Dysbiosis: Symptoms, Types, Causes and Treatment

Microbial communities, particularly those in our gut and on mucosal surfaces, play a pivotal role in our health. When these communities lose their balance—a state known as dysbiosis—our risk for many diseases rises, sometimes dramatically. This article explores what dysbiosis is, how it manifests, the main types and causes, and the current best approaches for restoring microbial harmony.

Symptoms of Dysbiosis

Dysbiosis doesn’t always announce itself with a single, telltale symptom. Instead, it presents a spectrum of signs—some obvious, others subtle. Many people with dysbiosis experience a mix of gastrointestinal discomfort, but the effects can also ripple outward, affecting immunity, mood, metabolism, and even neurological health. Understanding these symptoms is crucial, as early recognition can lead to better management and outcomes.

Symptom	Description	Associated Disease/Condition	Source
GI distress	Abdominal pain, bloating, diarrhea, constipation	IBS, IBD, SIBO	2, 4, 7
Systemic inflammation	Elevated markers like calprotectin or CRP	Autoimmune diseases (e.g., Sjögren’s, IBD)	1, 7, 4
Increased infection risk	Higher susceptibility to pathogenic overgrowth	Bacterial vaginosis, pediatric dysbiosis	6, 5
Neuropsychological symptoms	Anxiety, depression, cognitive changes	Depression, neurodegenerative disease	12, 15

Table 1: Key Symptoms

Gastrointestinal Symptoms

Gastrointestinal (GI) complaints are the hallmark of dysbiosis. These include:

• Abdominal pain and cramping
• Bloating and excessive gas
• Diarrhea or constipation, sometimes alternating
• Distension and discomfort after meals

Such symptoms are common in conditions like irritable bowel syndrome (IBS), small intestinal bacterial overgrowth (SIBO), and inflammatory bowel disease (IBD) 2 4 7. SIBO, for example, is a specific form of dysbiosis where bacteria abnormally proliferate in the small intestine, causing a suite of GI symptoms 2.

Systemic and Immune-Related Signs

Dysbiosis can stoke inflammation both locally and systemically. Markers like fecal calprotectin or C-reactive protein (CRP) are often elevated in patients with autoimmune diseases or severe dysbiosis 1 7. These inflammatory indicators correlate with disease activity in conditions like Sjögren’s syndrome and IBD 1 4.

Infections and Immune Dysfunction

When beneficial microbes are lost or pathogens gain ground, the risk of infections rises. For example, vaginal dysbiosis increases vulnerability to bacterial vaginosis, sexually transmitted infections, and even adverse pregnancy outcomes 6. Similarly, children exposed to antibiotics early in life may have altered immunity and infection risk due to pediatric dysbiosis 5.

Neuropsychological and Systemic Effects

The gut-brain axis means that dysbiosis can reverberate into the nervous system. Symptoms such as anxiety, depression, and cognitive changes have been linked to gut microbial imbalance 12 15. There’s also mounting evidence that dysbiosis may contribute to age-related neurological diseases, highlighting the breadth of its effects 15.

Types of Dysbiosis

Not all dysbiosis is alike. Scientists have identified several distinct patterns, each with unique characteristics and health implications. Understanding these types helps tailor treatment strategies for individuals.

Type	Defining Feature	Health Impact	Source
Loss of diversity	Reduced variety of species	Chronic disease risk	5, 10, 13
Loss of keystone taxa	Depletion of crucial beneficial bacteria	Immune dysfunction, metabolic issues	5, 7, 3
Pathogen bloom	Overgrowth of harmful microbes	Inflammation, infection	7, 6, 2
Functional shift	Metabolic or signaling changes	Systemic effects	3, 9, 13

Table 2: Major Types of Dysbiosis

Loss of Microbial Diversity

A healthy microbiome thrives on diversity. Loss of microbial diversity is a ubiquitous marker of dysbiosis, often seen after antibiotic use or in chronic illnesses such as obesity, diabetes, kidney disease, and IBD 5 10 13. This reduction in variety weakens resilience against pathogens and impairs key metabolic functions.

Loss of Keystone Taxa

Certain microbes, sometimes called “keystone taxa,” are fundamental to microbiome stability. Their loss (e.g., Faecalibacterium, Roseburia, Lactobacillus) can destabilize the entire ecosystem, undermining immune regulation and metabolic health 5 7 3. In the gut, the absence of such bacteria is linked to increased inflammation and disease susceptibility.

Pathogen Bloom

Sometimes, dysbiosis is driven by an overgrowth of one or more harmful species. For instance, Enterobacteriaceae or Enterococcus can predominate in the gut during severe dysbiosis, often in the wake of antibiotics or hospitalization, and are associated with higher inflammation 7. Similarly, bacterial vaginosis is characterized by anaerobic pathogen blooms in the vaginal microbiome 6. SIBO and intestinal methanogen overgrowth (IMO) are classic examples in the gut 2.

Functional Shifts

Dysbiosis isn’t always about which microbes are present; sometimes it’s about what they do. Functional dysbiosis refers to changes in the metabolic or signaling capabilities of the microbiome. For example, loss of vitamin D receptor function in the host can shift the microbiome’s metabolic profile, affecting nutrient synthesis, immune signaling, and even cancer risk 3 9.

Causes of Dysbiosis

Dysbiosis rarely occurs by chance. Numerous factors—some within our control, others not—shape the microbiome throughout life. Recognizing these contributors is the first step to preventing or reversing microbial imbalance.

