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Short-Chain Fatty Acids (SCFAs) for Inflammatory Bowel Disease (IBD) (2024 Review)

Inflammatory Bowel Disease (IBD) represents a group of intestinal disorders that cause prolonged inflammation of the digestive tract, primarily including Crohn’s disease and ulcerative colitis.

Recent research has highlighted the vital role of short-chain fatty acids (SCFAs) in mitigating IBD by maintaining intestinal health, regulating immune responses, and supporting the gut microbiome.

Traditional Chinese Medicine (TCM) and natural compounds have been identified as promising sources to modulate SCFAs, offering potential therapeutic avenues for IBD management.


  1. SCFAs, especially acetate, propionate, and butyrate, are crucial metabolites produced by gut microbiota, instrumental in gut health and immune regulation.
  2. Traditional Chinese medicines and natural compounds have shown potential in promoting SCFA production, thus alleviating symptoms of IBD in animal models.
  3. The therapeutic effects of SCFAs include enhancing intestinal barrier integrity, modulating immune responses, and maintaining gut microbiome balance.
  4. Future IBD treatment strategies could focus on targeting SCFA pathways, utilizing TCM, and natural compounds to develop personalized medicine approaches.

Source: Molecules (2024)

What are Short-Chain Fatty Acids (SCFAs)?

Short-chain fatty acids (SCFAs) are fatty acids with fewer than six carbon atoms, produced primarily through the fermentation of dietary fibers by the gut microbiota in the colon.

They play a pivotal role in gut health and have systemic effects on the body’s metabolism and immune function.

The most studied SCFAs include acetate, propionate, and butyrate, each offering unique benefits for health.

Functions of SCFAs

  • Energy Source: Butyrate serves as a primary energy source for colonocytes (colon cells), supporting their health and promoting the integrity of the gut lining.
  • Regulation of Inflammation: SCFAs help modulate the immune system, reducing inflammation by inhibiting pro-inflammatory cytokines and promoting the production of anti-inflammatory compounds.
  • Enhancement of the Gut Barrier: SCFAs contribute to the strengthening of the intestinal barrier by stimulating the production of mucus and enhancing the tight junctions between gut cells, preventing the translocation of harmful substances into the bloodstream.
  • Modulation of Gut Microbiota: By influencing the pH of the colon, SCFAs help maintain a favorable environment for beneficial bacteria and inhibit the growth of pathogenic bacteria.

Sources of SCFAs

SCFAs are not found in foods directly but are produced endogenously by the gut microbiota as they ferment indigestible dietary fibers and resistant starches.

Sources that promote SCFA production include:

  • Resistant Starches: Foods like cooked and cooled potatoes, green bananas, and legumes are rich in resistant starches that escape digestion and are fermented in the colon.
  • Dietary Fibers: Whole grains, fruits, vegetables, and nuts are excellent sources of dietary fibers that undergo fermentation.
  • Prebiotic Foods: Certain foods such as garlic, onions, leeks, asparagus, and Jerusalem artichokes contain prebiotics, which specifically fuel beneficial bacteria known to produce SCFAs.

Biological actions of SCFAs

SCFAs have several important actions within the gut and throughout the body, including:

  • Maintaining Gut Health: By nourishing colonocytes and enhancing the gut barrier, SCFAs help protect against gastrointestinal disorders.
  • Regulating Blood Sugar: SCFAs can influence the release of gut hormones that help regulate glucose metabolism, potentially improving insulin sensitivity.
  • Affecting Body Weight: Some research suggests that SCFAs can influence satiety and energy metabolism, potentially playing a role in weight management.
  • Supporting Immune Function: Through their anti-inflammatory effects and modulation of the gut microbiota, SCFAs contribute to a balanced immune response.

