10 Signs Your Gut Bacteria Are Out of Balance

Bloating is one of the most common signs that your gut bacteria aren't functioning optimally. When gut microbes ferment carbohydrates, they produce gases like hydrogen and methane, which can lead to bloating and discomfort. [3] 

You might notice your belly feels noticeably fuller after meals, even when you haven't eaten a large amount. The bloating may be worse at certain times of day or after specific foods. If this happens regularly, it could suggest your gut bacteria balance is off.

What to do: Keep a food and symptom diary for a week. Note which foods seem to make bloating worse. You may find that processed foods, high-sugar items, or foods high in fermentable carbohydrates trigger bloating more than others.

Changes in bowel movements—such as constipation, diarrhea, or alternating patterns—can reflect disruptions in gut microbiota and intestinal motility. [3] Healthy gut bacteria help regulate how quickly food moves through your digestive tract and maintain proper stool consistency.

If you've noticed a shift in your regular bathroom habits without an obvious cause like a recent illness or diet change, your microbiome may be asking for attention. This is especially true if the changes persist for more than a few weeks.

What to do: Pay attention to your baseline. How many times per day do you typically have a bowel movement? Is your stool consistency usually firm, soft, or somewhere in between? Any significant deviation warrants a conversation with your healthcare provider.

Feeling exhausted even after getting enough sleep? Your gut health may play a role. When your microbiome is out of balance, it can affect how your body processes nutrients and regulates metabolism, which may influence your overall energy levels. [4]

Additionally, imbalances in the gut microbiome can contribute to low-grade inflammation in the body, which has been linked to fatigue and reduced energy levels. [5,6]

You might find that no amount of rest seems to help, or that your energy crashes mid-afternoon despite a full night's sleep.

What to do: Before attributing fatigue solely to your gut, mention it to your healthcare provider. They can rule out other causes like thyroid dysfunction or anemia. Once those are excluded, your gut bacteria balance may be worth investigating.

Difficulty losing weight or gaining weight can be connected to dysbiosis. [7] Your gut bacteria influence how many calories you extract from food and play a role in metabolism and energy balance. [7]

When your microbiome is imbalanced, it can affect how your body processes energy and regulates metabolism, which may influence weight changes over time. [7]

What to do: Focus on eating a diverse range of whole foods—vegetables, fruits, legumes, and whole grains—that feed beneficial bacteria. These foods contain fiber that your good bacteria thrive on. Avoid excessive processed foods, which tend to promote dysbiosis-friendly bacteria instead.

Your gut microbiome plays a key role in supporting your body’s natural defenses. It helps regulate your immune system and protect against harmful microbes, while maintaining balance so your body doesn’t overreact to harmless ones. [8]

When this balance is disrupted, it can affect how efficiently your immune system responds to potential threats. Some research suggests that changes in the gut microbiome may influence susceptibility to infections and how the body responds to them. [9]

You might notice patterns such as getting sick more often than usual or taking longer to recover, which can sometimes reflect changes in overall immune resilience.

What to do: While rebuilding your microbiome takes time, support your immune system in the meantime. Prioritize sleep, manage stress, and consider whether you're taking antibiotics more frequently than necessary (as these can further damage your microbiome).

The connection between gut health and skin is so well-established that scientists refer to the "gut-skin axis"—the two-way communication between your digestive system and your skin. [10] When your microbiome is out of balance, inflammatory compounds can reach your bloodstream and trigger or worsen acne, eczema, rosacea, or other skin issues. [10]

You might notice that despite having a solid skincare routine, your skin isn't improving—or that it's actually getting worse. Sometimes the answer lies in your gut, not in your moisturizer. [10]

What to do: While topical skincare matters, also consider your internal health. Reducing inflammatory foods (like excess sugar and seed oils) and increasing foods rich in antioxidants and fiber can support both your skin and your microbiome.

