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Section 1 (PDF)

By Alex Vasquez, DC, ND, DO, FACN

Introduction: For the accurate understanding and effective treatment of any disease, all components of the disease should first be integrated into a cohesive and consistent model that explains all aspects of the disease, including risk factors, pathophysiologic findings, and responses to treatments. For fibromyalgia (FM), the most cohesive model centers on the disease’s genesis in the GI tract, resulting from overgrowth and/or imbalance of luminal bacteria. This short article will present gastrointestinal dysbiosis as the GUT – grand unified theory – of all aspects of fibromyalgia, based on previous and recent reviews by this author.1-5 The pathophysiology of FM is illustrated in Figure 1, and described in the sections that follow.




Patients with fibromyalgia have high rates of gastrointestinal dysbiosis in proportion to the severity of musculoskeletal pain.


Small intestine bacterial overgrowth (SIBO) – also referred to as “intestinal bacterial overgrowth” or simply “bacterial overgrowth” – provides the single best model for explaining the clinical and pathophysiological manifestations of FM, as well as irritable bowel syndrome (IBS). Although underappreciated by many clinicians, SIBO is common in clinical practice, affecting, for example, approximately 40% of patients with rheumatoid arthritis, 84% of patients with IBS, and 90-100% of patients with FM. In a study of 42 FM patients, all 42 patients showed laboratory evidence of SIBO, and the severity of the intestinal bacterial overgrowth correlated positively with the severity of the fibromyalgia, thus indicating the plausibility of a causal relationship.6

The links between FM and IBS are also strong; many IBS patients meet strict diagnostic criteria for FM, and many FM patients meet strict criteria for IBS. Lubrano et al7 showed that FM severity correlated with IBS severity among patients who met strict diagnostic criteria for both conditions. The high degree of overlap between these 2 diagnostic labels suggests that these conditions are 2 variations of a common pathophysiological process – SIBO.8 SIBO causes altered bowel function, immune activation, and visceral hypersensitivity, and it is the best causative explanation for the clinical and pathophysiological manifestations of IBS. For more details and citations, see the excellent review by Lin, published in JAMA in 2004.9 IBS is characterized by visceral hyperalgesia (hypersensitivity to pain), just as fibromyalgia is characterized by musculoskeletal hyperalgesia.

Given this strong evidence indicating that IBS is caused by SIBO and that IBS and FM are variations of the same pathophysiological process, it is reasonable to conclude that SIBO may cause FM. SIBO is highly prevalent in FM. Several studies6,10-13 have shown that 90-100% of fibromyalgia patients have evidence of SIBO; such relationships imply causality and must be integrated into any science-based model of fibromyalgia. As generally expected with GI dysbiosis, FM patients show evidence of increased intestinal permeability, so-called “leaky gut.”10

Successful treatments for GI dysbiosis include monotherapy with berberine from Berberis vulgaris14 and/or Origanum vulgare (emulsified oil of oregano, time-released for proper dispersion)15 and combined use of Artemisia dracunculus, Tinospora cordifolia, Equisetum arvense, Thymus vulgaris, Pau d’Arco, Anethum graveolens, Brucea javanica, Pulsatilla chinensis, Picrasma excelsa, Acacia catechu, Hedyotis diffusa, and Achillea millefolium.16

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The migraine-fibromyalgia protocol excerpted from Inflammation Mastery (PDF cover, PDF contents) has been developed and published since Dr Vasquez was professor of Orthopedics and Rheumatology at Bastyr University nearly 20 years ago. Since then, the protocol has been repeatedly verified and updated, including a commissioned continuing medical education (CME) monograph published by Institute for Functional Medicine in 2008. Dr Vasquez has presented this information to international audiences of healthcare providers and has published related information in journals such as Nature Reviews Rheumatology and Journal of the American Osteopathic Association.

The exact same migraine protocol is available in different formats, contexts, and under different titles, depending on whether you want 1) the entire protocol or just a smaller section, 2) migraine with fibromyalgia or just migraine alone, and 3) paper book or digital ebook:

  1. Inflammation Mastery 4th Edition: This is the complete protocol and context at 1,200 pages; also published separately as two volumes titled Textbook of Clinical Nutrition and Functional Medicine with Chapter 5 published as volume 2

  2. Pain Revolution in full-color, includes the protocols for migraine and fibromyalgia, since these conditions commonly occur together; available as paper book and digital ebook

  3. Brain Inflammation printed in discounted grayscale, ie, black and white; available as paper book and digital ebook

  4. Migraine and Headache Revolution: Digital ebook exclusively focused on migraine

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Inflammation Mastery 4th Edition (PDF cover, PDF contents) is the "master textbook" that details the functional inflammology protocol, described below. The full-color paper book is available for international shipping from ICHNFM.ORG while paper and digital versions are available from major bookstores such as (also in the UK and in Germany...) and Because the information in this book has already been time-proven via previous publications and extensive peer-review and thousands of citations to authoritative sources, it will not change nor be replaced in the foreseeable future. Any necessary updates will be provided by articles, videos, live webinars, and an extending separate "volume 3" described below.

