What are the symptoms of intestinal inflammation?

Intestinal inflammation is a common but complex contributor to gut symptoms such as digestive discomfort, bowel pain, gastrointestinal bloating, and abdominal swelling. This article explains what intestinal inflammation is, how it shows up, and why symptoms vary widely from person to person. You’ll learn the most frequent signs, the difference between acute and chronic processes, what symptoms can and cannot tell you, how the gut microbiome influences inflammation, and when deeper testing may help. By the end, you’ll understand the role of clinical evaluation and how microbiome insights can complement care when the root cause of intestinal irritation remains unclear.

Understanding Intestinal Inflammation: What You Need to Know

What Is Intestinal Inflammation?

Intestinal inflammation refers to immune activity within the lining of the small or large intestine. This process is part of the body’s defense system—helpful when it targets pathogens or repairs minor injuries, but problematic when it becomes excessive, persistent, or misdirected. Inflammation can cause the intestinal barrier to become more permeable, increase fluid secretion into the gut, and alter movement and sensation in the digestive tract, all of which may contribute to symptoms ranging from mild discomfort to severe pain.

Several conditions are associated with intestinal inflammation. Inflammatory bowel disease (IBD)—namely Crohn’s disease and ulcerative colitis—involves chronic, relapsing inflammation that can cause ulcers, bleeding, and scarring. Infectious colitis due to bacteria, viruses, or parasites may cause acute inflammation that resolves once the infection clears. Celiac disease (an immune reaction to gluten), ischemic colitis (reduced blood flow), radiation colitis, and some medication-related injuries can also inflame the intestines. Irritable bowel syndrome (IBS) is not primarily inflammatory, but low-grade immune changes and microbiome shifts can occur in some people, blurring symptom boundaries.

Clinically, it helps to distinguish between acute and chronic inflammation. Acute inflammation often develops quickly—commonly due to infection or toxin exposure—and may resolve within days to weeks. Chronic inflammation persists for months or longer and tends to wax and wane, as seen in IBD, celiac disease, or ongoing immune dysregulation. The time course, triggers, and associated findings guide clinicians toward the likely cause.

Why Gut Health Matters

The intestines are central to nutrient absorption, fluid balance, and the handling of trillions of microbes that coexist with human cells. A healthy intestinal lining forms a selective barrier: it allows nutrients and water to pass while keeping pathogens and large antigens at bay. Inflammation can disrupt this barrier, leading to increased permeability (“leaky gut”), impaired nutrient absorption, and changes in motility that contribute to diarrhea, constipation, or alternating patterns. Over time, chronic immune activation in the gut can influence systemic health by altering metabolism, hormone signaling, and immune function beyond the gut.

The gut-associated lymphoid tissue (GALT) houses a substantial proportion of the body’s immune cells. When the intestinal environment becomes imbalanced—due to infection, diet, stress, medications, or microbial shifts—immune signaling can intensify. This may produce symptoms such as gastrointestinal bloating, abdominal swelling, urgency, and bowel pain. Because the gut is richly innervated, even mild inflammation can heighten visceral sensitivity, making normal digestive processes feel uncomfortable. Appreciating these mechanisms underscores why recognizing—and appropriately investigating—symptoms of intestinal inflammation matters for overall health.

Recognizing the Signs and Symptoms of Intestinal Inflammation

Common Symptoms to Watch For

Symptoms vary, but several patterns are commonly reported when the intestinal lining is irritated or inflamed. The presence of any single symptom does not prove inflammation, and the constellation, duration, and severity are more informative than any isolated sign.

• Digestive discomfort: People often describe cramping, fullness, or a “sour” stomach sensation, especially after meals. Meal-related discomfort can reflect increased sensitivity, altered motility, or inflammatory effects on the mucosa.
• Bowel pain: This may be localized (e.g., right lower quadrant in terminal ileal involvement) or diffuse. Pain may accompany urgency, bowel movements, or persist between meals. In severe cases, pain can be colicky if the intestine is spasming or narrowed.
• Gastrointestinal bloating and abdominal swelling: Visible distension or a sensation of tightness can develop with gas accumulation, fluid shifts, or slowed transit. Inflammation can influence how gas is produced and cleared, and can sensitize nerves so bloating feels more intense.
• Abdominal tenderness or sensitivity: Pressing on the abdomen may elicit discomfort. Tenderness can be generalized or focal, and in some conditions, guarding (tensing of abdominal muscles) may occur.
• Altered bowel habits: Diarrhea is common in active inflammation due to fluid secretion and impaired absorption. Constipation may occur if inflammation disrupts coordinated motility or if scarring narrows segments. Some people alternate between diarrhea and constipation.
• Unexplained weight loss or fatigue: Chronic inflammation may increase metabolic demands and reduce appetite. Poor absorption of nutrients and iron can contribute to fatigue.
• Other signals: Fever, blood in the stool (bright red or darker/black), mucus, nighttime symptoms that wake you, or new incontinence can indicate more significant activity and merit prompt medical evaluation.

