Autoimmunity Unlocked

5 Keys to Transform Microbiome, Immune, and Digestive Health and Reclaim Your Life. A 5R+ Holistic System Encyclopedia with Tactics for Rheumatoid Arthritis, Lupus, and Crohn’s.

by Anar R Guliyev, M.D. www.autoimmunityunlocked.org

Appendix 2: References and Additional Reading

Hope in the Face of the Incurable
Immune System - The Good, the Bad, and the Ugly
- The Ugly: An Ailing Immune System
- The Good: The Holistic Way to Restore the Immune System
Key 1. Dysbiosis: Repopulate the Microbiome
Key 2. Inflammation: Reduce
Key 3. Leaky gut: Repair
Key 4. Lazy gut: Reawaken
Key 5. Factors Beyond Digestive Health: Recondition

Hope in the Face of the Incurable

Immune System - The Good, the Bad, and the Ugly

The Ugly: An Ailing Immune System

The Immune System and Cancer - An Inconspicuous Link

Ehrenfeld M. Autoimmune diseases and cancer. In: Anaya JM, Shoenfeld Y, Rojas-Villarraga A, et al., editors. Autoimmunity: From Bench to Bedside [Internet]. Bogota (Colombia): El Rosario University Press; 2013 Jul 18. Chapter 39. Available from: https://www.ncbi.nlm.nih.gov/books/NBK459441/
Isomäki, H. A., Hakulinen, T., & Joutsenlahti, U. (1978). Excess risk of lymphomas, leukemia and myeloma in patients with rheumatoid arthritis. Journal of chronic diseases, 31(11), 691–696. https://doi.org/10.1016/0021-9681(78)90071-1

Autoimmune Diseases - A Modern Epidemic

Lerner, A. , Jeremias, P. , & Matthias, T. (2015). The World Incidence and Prevalence of Autoimmune Diseases is Increasing. International Journal of Celiac Disease, 3(4), 151-155. http://pubs.sciepub.com/ijcd/3/4/8/#

Immune Illness On the Rise

Loh, W., & Tang, M. L. K. (2018). The Epidemiology of Food Allergy in the Global Context. International journal of environmental research and public health, 15(9), 2043. https://doi.org/10.3390/ijerph15092043
IDF Diabetes Atlas, 7th edn, International Diabetes Federation, 2015.
Burisch, J., Pedersen, N., Čuković-Čavka, S., Brinar, M., Kaimakliotis, I., Duricova, D., Shonová, O., Vind, I., Avnstrøm, S., Thorsgaard, N., Andersen, V., Krabbe, S., Dahlerup, J. F., Salupere, R., Nielsen, K. R., Olsen, J., Manninen, P., Collin, P., Tsianos, E. V., Katsanos, K. H., … EpiCom-group (2014). East-West gradient in the incidence of inflammatory bowel disease in Europe: the ECCO-EpiCom inception cohort. Gut, 63(4), 588–597. https://doi.org/10.1136/gutjnl-2013-304636
Prescott, S. L., Pawankar, R., Allen, K. J., Campbell, D. E., Sinn, J. K.h, Fiocchi, A., Ebisawa, M., Sampson, H. A., Beyer, K., & Lee, B. W. (2013). A global survey of changing patterns of food allergy burden in children. The World Allergy Organization journal, 6(1), 21. https://doi.org/10.1186/1939-4551-6-21
Platts-Mills T. A. (2015). The allergy epidemics: 1870-2010. The Journal of allergy and clinical immunology, 136(1), 3–13. https://doi.org/10.1016/j.jaci.2015.03.048
Weiss S. T. (2002). Eat dirt–the hygiene hypothesis and allergic diseases. The New England journal of medicine, 347(12), 930–931. https://doi.org/10.1056/NEJMe020092
Bach J. F. (2002). The effect of infections on susceptibility to autoimmune and allergic diseases. The New England journal of medicine, 347(12), 911–920. https://doi.org/10.1056/NEJMra020100
Jackson KD, Howie LD, Akinbami LJ. Trends in allergic conditions among children: United States, 1997–2011. NCHS data brief, no 121. Hyattsville, MD: National Center for Health Statistics. 2013. https://www.cdc.gov/nchs/data/databriefs/db121.pdf
Miller F. W. (2023). The increasing prevalence of autoimmunity and autoimmune diseases: an urgent call to action for improved understanding, diagnosis, treatment, and prevention. Current opinion in immunology, 80, 102266. https://doi.org/10.1016/j.coi.2022.102266

