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The Gut Microbiome and Rheumatology: How Integrative Approaches Can Improve Outcomes

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The Gut Microbiome and Rheumatology: How Integrative Approaches Can Improve Outcomes

Rheumatology-related symptoms, including chronic pain, affect a significant portion of people in the U.S. Millions of adults experience various rheumatic conditions. Given the prevalence of these concerns, addressing these symptoms should be a priority in functional health. The gut microbiome plays a central role in GI health, immune regulation, and body function, making it a key integrative approach to addressing these conditions.

This article aims to connect the dots between the gut microbiome and rheumatology. We will explore how integrative approaches such as clinical nutrition can lead to improved outcomes. Understanding the connection between these two areas is imperative as it allows us to uncover strategies to alleviate symptoms, improve well-being and promote overall health in these conditions. We will explore the diverse range of integrative approaches that hold promise in managing rheumatic diseases. We will also discuss the potential of integrative medicine and the gut microbiome in improving outcomes for rheumatology-related symptoms.


What is The Gut Microbiome?

The gut microbiome, also referred to as gut microbiota or gut flora, encompasses trillions of microorganisms residing in the gastrointestinal (GI) tract. These microorganisms colonize various body regions, with the highest concentrations found in the small and large intestines. The microbiome consists of multiple bacteria, viruses, protozoa, and fungi.

The gut microbiota is composed of a diverse array of microorganisms, encompassing both beneficial and potentially pathogenic species. In a state of health, a symbiotic relationship is established between the gut microbiota and the human host, wherein both entities mutually derive benefits from one another, and the microbial population coexists harmoniously without any notable conflicts.

Extensive research conducted in the past decade has shed awareness on the significant role of the microbiome and its impact on various physiological processes, including metabolism, immune responses, and neuroendocrine signaling. The gut microbiota can modulate metabolic functions, educate the immune system, and communicate with the neuroendocrine system, significantly influencing our overall physiology in health and disease states.

A prominent function of the gut microbiome is its involvement in nutrient absorption, including the modulation of enzymes, vitamins, and amino acids and the production of short-chain fatty acids (SCFAs). The gut microbiome contributes to the smooth functioning of the body's vital processes through these mechanisms.

What is Rheumatology?

Rheumatology, a medical specialty, involves diagnosing and comprehensively managing musculoskeletal disorders and systemic autoimmune conditions, collectively known as rheumatic diseases. These ailments encompass a broad spectrum of afflictions, impacting the joints, bones, and muscles, often causing discomfort, rigidity, and structural abnormalities. Additionally, these conditions can extend their grasp to affect diverse body systems, including the eyes, skin, nervous system, and internal organs. Notable examples of such disorders include arthritis, rheumatoid arthritis, gout, Systemic Lupus Erythematosus (SLE), and fibromyalgia.

What is The Gut Microbiome’s Role in Rheumatic Diseases?

The human body harbors trillions of bacteria, viruses, and fungi known as the microbiome. This diverse ecosystem plays a vital role in our well-being, aiding digestion, vitamin synthesis, drug metabolism, and immune regulation. Researchers are increasingly exploring the connection between the microbiome and autoimmune rheumatic diseases. In recent discussions at the American College of Rheumatology's 2021 annual meeting, researchers analyzed emerging findings in this research.

Dr. Yasmine Belkaid’s research, an expert in studying the interactions between the microbiome and the immune system, reveals the microbiome's dual role in controlling the immune response in the skin and gut. Harmless skin bacteria, ERVs (endogenous retroviruses), and specific T cells defend against pathogens and aid tissue repair but can also trigger inflammation influenced by diet.

Dr. Renuka Nayak's work highlights how the gut microbiome contributes to variations in drug response, particularly with methotrexate in rheumatoid arthritis. The composition of gut bacteria has been found to contribute to variations in patients' response to prescribed medications, including methotrexate, a standard RA treatment. Some gut bacteria can metabolize methotrexate, affecting its effectiveness and toxicity. The reaction to methotrexate also depends on the individual's microbiome makeup, with specific bacteria influencing its metabolism and therapeutic outcomes.