Note that these symptoms can arise in many conditions besides intestinal inflammation (for example, functional disorders, food intolerances, or medication side effects). Patterns over time, triggers, and associated features (like fever or bleeding) help narrow possibilities.

Associated Health Implications

When not addressed, ongoing inflammation can lead to complications depending on the cause. In IBD, chronic inflammation may cause strictures (narrowing), fistulas (abnormal connections), or deficiencies in nutrients such as iron, vitamin B12, and vitamin D. Recurrent flares can impair quality of life, disrupt work and social activities, and increase the risk of hospitalization. Even in non-IBD causes, prolonged intestinal irritation can exacerbate anxiety, disturb sleep, and strain day-to-day coping. The mental and social burden is real; many people adopt restrictive eating patterns or avoid activities due to fear of symptoms, which can, in turn, affect nutritional adequacy and psychosocial well-being.

Variability and Uncertainty in Symptoms

Two people with similar inflammation may experience very different symptoms. Factors that influence this variability include where in the gut inflammation occurs (small intestine vs. colon), severity and depth of inflammation, differences in nerve sensitivity, diet, stress, and the composition and activity of each person’s gut microbiome. Overlap with other gastrointestinal issues is common: IBS can present with pain, bloating, and altered bowel habits, and mild post-infectious changes can look like low-grade inflammation even when standard tests are normal. Because of this variability, self-diagnosis is unreliable, and symptom tracking is best used as a guide to seek appropriate evaluation rather than a substitute for it.

Why Symptoms Alone Cannot Confirm the Root Cause

Limitations of Symptom-Based Guesswork

While symptoms are the starting point, they rarely pinpoint the exact cause. Diarrhea and abdominal pain could stem from infection, celiac disease, IBD, bile acid malabsorption, small intestinal bacterial overgrowth (SIBO), pancreatic insufficiency, side effects from medications (e.g., NSAIDs, metformin), or functional bowel disorders. Bloating could reflect microbial gas production, carbohydrate malabsorption, motility disturbances, or hypersensitivity rather than inflammation per se. Relying on symptoms alone risks misinterpretation, delayed diagnosis, and inappropriate self-directed interventions that may worsen issues or mask important warning signs.

To move beyond guesswork, clinicians integrate symptoms with physical examination and targeted tests. Initial evaluations may include blood work (complete blood count, inflammatory markers such as C-reactive protein [CRP] or erythrocyte sedimentation rate [ESR]), stool tests (pathogen panels, fecal calprotectin or lactoferrin as markers of intestinal inflammation), celiac serology, and imaging or endoscopy when indicated. These tools clarify whether inflammation is present, help identify its location and potential cause, and guide next steps.

The Role of a Comprehensive Gut Health Assessment

Understanding the underlying cause is essential for effective management. For example, elevated fecal calprotectin often points toward inflammatory conditions of the bowel and can help distinguish IBD from IBS, whereas normal values make active intestinal inflammation less likely. Endoscopy with biopsy can reveal mucosal changes and confirm diagnoses such as Crohn’s disease, ulcerative colitis, or microscopic colitis. Breath testing may be used to evaluate SIBO in select cases. Symptom patterns—such as nocturnal diarrhea, weight loss, or rectal bleeding—also guide urgency and depth of investigation. A comprehensive assessment recognizes that similar symptoms can arise from biologically distinct pathways, calling for individualized evaluation rather than one-size-fits-all assumptions.