Potential Health Benefits of SCFAs

The potential health benefits of SCFAs extend beyond the gut, offering systemic effects that include:

  • Reduced Risk of Gastrointestinal Diseases: Including a reduced risk of inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), and colorectal cancer.
  • Improved Metabolic Health: SCFAs have been linked to lower risks of obesity, type 2 diabetes, and metabolic syndrome by regulating fat storage and glucose homeostasis.
  • Enhanced Immune Function: By modulating the immune response, SCFAs can help protect against autoimmune diseases and infections.
  • Neuroprotective Effects: Emerging research suggests SCFAs can cross the blood-brain barrier, influencing brain health and potentially reducing the risk of neurodegenerative diseases.

Findings: SCFAs & Traditional Chinese Medicines in IBD (2024 Review)

A comprehensive review on the impact of short-chain fatty acids (SCFAs) and traditional Chinese medicines (TCMs) on inflammatory bowel disease (IBD) underscores the pivotal role these metabolites play in gut health and disease modulation.

Below is an in-depth discussion of the findings, highlighting the specific roles of SCFAs, the impact of TCMs on SCFA production, and their collective influence on IBD pathophysiology.

1. Impact of SCFAs on Gut Health & IBD

SCFAs, particularly acetate, propionate, and butyrate, are key metabolites produced by the fermentation of dietary fibers by the gut microbiota. These fatty acids serve multiple beneficial roles in the gut environment, including:

  • Energy Source: SCFAs provide a primary energy source for colonocytes, supporting cellular metabolism and promoting gut barrier integrity.
  • Regulation of Immune Responses: SCFAs modulate the immune system, balancing pro-inflammatory and anti-inflammatory responses. Butyrate, for instance, inhibits nuclear factor-kappa B (NF-κB) pathways, reducing the production of pro-inflammatory cytokines.
  • Gut Barrier Enhancement: By strengthening the gut barrier, SCFAs prevent the translocation of pathogenic bacteria and reduce the risk of gut inflammation. They enhance the production of mucin, tight junction proteins, and antimicrobial peptides.
  • Microbiota Composition: SCFAs influence the composition of the gut microbiota, promoting the growth of beneficial bacteria and suppressing pathogenic species.

2. Traditional Chinese Medicines & SCFA Production

The review highlights the efficacy of various TCMs and natural compounds in modulating SCFA production, which in turn influences the severity of colonic inflammation in IBD models:

  • Baicalin and Berberine: These compounds were found to increase SCFA levels, particularly butyrate, altering the gut microbiota composition favorably and reducing inflammation.
  • Gegen Qinlian Decoction (GQD): GQD administration led to an increase in SCFA-producing bacteria, enhancing the overall SCFA profile in the gut. This was associated with reduced colonic inflammation through the inhibition of inflammatory pathways like NF-κB.
  • Mechanisms of Action: TCMs exert their effects through various mechanisms, including the modulation of immune responses (e.g., Treg/Th17 cell balance), enhancement of gut barrier function, and alteration of the gut microbiota composition to favor SCFA production. Specific pathways modulated by SCFAs include GPR43 activation and NF-κB inhibition, which are crucial for their anti-inflammatory effects.

3. Signaling Pathways & Molecular Mechanisms

SCFAs modulate several key signaling pathways and molecular mechanisms involved in IBD pathophysiology:

  • NF-κB Pathway: SCFAs, particularly butyrate, inhibit the NF-κB pathway, reducing the production of pro-inflammatory cytokines and mediators.
  • GPR43 Activation: SCFAs activate GPR43, a G-protein-coupled receptor, mediating anti-inflammatory effects and promoting gut barrier integrity.
  • Treg/Th17 Balance: SCFAs influence the balance between regulatory T cells (Tregs) and Th17 cells, crucial for maintaining immune homeostasis and preventing excessive inflammation.

SCFAs, TCMs, IBD Management (2024 Review)

Yuan Yao et al. conducted a review of short-chain fatty acids (SCFAs) and traditional Chinese medicines (TCMs) in addressing inflammatory bowel disease (IBD), with a specific focus on Crohn’s disease (CD) and ulcerative colitis (UC).

It underscored the significance of SCFAs—primarily acetate, propionate, and butyrate—produced via gut microbiota fermentation of dietary fibers, in sustaining gut health, modulating immune functions, and fueling colon cells.