The gut-brain connection is powerful. Your gut bacteria produce neurotransmitters like serotonin and GABA, which regulate mood and calm your nervous system. [11] Dysbiosis can disrupt this production, leaving you feeling anxious, depressed, or foggy.

You might experience increased anxiety, a persistent low mood, or subtle changes in mental clarity and focus. [11] 

What to do: Stress and mood changes can influence gut health through the gut–brain axis, potentially contributing to imbalances over time. [11] Supporting your microbiome often involves a combination of habits, including managing stress, prioritizing sleep, staying physically active, and eating a diet rich in fiber and whole foods.

If you've developed intolerances to foods you previously tolerated well, changes in your gut microbiome may play a role. [12] A damaged gut barrier allows partially digested food particles and bacterial toxins to enter your bloodstream, triggering inflammatory responses to foods that wouldn't normally cause problems. [12]

You might suddenly react to dairy, gluten, or other foods with bloating, brain fog, or skin issues. The frustrating part is that these reactions can feel unpredictable, making it hard to identify the pattern on your own. Learn more about the difference between food allergies and food sensitivities to better understand your symptoms.

What to do: An elimination diet can help identify trigger foods, but the real solution is healing your gut. Working with your healthcare provider on a structured approach—rather than eliminating foods indefinitely—is generally more effective and less restrictive long-term.

Dysbiosis doesn't stay confined to your gut. It can contribute to systemic inflammation, which may affect different parts of the body, including the joints. [5]

When inflammation levels rise, it can influence how your body feels overall, sometimes showing up as joint discomfort or increased sensitivity in areas already prone to inflammation. 

The connection between gut health and joint inflammation is sometimes referred to as the “gut–joint axis,” highlighting how changes in the microbiome may play a role in conditions beyond digestion.

If you’ve noticed new or worsening joint discomfort, it may be helpful to consider broader factors that influence inflammation and overall health, not just localized joint issues.

What to do: Supporting your body’s inflammatory balance can benefit both gut and joint health. Focus on anti-inflammatory dietary patterns, including omega-3-rich foods like fatty fish, along with leafy greens, berries, and other whole foods that help promote a healthier internal environment.

Your gut microbiome can influence sleep through its interaction with circadian rhythms and inflammatory processes. [13] Disruptions in this balance may affect how the body responds to sleep loss and circadian misalignment.

For example, research has shown that specific gut bacteria, such as Bifidobacterium longum, can modulate clock gene expression and reduce inflammation in sleep-deprived animal models, suggesting a role for the gut in regulating biological timing and resilience to sleep disruption [13].

While evidence in humans is still developing, this highlights a growing recognition that gut health and sleep are interconnected systems.

What to do: Create a sleep hygiene routine that also supports your gut: eat dinner earlier in the evening (giving your digestive system time to work before bed), limit screen time before sleep, and keep your bedroom cool and dark. These changes support both circadian rhythm balance and overall gut health.

Wondering what's really going on inside your gut? The Jona Gut Microbiome Test analyzes your gut bacteria composition from a simple home sample, giving you personalized insights into your microbiome balance and specific bacteria that may be out of proportion.

If you are experiencing persistent digestive symptoms, you should consult a healthcare provider. They may evaluate your condition, recommend appropriate medical tests, and suggest dietary or lifestyle changes to support gut health. [14]

Don't wait until symptoms become severe. Catching dysbiosis early and addressing it can prevent cascading effects on your digestion, immunity, mood, and overall health. Your healthcare provider may refer you to a registered dietitian who specializes in gut health for personalized dietary guidance.

Rebalancing your gut bacteria takes time and intentionality, but the payoff is worth it. Everlywell's Jona Gut Microbiome Test gives you a detailed picture of your bacterial composition from the comfort of home. Rather than guessing what might be wrong, you'll have actionable data about your specific microbiome—what's thriving and what needs support. With this information, you and your healthcare provider can create a targeted plan to restore balance and support your long-term health.