The Gut Microbiome: A Key Player in Intestinal Inflammation

The Microbiome and Gut Health

The human gut microbiome comprises trillions of bacteria, archaea, viruses, and fungi that live along the digestive tract, particularly in the colon. These microbes help digest complex carbohydrates, produce vitamins and short-chain fatty acids (SCFAs) like butyrate, train the immune system, and competitively exclude pathogens. Communication between microbes and the host occurs through metabolites, cell wall components, and direct interaction with the mucosal immune system. In a healthy state, the microbiome contributes to barrier integrity, modulates inflammation, and supports efficient digestion.

When this ecosystem loses resilience—due to diet low in fiber, illnesses, antibiotics or other medications, stress, or infections—microbial balance shifts. Beneficial species may decline while pathobionts (organisms that can provoke inflammation under certain conditions) expand. These changes may alter bile acid metabolism, increase fermentation gases, and influence immune receptors like Toll-like receptors (TLRs) that sense microbial signals. The result can be heightened inflammation, sensitivity, and symptoms like gastrointestinal bloating and bowel pain.

Microbiome Imbalances (Dysbiosis) and Their Impact

Dysbiosis refers to an imbalance in microbial composition or function. One hallmark is reduced diversity—fewer distinct microbes performing a narrower set of functions. Lower butyrate-producing bacteria can compromise epithelial energy supply and barrier maintenance, making the mucosa more vulnerable. Overgrowth of bacteria that produce inflammatory components (such as lipopolysaccharide, LPS) or excessive gas (hydrogen, methane) can intensify abdominal swelling and discomfort in susceptible individuals. Dysbiosis has been associated with IBD, IBS, metabolic conditions, and even extra-intestinal symptoms via the gut–brain axis, though associations do not always imply causation.

Importantly, dysbiosis looks different from person to person. One individual might have an overrepresentation of specific Proteobacteria linked with inflammatory signaling, while another may have low levels of beneficial genera like Faecalibacterium or Akkermansia. The same symptom—say, digestive discomfort—could reflect different microbial configurations and metabolic outputs, which is why personalized insight can be valuable when symptoms persist.

How Microbiome Testing Provides Insight

Microbiome testing typically involves a stool sample analyzed to characterize the types and relative abundances of microbes present. Methods vary: 16S rRNA gene sequencing profiles bacterial groups at varying taxonomic levels, whereas metagenomic sequencing can capture broader organisms and infer functional genes. While clinical diagnosis of conditions like IBD relies on medical evaluation, endoscopy, imaging, and laboratory markers, stool-based microbiome testing can complement that process by highlighting patterns of microbial imbalance, potential pathobiont overgrowth, and diversity levels that may relate to symptoms of intestinal irritation.

For people experiencing ongoing digestive discomfort without a clear cause, a carefully interpreted microbiome profile can guide thoughtful lifestyle and nutrition discussions with a clinician. It can help prioritize areas to explore (e.g., fermentable fiber tolerance, potential need for slow dietary transitions, consideration of targeted probiotics or prebiotics under professional guidance). If you are exploring this avenue, a stool-based microbiome test can provide a snapshot of your microbial community that you and your healthcare provider may use to inform next steps. Testing does not diagnose disease, but it can illuminate patterns relevant to symptom drivers.

What a Microbiome Test Can Reveal

• Microbial diversity: Indices that reflect how many different microbes are present and how evenly they are distributed. Lower diversity is often associated with reduced resilience and has been observed in some inflammatory states.
• Relative abundances: Levels of beneficial commensals (e.g., butyrate producers) versus potential pathobionts. Imbalances may correlate with symptoms like bloating or bowel pain.
• Functional potential: Inference about metabolic pathways (e.g., SCFA production, mucin degradation, bile acid metabolism) that can influence barrier function and immune tone.
• Signals of potential pathogens or parasites: Some platforms flag taxa associated with infection risk, though confirmatory clinical testing is required to establish active infection.
• Markers related to inflammation risk: While stool microbiome tests are not the same as clinical markers like fecal calprotectin, certain microbial patterns have been associated with inflammatory processes and may be discussed in reports.

Interpreting these findings should always be contextualized within symptoms, diet, medications, and clinical test results. Microbiome data adds a layer of personalization rather than replacing medical assessment.

Who Should Consider Microbiome Testing?

Not everyone with a short-lived stomach bug or occasional bloating needs microbiome testing. However, it can be informative for specific scenarios, especially when the goal is educational insight and personalized guidance rather than diagnosis.

