How To Heal Your Gut: 3 Steps Toward a Healthier You

How to heal your gut: Person holding red heart shape box

Abdominal pain, bloating, and chronic diarrhea or constipation are telltale signs that something is off with your gut. But the state of your gut health can also influence your hormones, mental health, immune health and skin. 

Poor gut health can lead to inflammation, nutritional deficiencies, and bad bacteria and other pathogens entering your bloodstream via tiny holes in your small intestine. 

In this article, we’ll explain the causes of poor gut health, the impact it can have on your overall wellness, and how to heal your gut and start feeling like yourself again.

Causes of Poor Gut Health

To better understand the causes of poor gut health, it’s important to know the role gut microbiota plays in your overall health.

Gut microbiota, also known as gut flora, are a collection of bacteria and other microorganisms that reside in your gastrointestinal tract. Gut bacteria play a role in maintaining a healthy immune system and regulating your metabolism [1].

When your intestinal flora are imbalanced, your gut lacks beneficial bacteria and grows too many harmful bacteria, much like a garden that’s been overrun by weeds. This imbalance is known as dysbiosis. Effects of gut dysbiosis include problems with your digestive system, inflammation, a dysregulated immune system (potentially leading to autoimmune diseases), hormonal imbalances, and a litany of other health issues. 

Today, gut dysbiosis is a very common occurrence due to standard dietary habits and lifestyle practices. The following causes of poor gut health are among the most common.

1. Poor Diet

Consuming inflammatory foods can encourage bacterial overgrowth and cause your immune system to overreach to these pathogens. Over time, the inflammatory process can damage your intestinal lining and result in leaky gut, a condition where bad bacteria and pathogens can enter your bloodstream via gaps in the small intestine.

These foods are known to be inflammatory and contribute to imbalanced gut flora and intestinal permeability. and:

  • Processed foods [2]
  • Sugar [3]
  • Artificial sweeteners [4, 5]
  • Alcohol [6, 7]

Gluten is a common trigger food and is inflammatory for those who are sensitive to it [8, 9]. This doesn’t mean that everyone should avoid gluten, just those who are sensitive to it.

2. Overuse of Antibiotics

Antibiotics are prescribed to help fight bacterial infections. They’re usually effective when administered and taken appropriately. However, overuse of antibiotics can change the composition and function of your gut microbiota [10, 11, 12]. 

Even when antibiotics are used correctly, they often may have direct gastrointestinal side effects such as diarrhea, nausea, and vomiting. 

3. Overuse of Antibacterial Soaps

Fervent hand-washing has become a must due to the pandemic. Washing your hands is one of the most effective ways to protect yourself from getting sick, but a popular ingredient in antibacterial soaps may negatively affect your gut health.

Triclosan is an antibacterial and antifungal agent that is present in nearly three-quarters of antibacterial soaps in the United States. It makes its way into your bloodstream when your skin absorbs the soap. Several studies have linked triclosan to gut dysbiosis, although further research is still required [13, 14, 15, 16].

4. Not Exercising or Exercising Too Much

A sedentary lifestyle can have a negative impact on your intestinal health. Regular exercise, when paired with a healthy diet, can help to prevent gut dysbiosis by generating a higher diversity of gut microorganisms and increasing the number of good bacteria [17, 18]. 

Too much exercise can be as detrimental to your gut health as not exercising enough. Evidence shows that as intensity and duration of exercise increases, so does the risk of damaging the gut lining [19].

5. Poor Sleep Habits

Emerging research shows that not getting enough sleep can negatively impact your gut microbiome [20, 21, 22].  A chronic lack of sleep (either poor sleep or too little sleep) can impact your gut health and lead to intestinal permeability [23].

Furthermore, another study has begun to measure the connection between sleep quality, gut microbiota, and cognitive flexibility in older adults [24]. Early findings show poor sleep quality may alter gut microbiome composition and lower cognitive ability. 

Signs and Symptoms of an Unhealthy Gut

How to heal your gut: Woman in pain lying on a sofa

An unhealthy gut can present itself in various ways. Stomach issues may be the most obvious indicators, but poor gut health can also manifest as ailments outside of the realm of your digestive system. 

