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How To Spot An Unhealthy Gut Microbiome And Its Effect On Weight Loss

Kara Holmes is an RN and health coach helping people heal their gut and lose weight sustainably. She is the author of the best-selling book 'Gut Health Reset'.

 
Executive Contributor Kara Holmes

Have you ever wondered why the weight isn’t coming off despite your disciplined diet and exercise routine? The answer might be hidden in your gut. Emerging research suggests that the health of your gut microbiome plays a critical role in regulating metabolism, hunger, and even fat storage. In this article, we'll reveal how a balanced gut can accelerate your weight loss journey, identify the warning signs of an unhealthy microbiome, and provide actionable steps to restore harmony in your digestive system. Discover how a thriving gut could be the ultimate key to unlocking your weight loss potential.


Doctor and holographic bowel scan projection with vital signs and medical records.

What does “gut health” mean?

The gut microbiome is a complex and diverse community of bacteria within your digestive system. Much like a flourishing garden depends on a variety of plants and creatures to create a symbiotic ecosystem, a healthy gut microbiome relies on a wide range of microorganisms and nutrients to promote overall wellness. Gut bacteria help digest food, regulate the immune system, and maintain the gut lining—a critical component of good digestive health. However, when balance in the gut is disrupted by stress, certain foods, or toxins, a condition called "dysbiosis" can occur. Dysbiosis happens when harmful bacteria grow disproportionately to the beneficial ones, potentially leading to health issues if left unchecked. This imbalance can cause a condition known as "leaky gut," where gaps develop between the cells of the gut lining. These gaps allow harmful substances to escape from the intestines into the bloodstream, potentially triggering inflammation and increasing the risk of health problems.


How gut health affects weight loss

Gut health can significantly impact weight loss by influencing how efficiently your body processes nutrients and regulates hunger hormones. A balanced gut microbiome optimizes digestion and nutrient absorption, which in turn affects metabolism and energy expenditure. An imbalance in gut bacteria can lead to inflammation or insulin resistance, both of which can hinder weight loss efforts. Research supports this connection– a study published in 2023 demonstrated that lower gut microbial diversity or an increase in certain beneficial bacteria promotes a healthier metabolism, ultimately helping to reduce obesity and maintain a healthy weight (Noor, 2023). Now, let’s explore some of the specific reasons poor gut health can impede weight loss.


The 3 reasons weight loss can suffer if your gut is unhealthy

There are three ways your gut health may be slowing down your weight loss efforts or ability to maintain a healthy weight:


  1. Gut dysbiosis: The phenomenon of "dysbiosis" refers to an imbalance in the gut where disease-promoting bacteria outnumber beneficial ones, leading to health issues. Conditions like candida overgrowth or SIBO (small intestinal bacterial overgrowth) are examples of gut dysbiosis

  2. Leaky gut: The gut can become inflamed and porous, a condition known as "leaky gut," where organisms, toxins, and small particles leak from the gut lumen into systemic circulation, potentially causing widespread inflammation.

  3. Hormonal imbalance: If your gut microbiome is imbalanced, with low diversity or an abundance of bacteria associated with obesity, it can alter how your gut processes nutrients and generates energy. Gut bacteria produce short-chain fatty acids, which provide energy and help repair organs. However, an over-accumulation of these energy compounds can lead to fat storage. This imbalance can also disrupt hunger and fullness hormones, as well as insulin signaling, causing you to eat more and feel full too late. Over time, this can lead to insulin resistance, where cells no longer respond to glucose, resulting in higher blood sugar levels. Excess glucose is then converted to fat and stored in adipose tissue (Leeuwendaal, 2021).


Signs and symptoms of an unhealthy gut

So how can you tell if an unhealthy gut is playing a major role in your weight loss challenges?


There are several red flags that might signal your gut health needs attention. Remember, it’s always wise to consult your doctor if you’re experiencing symptoms that feel unusual or persistent. But pay close attention to these ten signs—they may indicate it’s time to hit the 'reset' button for your gut microbiome.



10 signs that your gut health is unhealthy


1. You’re constantly bloated

One of the most obvious signs of an unhealthy gut is frequent bloating, even when you haven’t just eaten. Imbalances in your gut microbiome can disrupt digestion and absorption, leading to chronic bloating. Harmful bacteria may outnumber the beneficial ones, producing excess gas and inflaming your intestines. This leads to undigested food fermenting, causing bloating, discomfort, and eventually more severe gastrointestinal issues.


