. If there are foreign invaders (like bad gut microbes for too long), your immune system uses inflammation to attack it. So when chronic inflammation becomes widespread for a long time it starts to affect other organs throughout the whole body, not just the digestive tract. This is why the quality of your microbes, the integrity of the gut lining, and how much inflammation is percent is all interrelated. 

This is known as the leaky gut cycle:

  1. Dysbiosis causes leaky gut and inflammation
  2. Leaky gut causes inflammation and dysbiosis
  3. Inflammation causes damage to the lining of the intestines (leaky gut) and creates the environment for bad gut bugs to thrive (dysbiosis)

It’s kind of like the chicken or the egg example. Regardless of what came first, we get the end result of scrambled eggs. They are all a cause and effect of each other. See the trend? Regardless of which one you have first, you end up having all three. It is a never-ending cycle and often what keeps individuals on a frustrating hamster wheel. 

This same leaky gut cycle eventually causes chronic immune reactions, where the immune system attacks its own cells, leading to autoimmunity. Hence why it is so essential to heal the gut the right way in order to reverse an autoimmune condition. 

Leaky gut and inflammation connection to gut dysbiosis

The good news is that once you are able to identify your trifecta root causes and improve dysbiosis, the foreign invaders are no longer a threat and your immune system will calm down. The body is amazing at healing damaged tissue when the gut is balanced, and once the tissues heal, inflammation decreases. 

For those of you who don’t know my story, I got into the functional medicine space after I found out about my Celiac disease and other autoimmune conditions. Luckily doctors recognized the importance of food and eliminating gluten but I was told that was it and I would be fine. They sent me back into the world with no other recommendations.

The problem was that I didn’t get better after just eliminating the inflammatory gluten from my diet. It solved some of my problems, but I was developing even more autoimmune conditions and feeling defeated. The reason for that was because gluten wasn’t the end of my story! In fact, it was the imbalance of gut bacteria that caused the Celiac in the first place. Going gluten free wasn’t going to fix that! I needed to replace the bad gut bacteria with the good. I had to remove and replace other key components first before mending all the damage to the gut lining in order for my body to truly heal. 

And once I did just that, everything changed! My autoimmune conditions and the symptoms that accompanied them suddenly vanished. Yup, you heard that correctly. They are always in my medical chart but on paper, it looks as if they aren’t even there. This is possible when you get to the root cause of the dysbiosis and gut imbalances first. You can read more about my story here.

Methods to improve gut bacteria

There are cutting edge DNA stool tests that can identify dysbiosis and tell you if gut infections are present and need to be removed. Unfortunately conventional doctors aren’t using them. Functional practitioners, like me, use them all the time in practice.

As a functional medicine practitioner, I test my clients for gut imbalances because I see that it is the missing link to years of unanswered symptoms and questions. Most often, my go-to is the G.I. Map, which identifies levels of pathogenic (harmful) and healthy bacteria in the gut. This is a full-proof way to get an accurate idea of what’s going on inside your gut so that we aren’t just estimating what is actually going on.

This makes all the difference so that you aren’t continuing to spin your wheels wondering what to do for years, constantly trying to look up your symptoms and try the next new trend. The reason those tests are not used by most conventional practitioners is because they are more expensive typically not covered by most insurance plans. They are incredibly useful though! If you can’t afford one of these tests, looking at the warning signs above is usually enough to confirm dysbiosis if you have at least two of these signs and symptoms present. 


As you can see, the influence that gut bacteria have is enormous. Whether you suffer from chronic fatigue, skin problems, sugar cravings, or all of the above, I encourage you to take a long, hard look at what’s going on inside your gut. This is where the root cause originates and is the solution to most health problems. This is why I stress that if you want to fix your health you must start with your gut! 

If you’re struggling to get to the bottom of lingering, chronic health issues, consider addressing any gut dysfunction to promote healing from the inside-out! If you’re not sure where to start, I would love to walk alongside you in your healing journey. Visit my services page to learn more about how my team and I can help you balance your gut bacteria!

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"When it comes to balancing our body, healing the gut, reversing autoimmunity, and achieving optimal health—we are a lot like a car that won’t run right. In order to fix the problem once and for all instead of relying on jumper cables, we must get underneath the hood, run the diagnostics, and replace the battery so that it runs good as new."

-Nikki Yelton, RD

a note from nikki:

If you are ready to stop wasting precious time, get off the never-ending hamster wheel, and finally surrender trying to figure things out on your own—this is your moment. 

You don’t have to settle for just getting by and hoping tomorrow is a better day. We both know you are a woman who deserves better and are made for so. much. more.

are you ready?

Ready to resolve your GI distress, reverse autoimmunity, and live your extraordinary life?

I believe every woman can take back their health!

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