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dysbiosis
Dysbiosis describes a state of microbial imbalance within the gastrointestinal tract, characterized primarily by;
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The loss of beneficial microbes
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Overgrowth of opportunistic pathobionts
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A decline in overall microbial diversity [8,9].
Beneficial Microbes:
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Compete with pathogens for space and nutrients, preventing infections [2,3].
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Produce antimicrobial substances that kill or inhibit harmful microbes [2].
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Strengthen the mucus barrier to prevent toxins and microbes entering the blood [3].
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Ferment dietary fibers to produce beneficial short-chain fatty acids (SCFAs) [4].
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Support colon cell health by using SCFAs as energy and maintaining low gut pH [4].
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Train the immune system to respond to threats while avoiding unnecessary reactions [1,4].
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Promote immune tolerance by stimulating anti-inflammatory cells [1].
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Produce vitamins and nutrients, including B12, K, folate, and biotin [4].
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Influence brain health by producing neurotransmitter-like compounds [5].
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Modulate appetite and metabolism and influence insulin sensitivity [7].
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Form biofilms that protect the gut lining and support stable microbial communities [6].
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Altering gene expression through epigenetic signals like SCFAs [1].
Opportunistic Pathobionts:
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Trigger inflammation, leading to digestive complaints and diseases[10].
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Exploit weakened microbiomes, becoming opportunistic [11].
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Contribute to aging-related disease [12].
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Increase risk of systemic infections through intestinal permeability [13].
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Encourage antibiotic resistance [14].
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Disrupt nutrient absorption and metabolism [15].
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Cause and exacerbate various health conditions [16]
Microbial diversity
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Maintains gut homeostasis and prevents the overgrowth of harmful organisms. [17]
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Supports immune system development and immune tolerance. [18]
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Lower diversity increases risk of various chronic diseases [19]
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Enables digestion of complex foods and synthesis of nutrients. [20]
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Affects the gut-brain axis, influencing mood, anxiety, and cognitive function. [21]
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Provides a protective barrier against invading pathogens. [22]
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Helps in resilience and recovery after antibiotic use or illness. [23]
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Reduces gut inflammation through anti-inflammatory metabolites like butyrate. [24]
signs & symptoms
Tongue Coating + Colour Characteristics
A cross-sectional study of 158 adults, conducted over 5 months, photographed the tongue after an overnight fast using standardised imaging, collected pre-brushing tongue swabs for bacterial sequencing, and drew routine blood samples to test whether coating appearance reliably reflects microbiome dysbiosis and systemic inflammation. Tongue coatings were classified into four types detailed below, with the corresponding findings. [1]
Sparse White Coating
Tongues with a very sparse white coating, almost undetectable, demonstrated the most balanced microbiome, with higher α-diversity. This refers to an ecological system with stability and resilience, having more species sharing the space and fewer chances for one opportunist species taking over. This was further evident by the blood markers, which demonstrated no clear inflammation signals.
Thin Yellow Coating
Tongues with a thin yellow coating demonstrated the lowest α-diversity, meaning fewer kinds of microbes and a less even balance, and the weakest microbe–microbe network, so the community is less stable and more prone to imbalance.
Thin yellow coatings are also aligned with higher PLR levels, a simple blood marker that rises with systemic inflammation, and also tend to have higher blood levels of CRP (C-reactive protein), a protein that rises with systemic inflammation. Taken together, this coating type signals an unstable ecosystem, with a more inflammatory tone, which is not a beneficial state.
Thick White Coating
Tongues with a thick white coating, trended toward lower diversity and more disrupted networks than the healthy baseline. Thick white coatings demonstrated relatively more Prevotella salivae than the sparse white coatings, consistent with a shift toward dysbiosis.
Regarding inflammation, note was made of higher fibrinogen levels. Fibrinogen is an acute-phase reactant, when it is elevated it ordinarily signals ongoing inflammation. In this cohort, PLR inflammatory markers were not raised, but the fibrinogen association suggests vascular or inflammatory effects are still relevant for this pattern.