1. Digestive Problems

Digestive symptoms are a key indicator of gut dysbiosis. When your gut flora are imbalanced, bad bacteria consume the sugars in your diet, which then produce gases that cause bloating, abdominal pain, and bowel irregularities.  

Digestive issues associated with an unhealthy gut include:

  • Bloating
  • Constipation
  • Diarrhea
  • Heartburn 
  • Abdominal  pain
  • Food sensitivities [25, 26]

2. Autoimmunity

An autoimmune disease is when your immune system attacks its own healthy cells. They can be difficult to diagnose because symptoms may overlap with multiple conditions. Inflammation in the small intestine and bacterial overgrowths have been linked to autoimmunity [27, 28, 29].

The connection between autoimmunity and gut health has not been confirmed for all autoimmune diseases. However, these autoimmune diseases show a strong link to poor gut health:

  • Hashimoto’s disease and Graves’ disease [30, 31]
  • Celiac disease [32, 33]
  • Irritable bowel syndrome [34, 35]
  • Crohn’s disease and ulcerative colitis [36, 37]
  • Rheumatoid arthritis [38, 39]

3. Hormonal Imbalances

Gut inflammation can affect your body’s hormonal health, including thyroid health and gender-specific hormonal balance.

Research suggests a strong association between gut health and thyroid function, in what’s known as the gut-thyroid connection. Several studies show a link between bacterial overgrowths in the gut and thyroid autoimmunity [40, 41, 42, 43].

One study found that probiotics can reduce the need for thyroid medication and reduce fatigue in hypothyroid patients [44]. This is likely because probiotics fight bacterial overgrowths.

Hormonal imbalances from gut dysbiosis present differently in men and women.Research shows that gut dysbiosis can disturb estrogen levels and that women’s health conditions associated with unbalanced estrogen levels are associated with low bacterial diversity in the digestive tract [45, 46]. 

Symptoms and conditions associated with unbalanced female hormones include:

  • Increased PMS symptoms (such as bloating, irritability, and fatigue)
  • Changes in length or flow of your menstrual cycle
  • Low libido
  • Hot flashes
  • PCOS (polycystic ovary syndrome)
  • Obesity
  • Endometriosis
  • Cardiovascular disease
  • Breast cancer

There’s very little direct research into the connection between gut health and men’s hormonal health. However, several studies show a correlation between men’s sexual problems and poor gut health:

  • A very large study of 17,608 male patients found that men with IBS were 2.92 times more likely to have erectile dysfunction than non-IBS patients [47].
  • A research review found that IBS patients (both men and women) have more sexual health problems compared to control groups [48].
  • In a study of patients with IBD (Inflammatory bowel disease), most men had erectile dysfunction. Of 69 men with Crohn’s disease and ulcerative colitis, 39% had global sexual dysfunction and 94% had erectile dysfunction [49].

4. Cognitive and Mental Health Issues

Inflammation in the intestines can lead to inflammation in the brain, which affects your cognitive function and mental health  

Gut dysbiosis and inflammation are linked to the following symptoms:

  • Depression and anxiety [50, 51, 52]
  • Brain fog [53]
  • Insomnia and fatigue [54, 55]
  • Long-term risk of dementia [56]

5. Skin Conditions

A healthy gut equals healthy skin. If you’re experiencing problems with your skin despite following a well-curated skincare routine, poor gut health may be to blame [57, 58].

Skin conditions that may appear due to an unhealthy gut are:

  • Acne
  • Atopic dermatitis
  • Psoriasis 
  • Rosacea
  • Eczema

The above information can serve as a starting point for when you visit your doctor. An experienced functional medicine practitioner can help you get to the root of underlying health conditions.

The staff at Austin Functional Medicine specialize in gut-related disorders and can find the root causes of your symptoms and create a personalized treatment plan.

How To Heal Your Gut 

Eggs, chicken, vegetables with a Paleo Diet sign

Addressing a leaky gut and recalibrating an unbalanced gut microbiome will not only improve your gut health but can also alleviate associated symptoms and medical conditions. You can start to heal your gut by adjusting your diet and lifestyle and taking daily probiotics. 

From there, work with a functional medicine specialist to incorporate more advanced treatment methods if necessary.

1. Adopt a Healthier Diet and Lifestyle

While this may be the easiest and most immediate way to heal your gut, it’s not one to be taken lightly. The key is to work with your doctor to find the ideal diet for your gut. 