Sample PDF downloads: ​


Contents: Preamble/Contextualization, Chapters/subsections

  1. Patient Assessments, Laboratory Interpretation, Clinical Concepts, Patient Management, Practice Management and Risk Reduction: This chapter introduces/reviews/updates patient assessments, laboratory interpretation, musculoskeletal emergencies, healthcare paradigms; the common and important conditions hemochromatosis and hypothyroidism are also included in this chapter since these need to be considered on a frequent basis in clinical practice 

  2. Wellness Promotion & Re-Establishing the Foundation for Health: Reviewed here are diet, lifestyle, psychosocial health, and—given the pervasiveness of persistent organic pollutants and their increasingly recognized clinical importance—an introduction to environmental medicine

  3. Basic Concepts and Therapeutics in (Nondrug) Musculoskeletal Care and Integrative Pain Management: Nonpharmacologic management of musculoskeletal problems is preferred over pharmacologic (e.g., NSAID, Coxib, steroid, opioid) management because of the collateral benefits, safety, and cost-effectiveness associated with manual, dietary, botanical, and nutritional treatments. A brief discussion of the current crisis in musculoskeletal medicine is provided for contextualization and emphasis of the importance of expanding clinicians' knowledge of effective nondrug treatments

  4. The Major Modifiable Factors in Sustained Inflammation: Major components of the “Functional Inflammology Protocol” are reviewed here, from concepts and molecular biology to an emphasis on practical clinical applications: A few sections have been printed separately and are thus linked

    1. Food & Basic Nutrition  307

    2. Infections: Dysbiosis / Viral Infections  396 / 540

    3. Nutritional Immunomodulation  609

    4. Dysmetabolism, Mitochondrial Dysfunction/ERS/UPR, and mTOR  622

    5. Special Considerations: Sleep, Sociopsychology, Stress, Surgery  674

    6. Endocrine Imbalances  688

    7. Xenobiotic Immunotoxicity  699

  5. Clinical Applications 

    1. Hypertension  727

    2. Diabetes Mellitus  819

    3. Migraine & Headaches  863 (also published separately)

    4. Fibromyalgia  901 (also published separately)

    5. Allergic Inflammation  984

    6. Rheumatoid Arthritis  1019

    7. Psoriasis and Psoriatic Arthritis  1038

    8. Systemic Lupus Erythematosus  1053

    9. Scleroderma & Systemic Sclerosis  1074

    10. Vasculitic Diseases  1094

    11. Spondyloarthropathies & Reactive Arthritis  1108

    12. Sjögren Syndrome/Disease  1119

    13. Raynaud's Syndrome/Phenomenon/Disorder  1127

    14. Clinical Notes on Additional Conditions: Behçet's Disease, Sarcoidosis, Dermatomyositis and Polymyositis  1131

  6. Index & Appendix (PDF)

Available in one large volume or 2 smaller volumes, in paper or digital ebook for phones, iPads, computers: ​

  • Same content either all together or in 2 volumes: Because Inflammation Mastery 4th Edition is large at nearly 1,200 pages and because the previous version of chapters 1-4 had been published as "volume 1" in 2004, the book was also published separately as two volumes titled Textbook of Clinical Nutrition and Functional Medicine; this was done at the request of the students who use the book in their classes and clinical work and also to respect those who had purchased the previous version of chapters 1-4 and who simply needed to add chapter 5, which is published as volume 2

  • Paper book version: The general consensus is that people learn information at a deeper level when they read paper books because they interact with the material physically, can take notes directly on the page, and can easily flip pages to see other related information.

  • Digital ebook version: The digital ebook version for example via Amazon's Kindle platform allows the owner to read the book on phone, iPad and computer and to make highlights and notes that are synchronized across all devices. The Kindle app is free; download a *free* sample of Inflammation Mastery 4th Edition here via the *free* Kindle software from Amazon.


News and updates: ​

  • Volume 3 which will focus exclusively on dysbiosis and the microbiome and its clinical implications and treatments will be published in 2018 or more likely 2019. The information in this new 3rd volume will be completely new, derived from Dr Vasquez's 30-hour video course Human Microbiome and Dysbiosis in Clinical Disease.

  • See smaller updates and news at Dr Alex Vasquez 's Inflammation Mastery on

Bulk discounts (orders of 5 or more books shipped to the same address) are available for students, book clubs, and study groups by emailing

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