Cause	Example/Mechanism	Associated Risk/Outcome	Source
Antibiotics	Disruption of commensals	Loss of diversity, pathogen overgrowth	5, 10, 7
Diet	Low fiber, high fat/sugar	Reduced beneficial microbes	11, 12, 15
Immune dysfunction	Impaired regulation	Chronic inflammation, autoimmunity	3, 8, 9
Environmental exposures	Infection, toxins, hygiene	Shifts in microbiome composition	8, 10
Hormonal changes	Pregnancy, menopause	Vaginal and gut dysbiosis	6
Genetics	Host gene variants (e.g., VDR)	Altered microbial functions	9

Table 3: Primary Causes of Dysbiosis

Antibiotic Use

Antibiotics are double-edged swords. While essential for treating bacterial infections, they can devastate beneficial microbes, especially when used early in life or without clear indication. This disruption can persist, leading to long-term health consequences such as increased infection risk, allergies, and chronic diseases 5 10 7.

Diet and Lifestyle

Modern diets, particularly those low in fiber and high in fat and sugar, promote dysbiosis by starving beneficial bacteria and encouraging harmful species 11 12 15. Conversely, diets rich in plant fibers and polyphenols tend to nurture a more balanced microbiome.

Immune and Genetic Factors

The immune system and microbiome are in constant dialogue. Genetic mutations or immune dysfunction can tip this balance, fostering dysbiosis. For example, loss of the vitamin D receptor alters the gut microbial profile and impairs antimicrobial defenses 3 9. Immune-mediated diseases often both result from and contribute to dysbiosis 1 3 8.

Environmental and Hormonal Influences

Environmental toxins, infections, and even excessive hygiene can shift microbiome composition 8 10. Hormonal changes—during pregnancy, menopause, or puberty—especially affect the vaginal and gut microbiota, sometimes triggering dysbiosis and related health risks 6.

Treatment of Dysbiosis

Restoring microbial balance is both a science and an art. Treatments for dysbiosis depend on the context—whether addressing gut, vaginal, or systemic dysbiosis—and the underlying cause. Strategies are rapidly evolving, with promising new approaches on the horizon.

Treatment Approach	Method or Example	Indication/Benefit	Source
Probiotics	Live beneficial bacteria	Restore keystone taxa, reduce inflammation	11, 14, 12
Prebiotics	Non-digestible fibers	Feed beneficial microbes	11, 15, 12
Synbiotics	Combo of probiotics and prebiotics	Synergistic restoration	11, 12
Fecal microbiota transplantation (FMT)	Transfer of healthy donor stool	Severe/refractory gut dysbiosis (e.g., IBD, C. difficile)	13, 14, 11
Dietary modification	High fiber, plant-based diet	Support microbiome diversity	15, 12
Antibiotic stewardship	Judicious use of antibiotics	Prevent iatrogenic dysbiosis	5, 10
Novel biotherapeutics	Phage therapy, predatory bacteria	Targeted pathogen reduction	11

Table 4: Treatment Strategies for Dysbiosis

Probiotics, Prebiotics, and Synbiotics

• Probiotics are live microbes that can help reintroduce beneficial bacteria, particularly after antibiotic use or in mild to moderate dysbiosis 11 14 12.
• Prebiotics—non-digestible fibers—feed beneficial microbes, promoting their growth 11 15 12.
• Synbiotics combine both, aiming for a synergistic effect 11 12.

While generally safe, their effectiveness can vary by individual and condition.

Fecal Microbiota Transplantation (FMT)

FMT involves transferring stool from a healthy donor to a patient with severe dysbiosis, particularly for recurrent Clostridioides difficile infection or refractory IBD 13 14 11. FMT can restore diversity and keystone taxa, though its use remains controlled due to regulatory and safety concerns.

Dietary Approaches

A diet high in plant fibers, diverse whole foods, and low in processed ingredients supports a healthy, resilient microbiome 15 12. Dietary interventions are often the first step in managing mild dysbiosis and are crucial adjuncts in more serious cases.

Antibiotic Stewardship

Preventing unnecessary antibiotic use is key to avoiding dysbiosis, especially in children and at-risk populations 5 10. Stewardship programs help ensure antibiotics are used only when truly needed.

Novel and Emerging Therapies

• Phage therapy and predatory bacteria are promising new approaches for selectively targeting harmful microbes without disturbing beneficial communities 11.
• Personalized medicine, including targeted microbial consortia and precision dietary plans, is an exciting frontier 14.

Conclusion

Dysbiosis is a complex, multifaceted disruption of the body’s microbial communities, impacting health in profound ways. From gut complaints to mood disorders and autoimmune diseases, its fingerprints are everywhere. Fortunately, our understanding of dysbiosis—and how to counteract it—is growing rapidly.

Key Takeaways:

• Dysbiosis manifests with diverse symptoms, most commonly GI distress, inflammation, increased infection risk, and neuropsychological changes.
• There are distinct types of dysbiosis: loss of diversity, loss of keystone taxa, pathogen blooms, and functional shifts.
• The main causes include antibiotics, poor diet, immune and genetic factors, environmental exposures, and hormonal changes.
• Treatment strategies are varied but focus on restoring microbial balance via probiotics, prebiotics, FMT, dietary changes, and prudent antibiotic use.
• Ongoing research and new therapies promise more personalized, effective approaches to maintaining and restoring a healthy microbiome.

Empowering individuals and clinicians with knowledge about dysbiosis is vital for the future of personalized and preventive medicine. As science continues to unravel the mysteries of our microbial inhabitants, our ability to support and restore them will only improve.