It also emphasized the potential therapeutic benefits of modulating SCFA levels and utilizing TCMs to enhance their production, given their altered levels in IBD pathogenesis.


  • This review integrated findings from recent studies on SCFAs and TCMs, assessing their influence on SCFA production, colonic inflammation severity, and the mechanisms of action involved.
  • It particularly focused on the regulatory factors and signaling pathways affected by SCFAs.


  • The findings reveal that various TCMs and natural compounds, such as baicalin, berberine, and Gegen Qinlian Decoction (GQD), are effective in mitigating colonic inflammation in colitis animal models through SCFA production modulation.
  • The alterations in gut microbiota prompted by these TCMs lead to improved nutritional balance, strengthened gut barrier, enhanced immune system modulation, and suppression of pathogenic bacteria growth.
  • Notably, the review pinpoints specific signaling pathways influenced by SCFAs, including the NF-κB pathway involved in inflammatory responses and GPR43, a receptor that mediates the anti-inflammatory effects of SCFAs.


  • The necessity to pinpoint the active compounds within TCMs that enhance SCFA production.
  • The need for a deeper understanding of SCFAs’ complex interactions with host health and the determination of their optimal therapeutic concentrations to avoid adverse effects.
  • The challenge of standardizing TCM treatments due to variability in compositions.

Which TCMs May Provide Benefit in IBD?

The review highlights several Traditional Chinese Medicines (TCMs) and natural compounds with promising evidence for their effectiveness in managing inflammatory bowel disease (IBD) through the modulation of short-chain fatty acid (SCFA) production.

Here’s a breakdown of the specific TCMs mentioned and their potential mechanisms for aiding in IBD treatment, with a focus on those with the most substantial evidence.

1. Baicalin

  • Mechanism: Baicalin has been shown to modulate the gut microbiota, enhancing the production of butyrate, a key SCFA in maintaining gut health and modulating immune responses. It also plays a role in reducing oxidative stress and regulating the Th17/Treg balance, critical for managing inflammation.
  • Evidence: Strong evidence suggests baicalin’s effectiveness in reducing inflammation and supporting gut barrier integrity through SCFA production and immune regulation.

2. Berberine

  • Mechanism: Berberine impacts SCFA production by altering gut microbiota composition. It has been noted for its anti-inflammatory properties, ability to enhance barrier function, and potential to modify the gut microbiome in a way that favors SCFA production.
  • Evidence: Berberine has substantial backing for its role in increasing SCFA levels, particularly butyrate, and modulating inflammatory responses, making it a potent agent for IBD management.

3. Gegen Qinlian Decoction (GQD)

  • Mechanism: GQD has been found to increase the abundance of SCFA-producing bacteria, leading to elevated levels of acetate, propionate, and butyrate. These SCFAs contribute to the suppression of NF-κB pathway activity, reducing inflammation and enhancing intestinal barrier function.
  • Evidence: There’s strong evidence for GQD’s effectiveness in treating colitis models by modulating SCFA levels and impacting key inflammatory pathways.

Additional TCMs & Compounds for SCFAs & IBD

The review also mentions other TCMs and natural compounds like Qingchang Huashi Formula (QHF), Pulsatilla Decoction (PD), Astragalus Membranaceus and Codonopsis Pilosula (PAC), and Hericium Erinaceus Mycelium (HEM), which have shown promise in modulating SCFA production and alleviating colitis in animal models.

However, the specific mechanisms and the extent of evidence vary, with a need for further research to fully understand their therapeutic potential and application in IBD treatment.

Other Ways to Modulate Short-Chain Fatty Acid (SCFA) Production

These approaches aim to enrich the gut microbiota with beneficial bacteria capable of fermenting dietary fibers into SCFAs, thereby exerting positive effects on gut health and mitigating inflammatory conditions like IBD.