2. You have eczema, rash, or rosacea

Poor gut health often shows up on your skin due to the gut-skin axis—a direct connection between your gut and skin. Dysbiosis, or an imbalance of gut bacteria, can increase intestinal permeability, allowing toxins and inflammatory molecules into your bloodstream. This systemic inflammation can lead to skin conditions like eczema, rashes, or rosacea. Additionally, poor nutrient absorption can further aggravate these skin issues.


3. You get frequent stomach aches

Just like bloating, frequent stomach aches can be a sign of gut dysbiosis. The imbalance of gut bacteria causes inflammation and irritation, which can lead to stomach pain. This discomfort often stems from impaired digestion and the accompanying bloating. If you’re experiencing consistent belly aches, it could be a red flag that your gut health is out of balance.


4. Smelly flatulence

While it’s not a fun topic, excessively smelly flatulence can also signal gut dysbiosis. Certain bacteria in an imbalanced microbiome produce foul-smelling gases, especially sulfur-containing compounds like hydrogen sulfide, known for its "rotten egg" odor. When these bacteria overgrow, they ferment proteins and carbohydrates, producing these gases and causing unpleasant smells.


5. Joint aches and pains

Joint pain can become more pronounced when your gut is out of balance, thanks to the gut's connection to systemic inflammation. Dysbiosis can increase intestinal permeability (commonly called "leaky gut"), allowing toxins and undigested food particles to enter the bloodstream. This triggers an immune response and widespread inflammation, which often targets the joints, worsening pain and contributing to conditions like arthritis.


6. Depression and anxiety

There’s a strong connection between the gut and the brain, known as the gut-brain axis. Harmful bacteria can disrupt the production of crucial neurotransmitters like serotonin and dopamine, both of which regulate mood. In fact, about 90-95% of serotonin—the "feel-good" hormone—is produced in the gut (De Ponti, 2004). A leaky gut also allows inflammatory molecules to enter the bloodstream, potentially causing brain inflammation and impacting mood and cognitive function. This can create a vicious cycle, contributing to anxiety and depression.


7. Fatigue and brain fog

Fatigue and brain fog are common signs of gut dysbiosis or a leaky gut. This happens due to the intricate connection between the gut, the immune system, and mitochondria (the energy-producing centers of our cells). When leaky gut triggers chronic immune activation, it causes inflammation, diverting the body's energy and leading to fatigue.


Inflammation can also damage mitochondria, impairing their ability to produce ATP (the body’s main energy source), worsening exhaustion. As for brain function, systemic inflammation affects the nerves, disrupts the blood-brain barrier, and interferes with gut-brain communication through the vagus nerve, leading to memory problems, difficulty concentrating, and brain fog.


8. Itchiness

Leaky gut allows toxins to circulate through the body, triggering an immune response and systemic inflammation. This can manifest on the skin, which is closely connected to gut health. Inflammatory responses can lead to histamine release, causing itchiness, rashes, or other skin irritations. Additionally, an imbalanced gut can reduce the body’s ability to detoxify efficiently, leading to a buildup of irritants that further aggravate skin conditions.


9. Difficulty losing weight

An imbalanced gut can hinder weight loss, even if you're doing everything else right. Dysbiosis disrupts nutrient absorption and metabolism, contributing to chronic low-grade inflammation, which interferes with insulin sensitivity and promotes fat storage, especially around the abdomen. Gut imbalances can also affect hunger and satiety hormones like ghrelin and leptin, leading to increased cravings and a harder time managing appetite. Since the gut plays a key role in detoxification, a compromised gut can lead to toxin buildup, further slowing metabolism and making weight loss more challenging.


10. Irregular bowel patterns

Gut dysbiosis can affect bowel movements in both directions—speeding up transit, leading to diarrhea, or slowing it down, causing constipation. Bacterial overgrowth can irritate the gut lining and produce excess gas, which accelerates transit and results in loose stools. Alternatively, certain bacteria can slow down motility or produce gases like methane, which contributes to sluggish digestion and constipation. This imbalance also reduces the production of short-chain fatty acids, essential for regular bowel movements.


What you can do to heal your gut

If you’re noticing several symptoms that point to an unhealthy gut, it's time to focus on restoring balance to your microbiome and repairing the gut lining. Here are some steps to help you heal your gut:


  1. Incorporate Prebiotic, Probiotic Foods, and More Plants. Add fermented foods like sauerkraut, kimchi, miso, and kefir to support beneficial gut bacteria. Plant-based foods also play a key role in nurturing your microbiome. The American Gut Project showed that people who eat 30 or more different plant foods per week experience improved bacterial diversity. Foods like garlic, onions, leeks, and asparagus are rich in prebiotic fibers, feeding beneficial bacteria and supporting a healthy gut.

