Unhealthy Gut Signs: Symptoms to Watch For & How to Heal Your Gut

Gut health isn’t a medical diagnosis

The term ‘unhealthy gut’ won’t appear in scientific journals or peer-reviewed diagnostic criteria. ‘Unhealthy gut’ isn’t a medical diagnosis, but it is an umbrella term that represents underlying categories such as;

• Functional gastrointestinal disorders: disorders such as irritable bowel syndrome (IBS) are cases where symptoms such as stomach pain and bloating exist without visible structural damage. 
• Microbial shifts: are often referred to as dysbiosis, where the gut microbiome is unbalanced and leads to the reduction of beneficial microbes and a rise in the growth of opportunistic bacteria. The gut microbiota and shifts within it can influence our risk of developing gastrointestinal, and immune-related diseases.
•  Infections and inflammation: acute or chronic conditions such as bacterial gastroenteritis, inflammatory bowel disease or celiac disease. 
• Medication and supplements:  antibiotics, NSAIDs, proton pump inhibitors, and even certain herbal supplements can alter gut flora and gut motility.
• Food intolerances and sensitivities:  lactose, fructose, FODMAPs, or non-celiac gluten sensitivity can mimic signs of poor gut health without involving true allergies or autoimmune conditions.

Recognising the differences between these categories is crucial to identify and manage the underlying cause.

Top Signs Your Gut Health May Be Off

If you’re trying to identify signs of poor gut health, start taking note of persistent, ongoing issues and identifying patterns of how often and why these issues are occurring. Occasional digestive changes are normal, but recurring or worsening symptoms may indicate an unhappy gut. When the microbiome is unbalanced, beneficial bacteria are reduced and harmful microbes multiply. This contributes to digestive issues, inflammation, mental health issues and autoimmune conditions. 

 Here are the most common unhealthy gut symptoms and what they may indicate:

1. Frequent Bloating, Gas, or Abdominal Discomfort

Bloating occurs when the stomach feels tight and painful, and it can become visibly distended. Bloating and gut health are closely linked, but bloating isn’t always a matter of concern. It is when bloating persists alongside other digestive changes that may reflect a gut microbiome imbalance. Between 10% and 25% of healthy individuals reported occasional abdominal bloating. The most common cause of bloating is a build-up of gas in the stomach. Common contributors to bloating include eating too fast, carbonated drinks, high-FODMAPs diet or a diet high in processed, nutrient-poor foods. Bloating can also occur due to factors such as stress or poor sleep. Many women report feeling bloated at the beginning of their menstrual cycle.

 2. Constipation (Hard Stools, Straining, <3 Bowel Movements/Week)

The gut microbiota plays a role in the development of chronic constipation, along with other factors such as age, sex, diet, and psycho-psychological factors. Constipation is characterised by infrequent bowel movements, hard stools, and strain while defecating. It can be extremely painful and uncomfortable when these symptoms persist. Constipation has been closely linked to gut dysbiosis. Infrequent bowel movements can be a result of a low fibre diet, dehydration, sedentary habits, thyroid dysfunction, or medication use. 

3. Diarrhoea or Loose Stools That Keep Returning

Dysbiosis of the gut can often result in diarrhoea and loose stool. Disrupted fermentation is a leading cause of poor gut health and diarrhoea. When there is an overgrowth of certain types of bacteria that are less efficient at fermenting dietary fibres and carbohydrates, it can lead to irregular bowel habits such as diarrhoea. An imbalance in the gut can also affect the rate that food passes through the intestines and the rate of absorption. If diarrhoea persists beyond a few days or alternates with constipation, it warrants clinical evaluation to rule out inflammatory or infectious causes.

4. Heartburn / Reflux Symptoms

Acid reflux can significantly weaken the microbiota and allow for harmful bacteria to thrive and fungal overgrowth to occur. Acid reflux alters the environment of the upper digestive tract, changing the pH and the microbial make-up. Gut dysbiosis can cause severe inflammation, impair digestion, and weaken the oesophageal sphincter (the muscle that prevents stomach contents from flowing back up into the oesophagus). Proton pump inhibitors, which are taken to manage symptoms of reflux, can further disrupt microbial balance.

5. Unusual Fatigue or Disrupted Sleep

The gut-brain axis explains why poor gut health symptoms often extend beyond the abdomen. Research found that almost half of those with IBS also struggled with fatigue. The digestive system is responsible for absorbing nutrients from food and turning it into energy. If factors such as a poor diet impact the health of our gut microbiome, the ability for our bodies to convert food to energy may be impacted, because of the gut’s permeability is impacted. Digestive issues such as a H. pylori infection, fatty liver, and chronic constipation can all make it harder for the body to absorb nutrients, causing inflammation and promoting fatigue. If you have a diet low in fibre and high in processed foods, it may be the cause of feeling tired and irritable. If you’re still tired despite adequate sleep, gut dysfunction may be to blame. 