Thick Yellow Coating
Tongues with a thick yellow coating, pointed to community disruption. Its α-diversity was low and its β-diversity network structure clearly shifted towards increased Streptococcus anginosus and Moraxella catarrhalis numbers. Health-wise these strains are aligned with elevated BMI or waist size, more fat stored in the liver, insulin having to work harder, and inflammation-wise. This is also demonstrated with consistently elevated PLR levels, which is a simple blood marker that rises with systemic inflammatory responses.[1]
Dysbiosis Mediated Digestive Disorders
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Constipation
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Chronic Diarrhea
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Irritable Bowel Syndrome (IBS)
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Chron's Disease
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Diverticulitis
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Ulcerative colitis
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Gastritis
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Gastro-oesophageal Reflux Disease (GORD)
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Peptic Ulcers
A broad spectrum of conditions across the digestive, immune, metabolic, dermatological, and neurological systems are linked to an imbalance in the composition or function of the body's microbial communities.
This correlation arises because the microbiome is not only involved in digestion but also regulates immune signaling, maintains barrier integrity, produces neurotransmitters, and influences systemic inflammation and metabolism. When the balance of beneficial to harmful microbes is disrupted, it can lead to excess production of inflammatory molecules, loss of protective metabolites like short-chain fatty acids, greater permeability of mucosal barriers and cause several other imbalances.
Dysbiosis Mediated Immune Disorders
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Allergies
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Asthma
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Recurrent Respiratory Infections
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Food Intolerances
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Autoimmune Disease
Dysbiosis within the gut and upper airway microbiome can significantly alter immune regulation, increasing susceptibility to allergic, inflammatory, and recurrent infectious conditions. This occurs because the microbiome shapes immune tolerance, calibrates inflammatory pathways, influences antibody responses and assists in maintaining epithelial integrity within the respiratory tract.
When microbial balance is disrupted, the immune system becomes more reactive, less regulated, and less effective at defending against pathogens, resulting in heightened inflammation, hypersensitivity and recurrent respiratory symptoms.
Dysbiosis Mediated Skin Conditions
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Eczema
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Contact Dermatitis
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Folliculitis
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Acne
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Abscesses or Boils
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Psoriasis
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Rosacea
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Pityriasis Versicolor
A wide range of dermatological conditions are now recognised as being influenced by imbalances within the gut-skin and skin-surface microbiome ecosystems. The skin relies on microbial diversity to regulate local immunity, maintain barrier function, modulate inflammation, and protect against pathogenic organisms.
When dysbiosis occurs it can lead to an overactive immune response, impaired barrier repair, increased colonisation by harmful microbes and a rise in pro-inflammatory compounds that manifest on the skin.
Dysbiosis Mediated Genitourinary and Reproductive Disorders
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Urinary Tract Infections
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Candidiasis
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Bacterial Vaginosis
The vaginal, urinary, and reproductive microbiomes are highly sensitive ecosystems that rely on dominant beneficial species, particularly Lactobacilli, for protection, pH regulation, pathogen resistance and modulation of local immune responses. Dysbiosis in these regions, or systemic dysbiosis originating from the gut, can impair mucosal defences, increase adherence of opportunistic microbes, disrupt hormonal signalling and contribute to chronic inflammatory or infectious presentations. These imbalances often manifest as recurrent infections, altered discharge, pelvic discomfort or hormonal dysregulation.
Dysbiosis Mediated Neuroendocrine and Metabolic
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Serotonin Deficiency
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Insulin Resistance
The gut microbiome plays a pivotal role in neurochemical production, hormone metabolism, glucose regulation, and appetite control through the gut-brain-axis and gut-endocrine pathways. When dysbiosis occurs, it can reduce production of key neurotransmitters, such as serotonin, impair insulin signalling, increase systemic inflammation, and disrupt metabolic homeostasis. These changes can contribute to mood disturbances, altered stress responses, cravings, weight fluctuations and metabolic dysfunction.
Causes
Antibiotics
Antibiotics disrupt microbial balance by indiscriminately killing both pathogenic and beneficial bacteria. This results in decreased microbial diversity and long-term shifts in microbial communities.
