How to Tell If Your Bowels Aren't Working Properly?

If you've been experiencing symptoms like abdominal discomfort, irregular bowel movements, or chronic bloating, you may be dealing with underlying bowel problems. This blog post explores how to identify when your digestive system isn’t working properly, with a particular focus on how your gut microbiome plays a critical role in bowel health. Learn how gut microbiome testing can uncover hidden issues, how microbial imbalances manifest as bowel symptoms, and what steps you can take to restore your digestive health. Get answers to pressing questions about gut health and how to maintain optimal digestive function with personalized insights.

Introduction

Digestive health is the cornerstone of overall well-being, influencing not only how we break down food but also impacting immunity, mood, and energy levels. An optimally functioning gut ensures that nutrients are absorbed efficiently, waste is eliminated regularly, and harmful substances don't accumulate. However, the complexity of our digestive system can make it difficult to tell when something is wrong, especially when symptoms are subtle or overlap with other conditions.

At the center of our digestive health lies the gut microbiome—a vast ecosystem of trillions of bacteria, viruses, fungi, and other microorganisms that live in our intestines. These microbes aid in digestion, regulate the immune system, produce vital nutrients, and keep harmful pathogens in check. When this microbial community becomes imbalanced, it can disrupt digestive processes and lead to a range of bowel problems.

With the advent of advanced sequencing technologies, it's now possible to measure the diversity and function of your gut microbiome through gut microbiome testing. These insights can help determine whether your bowels are working properly and identify specific microbial imbalances that may be causing your symptoms. In this blog, we’ll explore how to recognize signs of unhealthy bowel function, the role of microbiome data in diagnosis and treatment, and actionable steps to improve your gut health.

1. Identifying Common Bowel Problems Through Gut Microbiome Testing

The gut plays a major role in your digestive capabilities, energy levels, and immune responses. When your bowels are not functioning efficiently, it often results in symptoms that are uncomfortable, persistent, and disruptive. Common issues such as bloating, diarrhea, and constipation are frequently linked to imbalances in the gut microbiome, also known as dysbiosis.

Bloating, for example, is often caused by the fermentation of food by bacteria that produce excess gas. When the wrong types of bacteria overpopulate your colon—especially methane-producing or sulfur-reducing bacteria—this process is amplified. Diarrhea can be linked to an overgrowth of pathogenic bacteria or a lack of microbial diversity. Conversely, constipation may stem from insufficient populations of fiber-fermenting bacteria that help form soft, easy-to-pass stools.

Gut microbiome testing works by analyzing a stool sample to identify the types and quantities of microorganisms present in your gut. This analysis offers insights into your microbial diversity—the variety of species in your gut—and any overrepresentation or underrepresentation of specific strains. Measuring this diversity is crucial because a more diverse microbiome is generally associated with better digestive health and resilience.

If you’re wondering whether poor microbial balance is contributing to your symptoms, ordering a gut microbiome test can provide critical insights. It not only detects pathogenic bacteria but also identifies deficiencies in important health-promoting bacteria such as Bifidobacterium and Lactobacillus. Understanding your microbial profile enables targeted dietary, supplemental, or lifestyle interventions to restore balance and improve bowel function.

In summary, gut microbiome testing is a powerful diagnostic tool that helps uncover the microbial causes behind common bowel problems, paving the way for personalized treatments and better digestive health outcomes.

2. Recognizing Signs of Digestive Health Issues That May Indicate Microbiome Imbalance

One of the challenges with digestive disorders is that their symptoms can be mild, vague, or attributed to stress, lifestyle, or diet without ever pinpointing the underlying root cause. Many people experience abdominal discomfort, fatigue, or inconsistent bowel habits without realizing that they may signify an imbalance in the gut microbiome. Recognizing these early signs is essential to avoiding more severe gut-related conditions down the line.

Some of the key physical symptoms suggestive of microbiome imbalance include:

• Chronic bloating or abdominal swelling after meals
• Recurrent gas that doesn’t improve with dietary changes
• Irregular bowel movements—alternating between constipation and diarrhea
• Undigested food particles in stool
• Persistent fatigue or low energy levels

The gut and brain are connected through the gut-brain axis, and as a result, imbalances in the microbiome often present with mood-related symptoms as well. These include anxiety, depression, irritability, and trouble concentrating. This occurs because certain gut bacteria produce neurotransmitters like serotonin, which regulate mood and cognitive function. A decrease in these bacteria might have cascading effects on mental clarity and emotional well-being.