Dr. Jose Scher's extensive work on the microbiome and its connection to psoriatic disease highlighted the impact of dysbiosis, an imbalance in the microbiome, on autoimmune rheumatic conditions. In psoriasis and psoriatic arthritis (PsA), disruption of a healthy microbiome and reduced levels of protective short-chain fatty acids (SCFAs) have been observed. SCFAs, produced by bacteria during fiber breakdown, help decrease gut inflammation and improve overall inflammatory arthritis. Exploring approaches to modulate the microbiome, including fecal microbial transplants, administration of beneficial bacteria strains, and dietary changes, holds promise for treating psoriatic disease.

Though achieving a balanced microbiome poses challenges, its potential to reduce arthritis symptoms and improve health is significant. The microbiome's intricate relationship with rheumatic diseases remains an area of intensive research. Ongoing research aims to uncover novel therapeutic approaches in rheumatology.

Functional Medicine Labs to Test The Gut Microbiome's Health

The following labs can help practitioners identify alterations in gut health:

Microbiome Labs

Microbiome Labs specializes in microbiome science and therapeutics, offering the BiomeFX test to explore the gut microbiome's vital functions. With accurate sequencing technology, it identifies pathogens and keystone species crucial to overall health. Their individualized testing results support practitioners and patients in managing microbiome function through nutrition, lifestyle, and supplements.

Gut Zoomer

The Gut Zoomer test provides a comprehensive analysis of gut health. This test identifies pathogens and dysbiosis crucial in the microbiome's health and helps unveil potential causes of chronic diseases. Gut microbiome imbalances can lead to various gastrointestinal and systemic conditions, from IBS and IBD to autoimmune disorders and inflammatory conditions.

Advanced Intestinal Barrier Assessment

The advanced IBA test provides a comprehensive gut health assessment by directly measuring critical markers related to gut permeability. It analyzes Zonulin, DAO, and LPS to evaluate leaky gut conditions, gut lining thickness, histamine degradation ability, and the presence of endotoxins. This test covers significant aspects of gut permeability to inform clinicians about the microbiome's health.

Food Sensitivity Panel

This food sensitivity panel combines measures of IgA and IgG antibodies to 180 commonly consumed food antigens. Clinicians often use food sensitivity testing to assess the health of the gut lining indirectly, as food sensitivities can affect the balance of the microbiome.

Vitamin D Test

Research has linked deficiencies in Vitamin D to fibromyalgia and chronic pain. Testing vitamin D levels using a Vitman D, 25-OH serum test is recommended so that supplementation can be individualized.

Integrative Nutrition for Rheumatic Diseases

The field of rheumatology benefits considerably from using integrative nutrition and applying advanced 'omics' technologies. These omics technologies, including genomics, transcriptomics, proteomics, metabolomics, and microbiomics, shed light on how nutrients influence our health. By studying the interplay between genetics, environmental triggers, nutrition, and conditions like rheumatoid arthritis (RA), we can discover the impact of specific nutrients and dietary patterns. Embracing integrative nutrition and leveraging 'omics' tools allows for personalized approaches and targeted interventions to improve health outcomes for individuals living with rheumatic diseases. The complex relationship between nutrition and rheumatological conditions is revealed through these cutting-edge techniques, leading to precise nutritional guidance and an enhanced understanding of the role of nutrition in rheumatology.

Supplements and Herbs for Rheumatic Diseases

Below are several evidence-based supplments for rheumatic diseases:


Probiotics support gut health by restoring microbiome balance, strengthening mucus production, preserving tight junctions, and reducing inflammation caused by protein damage and immune cell activation triggered by lipopolysaccharides (LPS). They offer potential relief for rheumatic conditions.