• People with persistent digestive discomfort, gastrointestinal bloating, or bowel pain without a clear explanation after initial medical evaluation.
• Individuals with chronic or recurrent symptoms of intestinal irritation who want to explore potential contributing imbalances in their gut ecosystem.
• Those with a history of gastrointestinal issues, including IBD in remission or IBS, who are seeking a data-informed conversation with their care team about supportive strategies.
• Anyone pursuing a personalized approach to gut health who wishes to understand microbial diversity, composition, and potential functional tendencies.

If you fall into these groups and would like a structured snapshot of your gut microbes, consider a reputable microbiome analysis as a complement to conventional care. Ensure you discuss results with a qualified healthcare professional to avoid over-interpreting findings outside clinical context.

Decision-Support: When Does Microbiome Testing Make Sense?

Indicators That Testing Is Recommended

Microbiome testing is most useful when it can inform action. Consider it when:

• Symptoms are ongoing or worsening despite basic dietary adjustments, stress management, or time-limited elimination trials under guidance.
• Initial medical evaluation is unrevealing and you and your clinician are weighing next steps for non-urgent, persistent symptoms.
• You want personalized insight before experimenting with probiotics, prebiotics, or larger dietary shifts, so that changes can be matched to your microbial profile.
• You are exploring root causes of abdominal swelling, intestinal irritation, or altered bowel habits, with the understanding that testing won’t diagnose disease but can surface patterns to address.

How Microbiome Testing Fits Into Gut Health Management

Think of microbiome testing as part of a layered approach. Clinical diagnostics like stool pathogen panels, fecal calprotectin, colonoscopy, or imaging are used to rule in or out specific diseases and assess active inflammation. Microbiome profiling can sit alongside those tools to offer a broader ecological perspective: are beneficial microbes depleted? Are there elevated levels of organisms associated with gas production or mucin degradation? Are diversity scores lower than typical? This information can help tailor nutrition strategies, guide careful introduction of fiber types, and shape probiotic discussions with your clinician.

For some, periodic testing can also be used to monitor changes over time, especially when dietary adjustments or other lifestyle interventions are underway. However, repeat testing should be purposeful—aimed at assessing whether targeted shifts are reflected in the microbiome and associated symptoms, rather than testing out of curiosity alone.

Biological Mechanisms Linking Microbes and Inflammation

Understanding how microbes modulate inflammation can make symptom patterns more intuitive:

• Barrier integrity: SCFAs like butyrate, produced by certain Firmicutes, fuel colonocytes and support tight junctions between cells. Reduced butyrate producers may weaken the barrier, allowing more luminal antigens to contact immune cells.
• Immune signaling: Microbial components (e.g., LPS, flagellin) activate pattern-recognition receptors (TLRs, NOD-like receptors). Balanced exposure trains tolerance, but dysbiosis may heighten pro-inflammatory signaling.
• Mucus layer dynamics: Some microbes degrade mucin; in excess, this can thin protective layers and expose the epithelium to stressors.
• Bile acid metabolism: Gut bacteria convert primary to secondary bile acids, which can influence motility, barrier function, and immune tone. Altered bile acid pools can contribute to diarrhea, urgency, or irritation.
• Gas and osmotic effects: Fermentation of carbohydrates yields gases (hydrogen, methane, carbon dioxide) and osmotic byproducts that draw water into the lumen, contributing to gastrointestinal bloating and bowel discomfort in sensitive individuals.

These mechanisms don’t act in isolation. Diet, stress hormones, sleep, medications, and genetics all interact with the microbiome and mucosal immune system, creating a unique landscape for each person’s symptoms of intestinal inflammation.

Red Flags and When to Seek Medical Care

While many episodes of digestive upset are self-limited, certain features warrant prompt evaluation by a clinician:

• Blood in the stool, black/tarry stools, or unexplained anemia.
• Persistent fever, severe abdominal pain, or signs of dehydration.
• Unintentional weight loss, nighttime symptoms that wake you, or progressive fatigue.
• New or worsening symptoms in individuals with known IBD, celiac disease, or immunocompromise.
• Recent travel, antibiotic use, or exposure to contaminated food with ongoing severe diarrhea.

If you experience these features, seek medical care. Microbiome testing is not a substitute for timely clinical assessment in urgent or worrisome situations.