The Good: The Holistic Way to Restore the Immune System

DILL+: Locks and Vicious Cycles

Guerreiro, C. S., Calado, Â., Sousa, J., & Fonseca, J. E. (2018). Diet, Microbiota, and Gut Permeability-The Unknown Triad in Rheumatoid Arthritis. Frontiers in medicine, 5, 349. https://doi.org/10.3389/fmed.2018.00349

Key 1. Dysbiosis: Repopulate the Microbiome

Mills, S., Stanton, C., Lane, J. A., Smith, G. J., & Ross, R. P. (2019). Precision Nutrition and the Microbiome, Part I: Current State of the Science. Nutrients, 11(4), 923. https://doi.org/10.3390/nu11040923

The Last Discovered Organ That Reshapes Our Understanding of Health

Marchesi, J. R., & Ravel, J. (2015). The vocabulary of microbiome research: a proposal. Microbiome, 3, 31. https://doi.org/10.1186/s40168-015-0094-5
Appanna, V. D. (2023). Microbiomes and their functions: Why organisms need microbes. CRC Press.

Microbial Forces Within Us

Kho, Z. Y., & Lal, S. K. (2018). The Human Gut Microbiome - A Potential Controller of Wellness and Disease. Frontiers in microbiology, 9, 1835. https://doi.org/10.3389/fmicb.2018.01835
FAQ: Human Microbiome. Washington (DC): American Society for Microbiology; 2013. Available from: https://www.ncbi.nlm.nih.gov/books/NBK562894/ doi: 10.1128/AAMCol.1-2013
Dietert, R. (2017). The human superorganism: How the microbiome is revolutionizing the pursuit of a healthy life. New York: W.W. Norton & Company.
O’Connor, J. P., & Sulzer, J. A. (2023). The invisible us: The human microbiome in health and disease. Science Repository, 1(1), 1-12. https://www.sciencerepository.org/the-invisible-us-the-human-microbiome-in-health-and-disease

A Busy, Adaptable Organ

Pieter Van den Abbeele, Willy Verstraete, Sahar El Aidy, Annelies Geirnaert, Tom Van de Wiele (2013). Prebiotics, faecal transplants and microbial network units to stimulate biodiversity of the human gut microbiome. Science Repository https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/1751-7915.12049
Morowitz, M. J., Carlisle, E. M., & Alverdy, J. C. (2011). Contributions of intestinal bacteria to nutrition and metabolism in the critically ill. The Surgical clinics of North America, 91(4), 771–viii. https://doi.org/10.1016/j.suc.2011.05.001
Rowland, I., Gibson, G., Heinken, A., Scott, K., Swann, J., Thiele, I., & Tuohy, K. (2018). Gut microbiota functions: metabolism of nutrients and other food components. European journal of nutrition, 57(1), 1–24. https://doi.org/10.1007/s00394-017-1445-8
Rembacken, B. J., Snelling, A. M., Hawkey, P. M., Chalmers, D. M., & Axon, A. T. (1999). Non-pathogenic Escherichia coli versus mesalazine for the treatment of ulcerative colitis: a randomised trial. Lancet (London, England), 354(9179), 635–639. https://doi.org/10.1016/s0140-6736(98)06343-0
Proal, A. D., Albert, P. J., & Marshall, T. G. (2013). The human microbiome and autoimmunity. Current opinion in rheumatology, 25(2), 234–240. https://doi.org/10.1097/BOR.0b013e32835cedbf
Rembacken, B. J., Snelling, A. M., Hawkey, P. M., Chalmers, D. M., & Axon, A. T. (1999). Non-pathogenic Escherichia coli versus mesalazine for the treatment of ulcerative colitis: a randomised trial. Lancet (London, England), 354(9179), 635–639. https://doi.org/10.1016/s0140-6736(98)06343-0
De Luca, F., & Shoenfeld, Y. (2019). The microbiome in autoimmune diseases. Clinical and experimental immunology, 195(1), 74–85. https://doi.org/10.1111/cei.13158