6. Mood or Stress Changes Alongside GI Symptoms

The gut-brain connection is a fascinating area of research that allows us to understand how our gut-health impacts how we think, our mood and how we feel. For example, have you ever felt a ‘pit’ in your stomach when you’ve heard some terrible news? That’s proof of the strong communication system our brain has with our gut. Studies have found that a significant number of people with IBS and other functional bowel problems also develop depression and anxiety. An estimated 90% of the body’s serotonin is produced in the gut. When gut dysbiosis occurs, neurotransmitter production, vagal nerve signalling, and systemic inflammation can be impacted, and symptoms such as anxiety, low mood, or heightened stress reactivity may be experienced. Gut bacteria imbalance symptoms frequently include cognitive fog and emotional instability.

7. Getting Sick Often (Frequent Minor Infections)

The strong link between gut health and our immune system is largely down to the fact that 70% to 80% of immune cells reside in the gut-associated lymphoid tissue (GALT). As a result, the intestinal microbiome acts as a training ground for our immune system.  In a state of dysbiosis, the effectiveness of gut immunity and systemic immune responses are impacted. This doesn’t just affect digestive comfort but also increases susceptibility to respiratory infections, prolongs recovery from illness and can cause reduced vaccine effectiveness.

8. Unintentional Weight Change or Appetite Shifts with GI Symptoms

Unintentional shifts in weight and a decrease or increase in appetite can be closely associated with the health of our gut. A relationship has been observed between the metabolism of nutrients, energy consumption, and gut flora. Mechanisms including the synthesis of short chain fatty acids, hormone stimulation, and persistent low-grade inflammation, have been believed to play a role in the onset of obesity.

9. Symptoms Flare After Antibiotics or New Medications/Supplements

Medications such as antibiotics have allowed for great advancements in medicine and saved millions of lives. However, certain medications such as antibiotics and proton pump inhibitors, have potential to alter the balance of bacteria in the gut. Microbiome changes are often temporary and subside shortly after taking the medication, however in some situations, our gut can become irritated for an extended period. Antibiotics are the most well-known for upsetting the gut. Broad spectrum antibiotics work by stopping the growth and kill bacteria – both good and bad. After the course of such medication, many people experience an imbalance of the gut microbiota.

10. Reacting to Foods You Used to Tolerate

If suddenly you find yourself unable to tolerate the food you once did, it could be reflecting changes in your intestinal barrier, microbiota changes or cumulative digestive overload. When the lining of the gut is compromised, common foods such as dairy, gluten or legumes may trigger diarrhoea, bloating or fatigue. Gut health issues can also manifest as skin conditions such as acne, eczema, or psoriasis which typically start with inflammation and can sometimes be improved by a diet or lifestyle changes.

When Unhealthy Gut Symptoms are a Red Flag

Most digestive discomfort can be alleviated by making lifestyle changes and identifying common triggers such as certain foods or stress. However, certain signs, such as the following, require prompt medical attention. 

• Blood in the stool: may indicate gastrointestinal bleeding, ulcers, or inflammatory conditions such as Irritable Bowel Disease (IBD). In some rare and more serious cases, it may be a symptom of colon cancer. 
• Unintentional weight loss: especially when paired with appetite changes or poor vitamin absorption. This could indicate a need for investigation into celiac disease or IBD.
• Severe or worsening abdominal pain/cramping: stomach discomfort is not uncommon, however, when it becomes severe or impacts your quality of life, this is where following up with a professional may be necessary.
• Fever along with GI symptoms: this may suggest infection or systemic inflammation which can require urgent assessment.
• Symptoms lasting weeks or progressively getting worse: if symptoms don’t subside with lifestyle changes or improving the quality of food in our diet, it is worth ruling out issues such as IBD, celiac disease or other malignancies. 

It is important to act promptly when something doesn’t feel right. Getting a second opinion from a healthcare professional is the first step when lifestyle changes and diet alterations are not enough.

Common Root Causes of Gut Symptoms

Understanding what causes poor gut health is just as important as recognising the symptoms. While individual triggers may vary, most cases fall into these five overlapping categories: 

1. Poor diet

A varied diet, high in fibre and nutrient rich food helps to promote a healthy gut. A lack of fibre, fruit and vegetables and a diet high in processed food can irritate the lining of the gut and cause digestive discomfort. Poor diet heavy in emulsifiers, artificial sweeteners, and refined sugars can promote inflammation and create a breeding ground for ‘bad’ bacteria to thrive. Research shows how the intestinal microbiota plays a role in the development of chronic inflammatory diseases such as IBD, and a poor diet has been closely linked to gut dysbiosis.