Boswellia Serrata

Incorporate Boswellia Serrata, or Frankincense, into your arthritis treatment plan for potential relief and improved joint health. This traditional herb with anti-inflammatory properties has been shown in a meta-analysis of seven studies to significantly reduce pain and stiffness and improve joint function in over 500 patients with osteoarthritis. Recommended dosage ranges from 100 to 1,000 mg, with a minimum treatment duration of 4 weeks for optimal results.

Omega 3

Omega-3 fatty acids offer relief from pain and inflammation in rheumatic conditions such as arthritis and fibromyalgia. The anti-inflammatory properties of EPA and DHA help reduce musculoskeletal pain and swelling. Studies indicate that taking daily omega-3 supplements of at least 2.7 grams for three months improves morning stiffness and tender joints, potentially reducing the reliance on NSAIDs.

Vitamin D

Vitamin D is vital in treating rheumatic conditions such as arthritis and fibromyalgia. Research has linked deficiencies in Vitamin D to chronic pain and fibromyalgia. Supplementing with vitamin D can alleviate pain and enhance mood. Testing vitamin D levels is recommended. The recommended daily dose for patients with low levels is 2,400 IU (as D3) or 1,200 IU for moderate levels.

Supplements and Herbs for Optimal Gut Health

Below are several evidence-based supplements for optimizing gut health:

Licorice Root (Glycyrrhiza glabra)

Glycyrrhiza is a potent anti-inflammatory herb known for its soothing effects on the digestive tract. While the whole root contains glycyrrhizin, which can increase blood pressure, a form of herb called DGL is commonly used to treat heartburn, GERD, and gastritis. DGL lacks glycyrrhizin but promotes mucus production, forming a protective barrier against acid and aiding in healing damaged tissues.


Curcumin, a compound present in turmeric, possesses remarkable anti-inflammatory, antioxidant, and anti-cancer properties. By regulating oxidative stress, curcumin effectively reduces inflammation in the body. Studies indicate that curcumin can alleviate symptoms of inflammatory bowel diseases (IBD) like ulcerative colitis (UC) and Crohn's disease (CD), as well as peptic ulcers. Incorporating curcumin into your regimen may provide a natural approach to managing gut inflammation.


Prebiotics are dietary fibers that nourish beneficial gut bacteria, producing short-chain fatty acids (SCFAs). These SCFAs offer anti-inflammatory effects throughout the body. By consuming prebiotics, you can enhance the diversity and population of beneficial bacteria in your gut, promoting better digestion, nutrient absorption, and gut lining strength. Common prebiotic forms in supplements include FOS, GOS, and inulin. However, individuals with SIBO (Small Intestine Bacterial Overgrowth) should avoid prebiotics, which can exacerbate symptoms like gas and bloating.

Slippery Elm

Slippery Elm, scientifically called Ulmus rubra, is an excellent botanical for promoting gut health, especially in children. It offers two main benefits in this regard. Firstly, it forms a protective barrier on the skin and gastrointestinal tract, preventing the entry of harmful pathogens. Secondly, its demulcent properties soothe inflamed gut tissue. Furthermore, Slippery Elm acts as a natural prebiotic, nourishing beneficial gut bacteria.


L-Glutamine, an amino acid, is vital in maintaining gut integrity and permeability. It offers three key benefits for gut health: balancing the gut microbiome, enhancing tight junctions in the gut lining, and reducing inflammation during gut distress.



With the prevalence of rheumatologic conditions and their related symptoms affecting millions worldwide, it is essential to provide ways to treat and manage these conditions effectively. Understanding the gut microbiome and its relation in rheumatology can give valuable insights for addressing and managing these conditions. By exploring the connection between the gut microbiome and rheumatology, we uncover the potential for integrative approaches to improve outcomes in individuals with rheumatologic diseases. Strategies such as clinical nutrition and utilizing evidence-based supplementation to optimize the gut microbiome may be beneficial in addressing rheumatologic symptoms.

As the number of individuals with these conditions continues to grow, it is crucial for further research into the role of gut microbes and their impact on the body systems, immune response regulation, and overall health. Through this research, we can better understand these conditions and discover personalized strategies for improved outcomes in rheumatologic management and other health conditions.

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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