Dimension 1: Microbiome Composition

Variety - Farmland vs Forest

Schnorr, S., Candela, M., Rampelli, S. et al. Gut microbiome of the Hadza hunter-gatherers. Nat Commun 5, 3654 (2014). https://doi.org/10.1038/ncomms4654
Conteville Liliane Costa, Oliveira-Ferreira Joseli, Vicente Ana Carolina Paulo (2019). Gut Microbiome Biomarkers and Functional Diversity Within an Amazonian Semi-Nomadic Hunter–Gatherer Group. Frontiers in Microbiology 2019-10. doi: 10.3389/fmicb.2019.01743 https://www.frontiersin.org/articles/10.3389/fmicb.2019.01743/full

Actively Repopulate

Building a Healthy Community

Spiller R. (2008). Review article: probiotics and prebiotics in irritable bowel syndrome. Alimentary pharmacology & therapeutics, 28(4), 385–396. https://pubmed.ncbi.nlm.nih.gov/18532993/
Sanders M. E. (2011). Impact of probiotics on colonizing microbiota of the gut. Journal of clinical gastroenterology, 45 Suppl, S115–S119. https://doi.org/10.1097/MCG.0b013e318227414a

Probiotics

M. Andrea Azcarate-Peril, Roland R. Arnold, José M. Bruno-Bárcena. (2019). How Fermented Foods Feed a Healthy Gut Microbiota. A Nutrition Continuum. (ISBN: 978-3-030-28737-5). https://link.springer.com/book/10.1007/978-3-030-28737-5
Marteau, P. R., de Vrese, M., Cellier, C. J., & Schrezenmeir, J. (2001). Protection from gastrointestinal diseases with the use of probiotics. The American journal of clinical nutrition, 73(2 Suppl), 430S–436S. https://doi.org/10.1093/ajcn/73.2.430s
Massimo Campieri, Paolo Gionchetti (1999). Probiotics in inflammatory bowel disease: New insight to pathogenesis or a possible therapeutic alternative? Gastroenterology 1999;116:1246-1249 https://doi.org/10.1016/S0016-5085(99)70029-6
Schultz, M., & Sartor, R. B. (2000). Probiotics and inflammatory bowel diseases. The American journal of gastroenterology, 95(1 Suppl), S19–S21. https://doi.org/10.1016/s0002-9270(99)00812-6
Richards, J. L., Yap, Y. A., McLeod, K. H., Mackay, C. R., & Mariño, E. (2016). Dietary metabolites and the gut microbiota: an alternative approach to control inflammatory and autoimmune diseases. Clinical & translational immunology, 5(5), e82. https://doi.org/10.1038/cti.2016.29
Narges Dargahi, Joshua Johnson, Osaana Donkor, Todor Vasiljevic, Vasso Apostolopoulos (2019). Immunomodulatory effects of probiotics: Can they be used to treat allergies and autoimmune diseases? Maturitas, Volume 119, 2019, Pages 25-38, ISSN 0378-5122, https://www.sciencedirect.com/science/article/pii/S0378512218305528
Suez, J., Zmora, N., Zilberman-Schapira, G., Mor, U., Dori-Bachash, M., Bashiardes, S., Zur, M., Regev-Lehavi, D., Ben-Zeev Brik, R., Federici, S., Horn, M., Cohen, Y., Moor, A. E., Zeevi, D., Korem, T., Kotler, E., Harmelin, A., Itzkovitz, S., Maharshak, N., Shibolet, O., … Elinav, E. (2018). Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT. Cell, 174(6), 1406–1423.e16. https://doi.org/10.1016/j.cell.2018.08.047
Wastyk, H. C., Perelman, D., Topf, M., Fragiadakis, G. K., Robinson, J. L., Sonnenburg, J. L., Gardner, C. D., & Sonnenburg, E. D. (2023). Randomized controlled trial demonstrates response to a probiotic intervention for metabolic syndrome that may correspond to diet. Gut microbes, 15(1), 2178794. https://doi.org/10.1080/19490976.2023.2178794
Farnworth, E. R. (Ed.). (2008). Handbook of fermented functional foods. CRC Press.