2. Stress, Sleep and Routine Disruption 

Being out of routine, not getting enough sleep, and experiencing stress can all contribute to an unhealthy gut and digestive issues. Adequate sleep is essential for the body to go into rest and repair mode. Like any other part of the body, the gut needs a break, especially from digesting food all day, which is where sleep becomes important. Stress is a great contributor to digestive issues and discomfort. For example, when people are stressed, they may experience stomach cramping and abdominal discomfort. This is a result of the strong connection of the gut-brain axis which sends signals to our body from our brain when stressed.

Being out of routine is normal occasionally, but over time, it can impact our diet, sleep, and stress response. This is why people often deal with abdominal discomfort or cramping when they go abroad or are travelling. 

3. IBS and Functional Gut Disorders 

Functional gut disorders such as IBS are conditions where the gastrointestinal symptoms associated with it cannot be attributed to structural or metabolic abnormality. Irritable Bowel Syndrome (IBS) is a functional disorder of gut-brain interaction characterized by abdominal pain and altered bowel habits. The root cause of IBS is dysregulation of the gut-brain axis, where communication between the digestive tract and the central nervous system is compromised and can become overly sensitive and reactive. It accounts for roughly 20% of outpatient gastroenterology clinic referrals of the main causes of the onset of IBS may be a gastrointestinal infection, antibiotic use, prolonged physiological stress, hormonal changes, or after surgery and illness. Contrary to popular belief, IBS isn’t typically associated with food intolerances, but when the gut-brain axis is irritated, digesting food itself can bring on symptoms.

Other functional gut disorders such as small intestinal bacterial overgrowth (SIBO), Crohn’s disease and Ulcerative Colitis can have a lasting effect on the health of our gut health.

4. Food Intolerances vs. Food Allergy 

Food intolerances are when an individual has difficulty digesting some food which results in symptoms such as bloating, stomach pain, or even skin rashes and itching. The cause of food intolerances is unclear and is usually identified through an elimination diet where the trigger is identified. A food allergy, on the other hand, is caused by a reaction of the immune system where the proteins found in food are seen as a threat. A food allergy can cause more severe reactions such as a rash, wheezing and itching. Allergies are often linked to food such as milk, eggs, fish or nuts. Research suggests that the gut microbiomes of individuals with food allergies differ from those without food allergies. Those with food allergy, more than likely will suffer from gut dysbiosis. 

5. Infections, Inflammation, or Other Conditions

If gut issues are severely impacting daily life, and lifestyle changes and dietary adjustments haven’t worked, it may be necessary to investigate some more serious conditions such as acute gastroenteritis, parasitic infections, H. pylori, celiac disease, or IBD. These conditions all present similar symptoms to an unhealthy gut.  It is important to rule these infections out when experiencing gut issues.

How to Improve Gut Health Using Science-Backed Steps

Step 1. Increase Fibre Gradually

Fibre is one of the most important nutrients in our diet for supporting a healthy gut. Dietary fibre supports beneficial bacteria in our gut and aids peristalsis which is the movement of food passing through our gut. A diet low in fibre can lead to dysbiosis, constipation, low energy levels and can also be a trigger of further diseases of the gut. Increasing fibre gradually is important as a rapid increase can cause worsening symptoms such as bloating and stomach pain. The recommended intake of dietary fibre is roughly 25-35g a day. When increasing dietary fibre, it is important to ensure you are drinking enough water to reduce symptoms such as bloating.

Step 2: Aim for Plant Diversity

Eat the rainbow! A diverse selection of vegetables, fruits, legumes, nuts and seeds is great for our gut. Our gut thrives off a variety of healthy food, and a greater plant diversity has been associated with microbiome diversity. A study carried by ZOE, saw positive effects when individuals eat 30 different plants a week. A diverse microbiome promotes enhanced functioning of the gut and improves resilience.

Step 3: Add fermented food (if tolerated) 

Fermented food such as sauerkraut, greek yogurt, kefir and kombucha are loved by our gut. They can improve gut health by introducing beneficial living microbes that support a healthy environment in our gut and allow for more microbiome diversity and lower inflammation. They are a great source of probiotics for our gut. Introducing even just one serving of fermented food to our diet can be a great place to start. 

Some of examples of fermented foods: 

• Kefir
• Plain yogurt
• Cottage cheese or farmer’s cheese
• Certain aged cheeses 
• Fermented vegetables
• Tempeh 
• Miso
•  Pickles
•  Sauerkraut kimchi
• Kombucha
• Apple cider

Step 4: Reduce Ultra-Processed Foods and Limit Alcohol

Ultra-processed foods are often high in sugar, salt, fat, additives, and preservatives. A diet high in processed foods can irritate the lining of the gut, while also providing no benefit to feeding our microbiome in a positive way. Alcohol consumption has been linked to the growth of pro-inflammatory bacteria in our gut. 