Molecularly, antibiotics reduce butyrate-producing bacteria, decreasing short-chain fatty acids (SCFAs). SCFAs serve as a primary energy source for colonocytes (colon cells), helping to maintain low intestinal pH to suppress the growth of pathogenic bacteria [34].
Poor Diet
Diets high in fat and sugar, whilst being low in fiber, alter the gut microbial ecosystem in favor of pro-inflammatory species.
Low dietary fiber reduces fermentation substrates for beneficial microbes, lowering short-chain fatty acid production, driving dysbiosis.
A high-fat diet increases bile acid secretion, fostering bile-tolerant species, which produce hydrogen sulfide. Excess hydrogen sulfide supports the growth of harmful bacteria that thrive in inflamed environments, while reducing beneficial microbes that produce short-chain fatty acids. As a result, the gut ecosystem becomes unbalanced [35].
Infections
Bacterial and viral infections displace normal flora, allowing pathogenic probiotics to dominate. These pathogens may release toxins or manipulate host immunity.
Infection activates pattern recognition receptors, stimulating NF-κB signaling and production of pro-inflammatory cytokines such as TNF-alpha. [36]. Therefore chronic infections create chronic inflammation, which subsequently inhibits beneficial microbes such as Akkermansia muciniphila, encouraging the expansion of pathobionts that thrive in oxygenated, inflamed environments [44]
Chronic Stress
Stress affects the gut-brain axis, altering gut motility, mucus production, and immune activity, all of which impact microbial populations.
Stress-induced HPA axis activation increases cortisol and norepinephrine, which impair gut immunity and barrier function. These hormonal changes reduce Akkermansia muciniphila [37], thereby encouraging the expansion of pathobionts [44].
Environmental Toxins
Exposure to pesticides, heavy metals, and food additives modifies microbial ecosystems and promotes dysbiosis.
Toxins generate oxidative stress through reactive oxygen species (ROS) production, damaging DNA and bacterial membranes. Some toxins activate AhR receptors, altering cytokine profiles and enhancing inflammatory responses that reshape the gut microbiome negatively [38].
Immune Dysregulation
Autoimmune conditions can both cause and result from dysbiosis. An impaired immune system fails to regulate microbial growth effectively. Loss of regulatory T cells and increased Th17 activity promotes a cycle of immune overactivation, which perpetuates microbial imbalance [39].
Genetic Predisposition
Genetic variants, such as NOD2 mutations alter the gut’s response to microbes. NOD2 mutations impair the recognition of bacterial cell walls, reducing antimicrobial peptide secretion. This weakens microbial surveillance and allows pathogenic overgrowth, linking host genetics directly to dysbiosis [40].
Hypochlorhydria - Low Stomach Acid
Low stomach acid levels fail to sterilize ingested pathogens allowing free passageway. Low stomach acid also impairs protein digestion, leaving large protein fragments that can remain undigested. These fragments can irritate the gut lining, contribute to inflammation, and disrupt the gut microbiome balance, leading to dysbiosis.
Furthermore, low stomach acid also reduces pepsin activation and disrupts nutrient assimilation, thereby altering microbial competition and contributing to dysbiosis [41,45].
Hepatic Insufficiency - Low Bile Production
Low bile production significantly contributes to dysbiosis through several interrelated mechanisms. Firstly bile acids, beyond their well-known role in fat digestion, have potent antimicrobial properties that help regulate the gut microbiota. When bile output is reduced this antimicrobial surveillance weakens, allowing for the overgrowth of opportunistic and pathogenic bacteria [42].
Bile acids normally inhibit the growth of gram-positive bacteria such as Clostridium and Enterococcus. Low bile production can thus lead to an overrepresentation of these species, shifting the microbial composition toward a pro-inflammatory and dysbiotic state [43].
Additionally, bile helps emulsify dietary fats, making them more accessible for digestion. Without sufficient bile, undigested fats remain in the gut lumen, serving as an unabsorbed substrate for harmful bacteria, further encouraging microbial imbalance [44].