Fermented Vegetables and Pickles

Arasu, M.V., Al-Dhabi, N.A., Rejiniemon, T.S. et al. Identification and Characterization of Lactobacillus brevis P68 with Antifungal, Antioxidant and Probiotic Functional Properties. Indian J Microbiol 55, 19–28 (2015). https://doi.org/10.1007/s12088-014-0495-3
Parvez, S., Malik, K., Ah Kang, S. and Kim, H.-Y. (2006), Probiotics and their fermented food products are beneficial for health. Journal of Applied Microbiology, 100: 1171-1185. https://doi.org/10.1111/j.1365-2672.2006.02963.x
Sudhanshu S. Behera, Aly Farag El Sheikha, Riadh Hammami, Awanish Kumar (2020). Traditionally fermented pickles: How the microbial diversity associated with their nutritional and health benefits? Journal of Functional Foods, Volume 70, 2020, 103971, ISSN 1756-4646, https://www.sciencedirect.com/science/article/pii/S175646462030195X

Fermented Dairy

Leeuwendaal, N. K., Stanton, C., O’Toole, P. W., & Beresford, T. P. (2022). Fermented Foods, Health and the Gut Microbiome. Nutrients, 14(7), 1527. https://doi.org/10.3390/nu14071527
Shiby, V. K., & Mishra, H. N. (2013). Fermented milks and milk products as functional foods–a review. Critical reviews in food science and nutrition, 53(5), 482–496. https://doi.org/10.1080/10408398.2010.547398
Nakazawa, Y., & Hosono, A. (1992). Functions of fermented milk: Challenges for the health sciences. Elsevier Science & Technology. https://www.cabdirect.org/cabdirect/abstract/19920455311
Mani-López, E., Palou, E., & López-Malo, A. (2014). Probiotic viability and storage stability of yogurts and fermented milks prepared with several mixtures of lactic acid bacteria. Journal of dairy science, 97(5), 2578–2590. https://doi.org/10.3168/jds.2013-7551

Cheese

Homayouni Aziz , Ansari Fereshteh , Azizi Aslan , Pourjafar Hadi *, Madadi Masuod (2020). Cheese as a Potential Food Carrier to Deliver Probiotic Microorganisms into the Human Gut: A Review, Current Nutrition & Food Science 2020; 16(1) . https://dx.doi.org/10.2174/1573401314666180817101526

Fecal Microbial Transplantation: Success or Temporary Fix?

Stripling, J., & Rodriguez, M. (2018). Current Evidence in Delivery and Therapeutic Uses of Fecal Microbiota Transplantation in Human Diseases-Clostridium difficile Disease and Beyond. The American journal of the medical sciences, 356(5), 424–432. https://doi.org/10.1016/j.amjms.2018.08.010
Han-Wen Kuo, Wang-Hsien Ding (2004). Trace determination of bisphenol A and phytoestrogens in infant formula powders by gas chromatography–mass spectrometry. Journal of Chromatography A, Volume 1027, Issues 1–2, 2004, Pages 67-74, ISSN 0021-9673. https://www.sciencedirect.com/science/article/abs/pii/S0021967303016261