A good rule of thumb is to try a diet for 2-3 weeks. If there’s no positive change in your symptoms, transition to another diet.

Two diets that promote gut health are the Paleo diet and the low-FODMAP diet.

Paleo Diet

The Paleo diet is usually the best place to start for patients without a structured diet in place because it’s easy to implement and doesn’t require strict adherence. The Paleo diet is free of foods associated with inflammatory responses and is heavy in whole foods [59, 60].

Key characteristics of the paleo diet include:

  • Eating fresh vegetables and fresh fruits (in moderation)
  • Consuming grass-fed lean meats and fresh fish instead of processed meals
  • Indulging in healthy fats (such as coconut oil) and eliminating unhealthy fats (such as corn oil)
  • Avoiding dairy products, grains and artificial sweeteners


Another diet that can help heal your gut is the more-restrictive low-FODMAP diet. This diet helps reduce bacterial overgrowth by eliminating foods that feed bacteria. The low-FODMAP diet is particularly beneficial for patients with irritable bowel syndrome [61, 62, 63].

The low-FODMAP diet is free of fermentable carbs that can increase bacterial overgrowth:

  • Oligosaccharides: Found in bread, cereals, pasta, and legumes (whole grains)
  • Disaccharides: Found in dairy products (lactose) and other beverages
  • Monosaccharides: Found in certain fruits and sweeteners that contain fructose
  • Polyols: Found in select fruits and vegetables plus some artificial sweeteners

General Gut Healing Foods

Elimination diets are not meant to be followed long-term. While some healthy, whole foods may be restricted on an elimination diet, You can gradually reintroduce these, provided they do not trigger inflammatory responses or digestive symptoms. 

Incorporate these foods into your diet to help heal your gut naturally:

  • Probiotic foods that introduce good bacteria into your body (sauerkraut, kimchi, miso, and kefir)
  • Prebiotic foods to feed healthy bacteria (artichokes, leeks, and garlic). People with gut issues cannot tolerate prebiotic foods, so go carefully with these.
  • Polyphenol-rich foods to act as a prebiotic (dark chocolate, apples, and red wine)
  • Collagen-containing foods to repair damaged gut lining (bone broth, lean meat and, fish)

Positive Lifestyle Changes

Diet is only one piece of the puzzle when healing your gut. Aim for at least 30 minutes of physical activity each day and get 7-8 hours of sleep each night.

Probiotic Protocol

Supplementing your diet with a probiotic supplement is an effective way to bring your gut microbiome back into balance. Over 500 clinical trials support the role of probiotics for restoring gut health and reducing symptoms. ..

These are the three main probiotic categories to consider when choosing the best supplement:

  • Lactobacillus and bifidobacterium: Improves the health of the host without colonizing the host [64, 65]
  • Saccharomyces Boulardii: Not a normal part of human microbiota but improves the health of the host [66]
  • Soil-based probiotics: Can colonize and improve the health of the host [67]

A combination of high-quality supplements from the three main probiotic categories may yield the best results. Monitor your results and once your symptoms have plateaued, gradually reduce your daily dose of probiotics until you’ve found the minimal effective dose.

2. Find a Functional Medicine Doctor 

While some people can heal their gut through simple dietary and lifestyle changes, others may have more long-standing gut issues that need additional treatment.

Unlike traditional medicine, functional medicine seeks to treat the whole body and find the root causes of illness. A knowledgeable functional medicine doctor will be able to diagnose and treat gut issues that can contribute to gut symptoms, hormonal health issues, immune dysfunction and other conditions. 

Heal Your Gut and Improve Your Health Today

Runners on the beach

In order to maintain a high level of health, it’s crucial to pay attention to the health of your gut. Fortunately, for some people, healing your gut may be as simple as cleaning up your diet and adopting a healthier lifestyle. For others, consulting with an experienced functional medicine practitioner can help you achieve the results you want.

The information presented in this article is not a substitute for medical advice. However, the staff at Austin Functional Medicine includes specialists in gastrointestinal health, nutrition, and health coaching. Dr. Ruscio, DC and his team are currently accepting new patients in-person and via telemedicine. Schedule an appointment today and be well on your way towards healing your gut.


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