Symptom Patterns That Can Guide Further Investigation

Patterns can help organize a conversation with your healthcare provider:

• Meal-triggered pain or bloating: May suggest carbohydrate malabsorption, bile acid issues, or visceral hypersensitivity; inflammation can amplify these responses.
• Diarrhea with urgency and blood: Suggests active colonic inflammation and merits prompt evaluation for IBD or infectious colitis.
• Right lower quadrant pain with weight loss: May raise suspicion for terminal ileal involvement (Crohn’s pattern) but requires diagnostic imaging/endoscopy.
• Bloating with constipation and incomplete evacuation: Could reflect motility issues, methane-dominant gas production, or pelvic floor dysfunction; inflammation is not always the driver.
• Symptoms after antibiotics: May indicate a transient microbiome shift; most resolve, but some persist and benefit from focused evaluation.

These examples illustrate why symptoms alone don’t confirm cause. Rather, they highlight questions to pursue with testing and professional input.

Practical Steps While You Seek Answers

While awaiting evaluation, simple, non-restrictive strategies can help track patterns without risking nutritional compromise:

• Symptom diary: Briefly record meals, stress levels, sleep, bowel habits, and symptoms. Look for repeatable patterns, not one-off events.
• Hydration and balanced meals: Maintain adequate fluids and include a mix of proteins, healthy fats, and tolerable carbohydrates. Extreme elimination diets should be avoided unless medically indicated.
• Medication review: Discuss with your clinician whether any current medications could contribute to intestinal irritation.
• Stress and sleep: Stress can heighten gut sensitivity through the brain–gut axis; consistent sleep and basic stress-reduction practices may help moderate symptoms.

Use these steps as supportive measures, not as stand-alone solutions, especially if red flags are present.

How Clinicians Typically Evaluate Suspected Intestinal Inflammation

A structured approach reduces uncertainty and improves care quality. Depending on your presentation, your clinician may consider:

• Blood tests: Hemoglobin, iron studies, CRP/ESR, basic metabolic panel, vitamin levels (B12, D) when relevant.
• Stool tests: Pathogen PCR panels, culture, ova and parasite exams for travel or exposure risks, and fecal calprotectin/lactoferrin for mucosal inflammation.
• Serology: Celiac antibodies (tTG-IgA, total IgA); additional tests if initial findings are equivocal.
• Endoscopy and imaging: Colonoscopy with biopsies to assess mucosa; small bowel imaging (MR enterography, CT enterography, or capsule endoscopy) when small intestine disease is suspected.
• Functional testing: Breath tests for SIBO in select cases, anorectal manometry for outlet dysfunction, or other motility studies as needed.

Results are interpreted in the context of your history and physical exam. If no clear cause is found and symptoms persist, adjunctive insights—like those from microbiome profiling—may help refine non-pharmacologic strategies.

Putting It Together: Symptoms, Biology, and Personalized Insight

Intestinal inflammation does not look the same in everyone. The same trigger can produce different outcomes depending on immune tone, barrier robustness, diet, and the resident microbiome. This variability is why similar symptoms can have different root causes—and why two people may respond very differently to the same intervention. When a careful medical workup rules out urgent conditions but symptoms continue, microbiome testing can add an ecological lens to the picture, helping you and your clinician prioritize realistic, individualized next steps that align with your biology and preferences.

Key Takeaways

• Intestinal inflammation is an immune response in the gut lining that can alter digestion, barrier function, and motility.
• Common symptoms include digestive discomfort, bowel pain, gastrointestinal bloating, abdominal swelling, altered bowel habits, fatigue, and sometimes fever or bleeding.
• Symptoms alone cannot confirm the cause; many conditions overlap, and medical evaluation is important to identify or exclude specific diseases.
• The gut microbiome influences inflammation via barrier support, immune signaling, mucus dynamics, bile acid metabolism, and gas production.
• Dysbiosis (microbial imbalance) is highly individual and may contribute to symptom patterns even when standard tests are inconclusive.
• Microbiome testing does not diagnose disease but can provide personalized insights that complement clinical care.
• Consider testing when symptoms persist despite initial steps and you want data to inform nutrition and lifestyle strategies.
• Red flags—bleeding, significant weight loss, persistent fever, or severe pain—require prompt medical attention.
• Integrating clinical results with microbiome insights supports a more nuanced, person-centered approach to gut health.

Frequently Asked Questions

Does gastrointestinal bloating always mean I have intestinal inflammation?