Feeding your Allies

Tuohy, K. M., Conterno, L., Gasperotti, M., & Viola, R. (2012). Up-regulating the human intestinal microbiome using whole plant foods, polyphenols, and/or fiber. Journal of agricultural and food chemistry, 60(36), 8776–8782. https://doi.org/10.1021/jf2053959

Prebiotics

Holscher H. D. (2017). Dietary fiber and prebiotics and the gastrointestinal microbiota. Gut microbes, 8(2), 172–184. https://doi.org/10.1080/19490976.2017.1290756

Dead or Alive - Enzymes in Your Food

Carmody, R. N., Bisanz, J. E., Bowen, B. P., Maurice, C. F., Lyalina, S., Louie, K. B., Treen, D., Chadaideh, K. S., Maini Rekdal, V., Bess, E. N., Spanogiannopoulos, P., Ang, Q. Y., Bauer, K. C., Balon, T. W., Pollard, K. S., Northen, T. R., & Turnbaugh, P. J. (2019). Cooking shapes the structure and function of the gut microbiome. Nature microbiology, 4(12), 2052–2063. https://doi.org/10.1038/s41564-019-0569-4

Frozen, Dried, Salted - Preserving Raw Produce

Sarron, E., Gadonna-Widehem, P., & Aussenac, T. (2021). Ozone Treatments for Preserving Fresh Vegetables Quality: A Critical Review. Foods (Basel, Switzerland), 10(3), 605. https://doi.org/10.3390/foods10030605

Polyphenols: The Colorful Path to a Diverse Microbiome

Kumar Singh, A., Cabral, C., Kumar, R., Ganguly, R., Kumar Rana, H., Gupta, A., Rosaria Lauro, M., Carbone, C., Reis, F., & Pandey, A. K. (2019). Beneficial Effects of Dietary Polyphenols on Gut Microbiota and Strategies to Improve Delivery Efficiency. Nutrients, 11(9), 2216. https://doi.org/10.3390/nu11092216
Oliveira, A. L. B., Monteiro, V. V. S., Navegantes-Lima, K. C., Reis, J. F., Gomes, R. S., Rodrigues, D. V. S., Gaspar, S. L. F., & Monteiro, M. C. (2017). Resveratrol Role in Autoimmune Disease-A Mini-Review. Nutrients, 9(12), 1306. https://doi.org/10.3390/nu9121306
Fernando Cardona, Cristina Andrés-Lacueva, Sara Tulipani, Francisco J. Tinahones, María Isabel Queipo-Ortuño (2013). Benefits of polyphenols on gut microbiota and implications in human health. The Journal of Nutritional Biochemistry, Volume 24, Issue 8, 2013, Pages 1415-1422, ISSN 0955-2863, https://doi.org/10.1016/j.jnutbio.2013.05.001
Gunathilake, K. D. P. P., Ranaweera, K. K. D. S., & Rupasinghe, H. P. V. (2018). Effect of Different Cooking Methods on Polyphenols, Carotenoids and Antioxidant Activities of Selected Edible Leaves. Antioxidants (Basel, Switzerland), 7(9), 117. https://doi.org/10.3390/antiox7090117
Manach, C., Scalbert, A., Morand, C., Rémésy, C., & Jiménez, L. (2004). Polyphenols: food sources and bioavailability. The American journal of clinical nutrition, 79(5), 727–747. https://doi.org/10.1093/ajcn/79.5.727