Additionally, immune dysregulation can result in food sensitivities and inflammatory reactions. If your body seems to be reacting to foods you previously tolerated well—such as dairy, gluten, or certain vegetables—it may signal that your gut lining is compromised, or your microbiome balance has shifted toward pathogenic bacteria.

With microbiome testing, you can uncover hidden patterns in your gut flora that may explain why these symptoms are occurring. A test will highlight potentially harmful species overgrowing in the gut, as well as beneficial strains that may be lacking. More importantly, it provides a roadmap for treatment: whether through introducing specific species via probiotics, dietary adjustments, or addressing underlying inflammation.

By taking a proactive approach with gut microbiome testing, you can turn ambiguous digestive complaints into actionable insights, ultimately supporting both your physical and mental health.

3. Spotting Bowel Movement Irregularities and Their Microbial Roots

One of the most direct signs your bowels may not be functioning properly is irregular bowel movements. Understanding the pattern, frequency, and consistency of your stool can provide insight into how well your digestive system is functioning—and, more specifically, what’s happening within your gut microbiome.

Irregularities usually manifest in three basic categories: constipation, diarrhea, and alternating patterns (as seen in conditions like Irritable Bowel Syndrome or IBS).

Constipation is generally defined as having fewer than three bowel movements per week. But just as important is stool consistency—dry, hard, or pellet-like stools that are painful to pass. Gut microbiota influence motility (the movement of food and waste through the digestive tract) by producing short-chain fatty acids (SCFAs) like butyrate. These SCFAs help maintain colon health and act as a fuel source for the cells lining your colon. A lack of key fiber-digesting microbes can lead to inefficient fermentation, reduced production of SCFAs, and ultimately slow transit time.

On the opposite end of the spectrum, diarrhea can occur when pathogenic bacteria or viruses irritate the gut lining, stimulate excess fluid secretion, or disrupt the normal absorption of water in the colon. Certain bacterial profiles—especially an increase in Proteobacteria—have been closely linked with chronic diarrhea and inflammatory gut disorders like ulcerative colitis.

People with alternating bowel patterns may experience a mix of constipation and diarrhea over time. This fluctuation often reflects a highly volatile microbial ecosystem, where harmful species can intermittently dominate. These shifts are commonly observed in IBS, small intestinal bacterial overgrowth (SIBO), or after antibiotic use, which drastically changes microbial populations.

Microbiome testing breaking down the composition and resilience of your bacterial communities can help identify the leading causes of these irregularities. Once microbial imbalances are mapped out, you can formulate a plan to restore microbial harmony, increase colon motility, and reestablish regular bowel movements.

In essence, stool patterns are not just bodily functions—they are reflective of your microbiome and overall health. Identifying irregularities with data provides control over symptoms many accept as “normal” but are often signals of something deeper.

4. Detecting Gastrointestinal Dysfunction That May Be Linked to Microbial Imbalances

Gastrointestinal dysfunction can often go unnoticed until it starts affecting quality of life. Issues such as indigestion, chronic bloating, acid reflux, and early satiety (feeling full quickly) are more than inconveniences—they may signify deeper microbial imbalances. When the gut microbiome is disturbed, the downstream effects can reach every part of your digestive system.

Dysbiosis, or an imbalance in the microbiome, is often accompanied by decreased levels of beneficial microbes that aid in breaking down complex carbohydrates and proteins. Without these organisms, undigested food components can remain in the GI tract longer than normal, undergoing abnormal fermentation processes that result in gas, discomfort, and reflux.

Reflux specifically may be triggered by fermenting microbes that increase abdominal pressure through gas production, pushing stomach contents back up into the esophagus. Additionally, certain gut microbes interact with the vagus nerve, influencing gut motility and signal function, which can disrupt coordinated contractions of the digestive system.

Testing the microbiome offers a clear path toward understanding these complex dynamics. With modern stool sequencing tools, you can find:

• Overgrowth of gas-producing species like Methanobrevibacter smithii
• Deficiencies in SCFA-producing strains like Faecalibacterium prausnitzii
• Presence of opportunistic bacteria that interfere with nutrient absorption

Equipped with this data, targeted strategies including probiotics, prebiotics, and enzyme supplements can be used to support optimal microbial balance and reduce dysfunction. The right strains of probiotics can promote gastric emptying, improve nutrient assimilation, and strengthen the intestinal lining against inflammation and permeability (known as leaky gut).

Identifying and treating these gastrointestinal symptoms early through gut microbiome testing can help prevent escalation into chronic conditions such as GERD, gastritis, and SIBO. By treating the microbial root cause, you can enjoy lasting relief and a more comfortable digestive experience.