Pancreatic Enzyme Deficiency
Pancreatic enzyme deficiency involves lowered digestive enzymes, which are essential for breaking down fats, proteins, and carbohydrates. When these enzymes are insufficient, incomplete digestion leaves macronutrients undigested, creating a nutrient-rich environment that favors the overgrowth of opportunistic and pathogenic bacteria [46].
This undigested food alters the colonic environment, increasing fermentation by non-beneficial microbes and shifting the microbiota profile. In particular, excessive protein fermentation can produce toxic metabolites like ammonia, phenols, and hydrogen sulfide which disrupt the microbial balance, and impair mucosal immunity. [47].
Additionally, insufficient enzymatic digestion affects gut pH balance, increasing luminal pH. This alteration disrupts the ideal acidic environment that supports beneficial bacterial populations like Lactobacillus and Bifidobacterium, while enabling the growth of bacteria associated with dysbiosis, [48].
References
[1] https://www.cell.com/fulltext/S0092-8674(14)00330-5
[2] https://www.cell.com/fulltext/S0092-8674(15)00209-6
[3] https://gut.bmj.com/content/66/5/813
[4].https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2025.1585090/full
[5].https://www.frontiersin.org/journals/psychiatry/articles/10.3389/fpsyt.2024.1524555/full
[6].https://www.frontiersin.org/journals/medicine/articles/10.3389/fmed.2025.1504460/full
[7] https://pmc.ncbi.nlm.nih.gov/articles/PMC11718612/
[8].https://www.sciencedirect.com/science/article/pii/S0944501324002337
[9] https://onlinelibrary.wiley.com/doi/abs/10.1002/eji.202451594
[10].https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2025.1547303/full
[11] https://www.nature.com/articles/s41598-025-96514-5
[12].https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2025.1585090/full
[13].https://www.journalofbabylon.com/index.php/JUBPAS/article/view/5651
[14] https://dc.etsu.edu/boland-research-day/2025/presentations/148/
[15] https://www.nature.com/articles/s41392-025-02146-6
[16] https://www.researchgate.net/publication/390873323
[17] https://pmc.ncbi.nlm.nih.gov/articles/PMC12006732/
[18].https://www.sciencedirect.com/science/article/pii/S0944501324002337
[19] https://www.journalofinfection.com/article/S0163-4453(25)00002-7/fulltext
[20] https://www.annualreviews.org/content/journals/10.1146/annurev-med-042423-042542
[21] https://docta.ucm.es/entities/publication/dfa36b23-096d-422f-9138-032523135fc5
[22].https://www.sciencedirect.com/science/article/pii/S0924857924002024
[23] https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0307781
[24] https://pmc.ncbi.nlm.nih.gov/articles/PMC11718612/
[25] https://www.mdpi.com/2227-9059/10/2/289
[26] https://www.mdpi.com/2079-9721/7/4/58
[27].https://www.sciencedirect.com/science/article/pii/S0753332223007758
[28] https://www.mdpi.com/1422-0067/23/7/3464
[29] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7786094/
[30].https://www.sciencedirect.com/science/article/pii/S2212877816300539
[31] https://www.frontiersin.org/articles/10.3389/fimmu.2022.906258/full
[32] https://onlinelibrary.wiley.com/doi/pdf/10.1155/2018/2037838
[33] https://www.nature.com/articles/nri.2017
[34] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7608204/
[35] https://www.nature.com/articles/s41575-019-0126-8
[36] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8106791/
[37] https://www.frontiersin.org/articles/10.3389/fnins.2017.00060/full
[38] https://www.frontiersin.org/articles/10.3389/fmicb.2020.573118/full
[39] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5855203/
[40] https://www.cell.com/cell-host-microbe/fulltext/S1931-3128(14)00201-8
[41] https://www.mdpi.com/1422-0067/20/23/6031
[42] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7690325/
[43] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7389850/
[44] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8150066/
[45] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6163871/
[46] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7239282/
[47] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5853774/
[48] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7690325/
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