  • Diet Changes: Consumption of a diet rich in dietary fibers, particularly resistant starches, non-digestible carbohydrates, and prebiotics, fosters the growth of SCFA-producing bacteria. Foods such as whole grains, fruits, vegetables, and legumes are potent sources of such fibers. Incorporating fermented foods like yogurt, kefir, sauerkraut, and kimchi, which contain live microorganisms, can promote the proliferation of beneficial gut bacteria that produce SCFAs.
  • Probiotic Supplementation: Supplementing the diet with probiotics, especially those strains known to enhance SCFA production (e.g., Lactobacillus and Bifidobacterium species), can directly increase SCFA levels in the gut.
  • Herbs & Traditional Chinese Medicines: Various TCMs, including herbal extracts and compounds like Gegen Qinlian Decoction and berberine, have been shown to modulate the gut microbiota favorably, increasing the abundance of SCFA-producing bacteria.

How SCFAs May Improve IBD & Related Conditions (Mechanisms)

SCFAs, particularly acetate, propionate, and butyrate, exert multiple beneficial effects on the gut environment and immune system, offering a multifaceted approach to managing IBD and related conditions.

  • Tight Junction Protein Expression: SCFAs upregulate the expression of tight junction proteins (e.g., claudins and occludin), strengthening the gut barrier and preventing the translocation of pathogens and inflammatory mediators into the systemic circulation.
  • Mucin Production: Butyrate stimulates the production of mucin by goblet cells, enhancing the mucus layer’s protective function against pathogens and mechanical damage.
  • Anti-inflammatory Effects: SCFAs modulate the immune system by inhibiting pro-inflammatory cytokines’ production (e.g., TNF-α, IL-6) and stimulating anti-inflammatory cytokines (e.g., IL-10). This effect is partly mediated through the inhibition of the NF-κB pathway.
  • Regulation of T Cell Differentiation: SCFAs influence the differentiation and function of T cells, promoting the development of regulatory T cells (Tregs) while inhibiting the differentiation of pro-inflammatory Th17 cells, thereby restoring immune balance and reducing inflammation.
  • Promoting Beneficial Bacteria: SCFAs can alter the gut microbiota’s composition, promoting the growth of beneficial bacteria while inhibiting pathogenic species. This effect supports a healthy gut ecosystem and reduces dysbiosis associated with IBD.
  • Energy Source for Colonocytes: Butyrate serves as a primary energy source for colonocytes, supporting their health and function. This energy provision is crucial for maintaining cellular integrity and the overall health of the gut lining.
  • Activation of G-Protein-Coupled Receptors (GPRs): SCFAs activate GPRs (e.g., GPR41, GPR43) on intestinal epithelial cells and immune cells, triggering signaling pathways that promote anti-inflammatory responses and gut barrier function.

By modulating SCFA production through dietary and medicinal interventions and leveraging SCFAs’ mechanisms of action, it’s possible to improve the management of IBD and related conditions, offering a promising avenue for research and therapeutic development.

Takeaways: SCFAs, Traditional Chinese Medicine (TCM), Inflammatory Bowel Disease

The study underscores the pivotal role of short-chain fatty acids (SCFAs) and Traditional Chinese Medicines (TCMs) in the therapeutic landscape of inflammatory bowel disease (IBD), including Crohn’s disease and ulcerative colitis.

By modulating the production of SCFAs, such as acetate, propionate, and butyrate, TCMs offer a promising avenue for managing IBD through the enhancement of gut health, immune regulation, and maintenance of the intestinal barrier.

Among the explored TCMs, Berberine and Gegen Qinlian Decoction (GQD) emerge with strong evidence supporting their effectiveness in modulating gut microbiota and SCFA levels, thereby attenuating inflammation and improving colonic health.

However, the review also highlights significant gaps in our understanding of the specific active compounds within TCMs that drive SCFA production, the optimal concentrations for therapeutic efficacy, and the complex interactions between SCFAs and host health.

Future research is warranted to address these limitations, with a focus on identifying precise mechanisms of action, optimizing treatment formulations, and conducting rigorous clinical trials to validate the clinical applicability of TCMs in IBD treatment.

The potential of TCMs to complement existing IBD therapies by leveraging the beneficial effects of SCFAs opens new pathways for holistic and personalized treatment strategies in gastrointestinal health.


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