Swapping out ultra processed foods in our diet for healthier alternatives is a good step towards a healthy gut. Reducing alcohol consumption and staying within the recommended alcohol consumption limits is a good place to start. It is important to have alcohol free days each week to give the body, especially the gut, a chance to recover from any inflammation or irritation. 

Step 5: Support Your Gut with Movement and Sleep

Getting daily exercise and movement is not only important for our mental wellbeing but also promotes a healthy gut. The modern-day sedentary lifestyle is a significant contributor to gut problems. Sitting down for long periods of time impacts the gut’s ability to pass food, leading to constipation. 

Adequate sleep is essential for the gut to rest and repair. Just like any other organ, our gut needs a break from digesting food and absorbing nutrients. A diverse gut microbiome is a contributor to better quality sleep, while adequate sleep supports a healthy gut. A good night’s sleep and a healthy gut have a symbiotic relationship! Lack of sleep promotes inflammation of the gut and reduces microbial diversity. On the other hand, an unhealthy gut can lead to sleep disorders that can impact our day-to-day functionality. 

Step 6: If Symptoms Persist, Get Evaluated

If you have tried and tested steps 1-6, with no relief from gut issues and discomfort, it may be time to get evaluated by a healthcare professional. If you are experiencing severe gut discomfort along with other symptoms such as rectal bleeding, unexplained weight loss, or persistent diarrhoea or constipation, it may indicate serious conditions such as IBD, infections or cancer. These serious conditions require prompt medical attention by a healthcare professional. 

Common Myths About Gut Health

“A detox cleans your gut”

False – our bodies are clever and already have a built-in detoxification system which includes the liver, kidneys, lungs, digestive system, and immune system. If you want to detoxify your gut, good news is that you’re already doing it! The mainstream media has pushed the idea of a detox, however, there is no scientific evidence supporting these products’ effectiveness on improving gut health. 

“Everyone needs a probiotic”

False – not everyone needs to be taking a probiotic. For most healthy individuals, eating healthy nutritious foods, while minimising alcohol and ultra processed foods is sufficient. Probiotics are most useful when they are targeted to address a specific issue. They are ideal for individuals after taking antibiotics to help rebuild beneficial bacteria in the gut, or for those with digestive conditions such as IBS or IBD. 

“Bloating always means your gut is unhealthy”

False – occasional bloating is completely normal. It’s a physiological response that can occur when we eat food too quickly, ingest a lot of air, or drink carbonated beverages. It can also occur naturally by digesting foods and can be influenced by hormonal changes, particularly for women going through the menstrual cycle. Bloating isn’t necessarily a concern, unless it is very frequent, chronic or painful.

Final Thoughts

Gut health is complex and the symptoms of poor gut health are often subtle and overlapping. This doesn’t mean that actionable steps can’t be taken to figure out the cause of poor gut health and identify and eliminate triggers. 

Instead of chasing quick fixes and spending money on unnecessary supplements and ‘gut health’ products, focusing on achieving a healthy diet, improving lifestyle habits and striving for consistency over perfection is a good place to start.

A great amount of knowledge about the gut microbiome and digestive health continues to evolve through ongoing research. Atlantia Clinical Trials plays a key role in advancing this evidence base by conducting human studies on nutrition, gut health, and functional foods. This research helps move beyond trends and toward scientifically validated approaches to improving gut health.

Frequently Asked Questions

How do I know if my gut is unhealthy? 

Knowing and looking out for the signs and symptoms of poor gut health is important. These may include chronic bloating, abdominal pain, diarrhoea or constipation, and fatigue.

How long does it take to improve gut health? 

This may differ from person to person, but some changes, such as less bloating can happen relatively quickly, by cutting out trigger foods or carbonated drinks. On the other hand, achieving changes in the gut microbiome may take up to a couple of months to a year to achieve. 

What are the best foods for gut health? 

Prebiotic food such as onions, garlic and oats which are high in fibre are great for the gut! Similarly, probiotic foods such as fermented foods have been proven to support a diverse and healthy gut microbiota.

Do I need probiotics or can food be enough?

Unless you have a specific health concern, or just finished a round of antibiotics, and are concerned for their impact on your gut, food is typically enough for a healthy individual. 

Is it normal to have bloating every day? 

No, bloating every once and a while after a big meal or carbonated beverages is normal, but if you are bloating daily, it may indicate an imbalance in the gut or an intolerance that could be worth getting checked out!

Can poor gut health cause fatigue? 

Yes, poor gut health can cause fatigue, typically because of inflammation, poor sleep, and poor nutrient absorption. 

Can gut health affect mood?

Yes, the gut-brain axis links gut function with mood and mental health. Additionally, hormones which are in control of our mood and happiness are mostly produced in the gut. 

Co-authored by – Chloe McDonough