Vitamin K

Ellis, J. L., Karl, J. P., Oliverio, A. M., Fu, X., Soares, J. W., Wolfe, B. E., Hernandez, C. J., Mason, J. B., & Booth, S. L. (2021). Dietary vitamin K is remodeled by gut microbiota and influences community composition. Gut microbes, 13(1), 1–16. https://doi.org/10.1080/19490976.2021.1887721
Lai, Y., Masatoshi, H., Ma, Y., Guo, Y., & Zhang, B. (2022). Role of Vitamin K in Intestinal Health. Frontiers in immunology, 12, 791565. https://doi.org/10.3389/fimmu.2021.791565
Mathers, J., Fernandez, F., Hill, M., McCarthy, P., Shearer, M., & Oxley, A. (1990). Dietary modification of potential vitamin K supply from enteric bacterial menaquinones in rats. British Journal of Nutrition, 63(3), 639-652. doi:10.1079/BJN19900150 https://www.cambridge.org/core/journals/british-journal-of-nutrition/article/dietary-modification-of-potential-vitamin-k-supply-from-enteric-bacterial-menaquinones-in-rats/AEB49A361AC03D5F80B952B34C4D6F94
Zhang Y., Ma C., Zhao J., Xu H., Hou Q., Zhang H. Lactobacillus casei Zhang and vitamin K2 prevent intestinal tumorigenesis in mice via adiponectin-elevated different signaling pathways. Oncotarget. 2017; 8: 24719-24727. Retrieved from https://www.oncotarget.com/article/15791/text/
van Ballegooijen, A. J., Pilz, S., Tomaschitz, A., Grübler, M. R., & Verheyen, N. (2017). The Synergistic Interplay between Vitamins D and K for Bone and Cardiovascular Health: A Narrative Review. International journal of endocrinology, 2017, 7454376. https://doi.org/10.1155/2017/7454376

The Myth of Healthy Toppings on Junk Food

Kaczmarek, J. L., Liu, X., Charron, C. S., Novotny, J. A., Jeffery, E. H., Seifried, H. E., Ross, S. A., Miller, M. J., Swanson, K. S., & Holscher, H. D. (2019). Broccoli consumption affects the human gastrointestinal microbiota. The Journal of nutritional biochemistry, 63, 27–34. https://doi.org/10.1016/j.jnutbio.2018.09.015
Shahinozzaman, M.; Raychaudhuri, S.; Fan, S.; Obanda, D.N. (2021). Kale Attenuates Inflammation and Modulates Gut Microbial Composition and Function in C57BL/6J Mice with Diet-Induced Obesity. Microorganisms 2021, 9, 238. https://doi.org/10.3390/microorganisms9020238
Turner, Alexandria, Chijoff, Eileen, Veysey, Martin, Keely, Simon, Scarlett, Christopher J., Lucock, Mark, and Beckett, Emma L. (2019). Interactions between taste receptors and the gastrointestinal microbiome in inflammatory bowel disease. Journal of Nutrition and Intermediary Metabolism 18 100106 100106. https://doi.org/10.1016/j.jnim.2019.100106
Guo, S., Geng, W., Chen, S., Wang, L., Rong, X., Wang, S., Wang, T., Xiong, L., Huang, J., Pang, X., & Lu, Y. (2021). Ginger Alleviates DSS-Induced Ulcerative Colitis Severity by Improving the Diversity and Function of Gut Microbiota. Frontiers in pharmacology, 12, 632569. https://doi.org/10.3389/fphar.2021.632569
Anna Prizment, Timothy R. Church, Dorothy Hatsukami, Robert Madoff, Christopher Staley, Robert J. Straka, Allison Iwan, Jenn Stromberg, Ya-Feng Wen, Cheryl Stibbe, Marie Rahne; (2020). Abstract A26: Pilot trial to examine the effect of ginger on the gut microbiome: The Minnesota Cancer Clinical Trials Network. Cancer Epidemiol Biomarkers Prev 1 September 2020; 29 (9_Supplement): A26. https://doi.org/10.1158/1538-7755.MODPOP19-A26

Food Diversity

Heiman, M. L., & Greenway, F. L. (2016). A healthy gastrointestinal microbiome is dependent on dietary diversity. Molecular metabolism, 5(5), 317–320. https://doi.org/10.1016/j.molmet.2016.02.005
https://thefuturemarket.com/biodiversity
FAO: What is Happening to Agrobiodiversity? https://www.fao.org/3/y5609e/y5609e02.htm#bm2