  2. Reduce Alcohol, Processed Foods and Sugars: Rather than focusing solely on cutting out gluten and dairy, prioritize reducing highly processed foods, alcohol, seed oils, and sugars. Ultra-processed foods make up nearly 90% of the sugar intake in the U.S. (Martínez Steele, 2016) and are loaded with preservatives and additives linked to inflammation and gut stress (Sawala, 2023). Sugars feed harmful bacteria, while processed fats contribute to inflammation and mitochondrial damage. Focus on whole, nutrient-dense foods for better gut health.

  3. Manage Stress: Chronic stress negatively impacts gut health, so prioritize stress management. Regular exercise, daily breathing exercises, spiritual practices like prayer, and spending time in nature can all help keep stress levels down.

  4. Stay Hydrated: Water supports digestion and maintains the mucosal lining of your intestines. Interestingly, the less water you drink, the less thirsty you feel—but as you increase your water intake, your body will trigger thirst cues more often.

  5. Consider Targeted Supplements: Supplements like digestive enzymes, L-glutamine, and omega-3 fatty acids can help repair the gut lining and reduce inflammation.

  6. Get Regular Exercise: Physical activity reduces inflammation, boosts mood, and promotes regular bowel movements, all of which contribute to gut health.

  7. Prioritize Sleep: Quality sleep is essential for gut healing. Your body needs time to repair, and a well-rested system promotes better gut function.

  8. Limit Antibiotic Use: Antibiotics wipe out both harmful and beneficial bacteria, so only use them when necessary.

  9. Consult a health coach or Integrative Practitioner: If you’re unsure where to start, working with a healthcare professional who understands gut health can help you develop a personalized plan to restore balance to your microbiome.


By following these steps, you can begin to restore balance to your gut, lower inflammation, and improve your overall health, including weight loss.


Ready to heal your gut, shed 10 pounds or more, and gain lasting confidence with real, sustainable results? Apply for a free health coaching breakthrough call with Kara here, or grab a copy of her book “Gut Health Reset: An Easy 4-Week Plan to Help Beginners Restore Their Mind and Microbiome, Lose Weight, and Relieve Anxiety.”


Follow me on Facebook, Instagram, LinkedIn, and visit my website for more info!

Read more from Kara Holmes

 

Kara Holmes, Health Coach, RN, Author

Kara is a rising voice calling attention to how the health of our gut and internal systems affects our mind, the body’s appetite, our ability to manage weight, and regulate other components of our health. Her story of dealing with an 11-year battle with disordered eating and mysterious health ailments highlights the importance of gut health in having a thriving, healthy body that will give you the best chance at aging well and achieving a life of your greatest potential. Her mission is to make gut health and nutrition approachable and understandable to everyone so that they can take control of their health and deal with issues at the source.

 

References:


  1. Noor, J., Chaudhry, A., Batool, S., Noor, R., & Fatima, G. (2023). Exploring the Impact of the Gut Microbiome on Obesity and Weight Loss: A Review Article. Cureus, 15(6), e40948.

  2. Leeuwendaal, N. K., Cryan, J. F., & Schellekens, H. (2021). Gut peptides and the microbiome: focus on ghrelin. Current opinion in endocrinology, diabetes, and obesity, 28(2), 243–252.

  3. De Ponti F. (2004) Pharmacology of serotonin: what a clinician should knowGut 2004;53:1520-1535. 10.1136/gut.2003.035568

  4. McDonald, D., Hyde, E., Debelius, J. W., Morton, J. T., Gonzalez, A., Ackermann, G., Aksenov, A. A., Behsaz, B., Brennan, C., Chen, Y., DeRight Goldasich, L., Dorrestein, P. C., Dunn, R. R., Fahimipour, A. K., Gaffney, J., Gilbert, J. A., Gogul, G., Green, J. L., Hugenholtz, P., Humphrey, G., … Knight, R. (2018). American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems, 3(3), e00031-18.

  5. Sawalha, K., Tripathi, V., Alkhatib, D., Alalawi, L., Mahmood, A., & Alexander, T. (2023). Our Hidden Enemy: Ultra-Processed Foods, Inflammation, and the Battle for Heart Health. Cureus, 15(10), e47484.

  6. Martínez Steele, E., Baraldi, L. G., Louzada, M. L., Moubarac, J. C., Mozaffarian, D., & Monteiro, C. A. (2016). Ultra-processed foods and added sugars in the US diet: evidence from a nationally representative cross-sectional study. BMJ open, 6(3), e009892.

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