No. Bloating is common and can result from gas production, slow transit, or hypersensitivity without overt inflammation. However, inflammation can amplify bloating by affecting motility and nerve sensitivity. If bloating persists, especially with other symptoms (pain, weight loss, bleeding), seek evaluation.

How can I tell the difference between IBS and IBD based on symptoms?

Symptoms overlap, but IBD more often features red flags such as blood in stool, persistent fever, nighttime diarrhea, and weight loss. IBS typically lacks objective inflammatory markers and red flags. Ultimately, testing—especially fecal calprotectin and, when indicated, endoscopy—is needed to distinguish them.

What are the most concerning signs that warrant urgent medical care?

Rectal bleeding, black or tarry stools, severe or worsening abdominal pain, persistent high fever, signs of dehydration, and unintentional significant weight loss require prompt evaluation. New or escalating symptoms in those with known IBD also warrant timely care.

Can stress cause intestinal inflammation?

Stress does not typically cause major mucosal inflammation by itself, but it can heighten visceral sensitivity, alter motility, and influence the microbiome. These changes can worsen symptoms and may interact with low-grade immune activity. Stress management can be supportive alongside medical care.

What clinical tests help confirm intestinal inflammation?

Fecal calprotectin or lactoferrin are stool markers that correlate with neutrophil activity in the gut and can indicate mucosal inflammation. Blood markers like CRP/ESR reflect systemic inflammation. Endoscopy with biopsies remains the gold standard to assess and diagnose specific inflammatory conditions.

Is microbiome testing the same as a stool test for infection?

No. Pathogen panels look for active infections from specific organisms. Microbiome tests profile the broader community and its diversity. They provide ecological insights but are not used alone to diagnose infections or inflammatory diseases.

Will a microbiome report tell me exactly what to eat?

Most reports highlight patterns—such as low diversity or low butyrate producers—that can inform nutrition discussions. They don’t prescribe a one-size-fits-all diet. Using results with a clinician or dietitian helps tailor sustainable, individualized strategies.

Can antibiotics fix intestinal inflammation?

Antibiotics treat bacterial infections, but they can also disrupt the microbiome and sometimes worsen symptoms if not indicated. In some specific conditions, certain antibiotics may be considered under medical supervision. Decisions should always be guided by diagnosis and risk–benefit considerations.

Does finding blood in the stool always mean severe disease?

Not always—hemorrhoids or minor tears can also cause bleeding. However, any unexplained blood in stool should be evaluated to rule out inflammatory, infectious, or other serious causes. Timely assessment is important.

Can diet alone resolve intestinal inflammation?

Diet can meaningfully influence symptoms and the microbiome, and specific dietary approaches may support clinical care. However, diet alone is not a replacement for medical evaluation, especially if red flags are present or a chronic inflammatory condition is suspected.

How often should I repeat microbiome testing?

There’s no universal schedule. If you and your clinician use testing to inform a targeted change, retesting after a reasonable interval (often months) can assess trends. Testing should be purposeful rather than routine.

Are probiotics helpful for intestinal irritation?

Some probiotics may support certain symptoms or contexts, but effects are strain-specific and variable between individuals. It’s best to discuss options with a clinician who can consider your symptoms, test results, and goals before you experiment.

Conclusion: Connecting Symptoms, Microbiome, and Personal Gut Health

Symptoms such as digestive discomfort, bowel pain, and gastrointestinal bloating can signal intestinal inflammation, but they do not reveal the root cause on their own. A careful medical evaluation clarifies whether and where inflammation is present and identifies conditions that need targeted treatment. Because each person’s microbiome and immune responses are unique, similar symptoms can arise from different biological pathways. When routine tests leave unanswered questions, microbiome testing can add constructive, personalized insight into microbial balance, functional tendencies, and diversity—useful information for refining nutrition and lifestyle strategies with your clinician. A thoughtful, evidence-informed approach that integrates clinical findings and individualized microbiome data offers a practical path toward understanding and supporting your gut health.

Keywords

intestinal inflammation, digestive discomfort, bowel pain, gastrointestinal bloating, abdominal swelling, intestinal irritation, gut microbiome, dysbiosis, microbial diversity, fecal calprotectin, IBD, Crohn’s disease, ulcerative colitis, celiac disease, IBS, SIBO, mucosal immunity, butyrate, SCFAs, bile acids, leaky gut, personalized gut health, stool microbiome testing, symptom variability