Dimension 2: Microbiome Distribution

Dieterich, W., Schink, M., & Zopf, Y. (2018). Microbiota in the Gastrointestinal Tract. Medical sciences (Basel, Switzerland), 6(4), 116. https://doi.org/10.3390/medsci6040116
Sekirov, I., Russell, S. L., Antunes, L. C., & Finlay, B. B. (2010). Gut microbiota in health and disease. Physiological reviews, 90(3), 859–904. https://doi.org/10.1152/physrev.00045.2009

SIBO, IBS, IBD, Ulcers: Many Faces of Microbiome Maldistribution

Small Intestinal Bacterial Overgrowth (SIBO)

Sachdev, A. H., & Pimentel, M. (2013). Gastrointestinal bacterial overgrowth: pathogenesis and clinical significance. Therapeutic advances in chronic disease, 4(5), 223–231. https://doi.org/10.1177/2040622313496126
Roland, B. C., Ciarleglio, M. M., Clarke, J. O., Semler, J. R., Tomakin, E., Mullin, G. E., & Pasricha, P. J. (2015). Small Intestinal Transit Time Is Delayed in Small Intestinal Bacterial Overgrowth. Journal of clinical gastroenterology, 49(7), 571–576. https://doi.org/10.1097/MCG.0000000000000257

Below the Waterline: Subclinical SIBO

Khoshini, R., Dai, S. C., Lezcano, S., & Pimentel, M. (2008). A systematic review of diagnostic tests for small intestinal bacterial overgrowth. Digestive diseases and sciences, 53(6), 1443–1454. https://doi.org/10.1007/s10620-007-0065-1

Ulcers and Helicobacter pylori

Bruno, G., Rocco, G., Zaccari, P., Porowska, B., Mascellino, M. T., & Severi, C. (2018). Helicobacter pylori Infection and Gastric Dysbiosis: Can Probiotics Administration Be Useful to Treat This Condition?. The Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale, 2018, 6237239. https://doi.org/10.1155/2018/6237239
Zhang, L., Zhao, M., & Fu, X. (2023). Gastric microbiota dysbiosis and Helicobacter pylori infection. Frontiers in microbiology, 14, 1153269. https://doi.org/10.3389/fmicb.2023.1153269

Healthy Digestion to Fix Microbiota Distribution

Don’t Rush the Reactor

Surgical Procedures to Avoid

Dolan, R. D., Baker, J., Harer, K., Lee, A., Hasler, W., Saad, R., & Schulman, A. R. (2021). Small Intestinal Bacterial Overgrowth: Clinical Presentation in Patients with Roux-en-Y Gastric Bypass. Obesity surgery, 31(2), 564–569. https://doi.org/10.1007/s11695-020-05032-y
Sabate, J. M., Coupaye, M., Ledoux, S., Castel, B., Msika, S., Coffin, B., & Jouet, P. (2017). Consequences of Small Intestinal Bacterial Overgrowth in Obese Patients Before and After Bariatric Surgery. Obesity surgery, 27(3), 599–605. https://doi.org/10.1007/s11695-016-2343-5

Stomach Acid

Acid - The Protective Firewall

Beasley, D. E., Koltz, A. M., Lambert, J. E., Fierer, N., & Dunn, R. R. (2015). The Evolution of Stomach Acidity and Its Relevance to the Human Microbiome. PloS one, 10(7), e0134116. https://doi.org/10.1371/journal.pone.0134116
Martinsen, T. C., Fossmark, R., & Waldum, H. L. (2019). The Phylogeny and Biological Function of Gastric Juice-Microbiological Consequences of Removing Gastric Acid. International journal of molecular sciences, 20(23), 6031. https://doi.org/10.3390/ijms20236031

Antacids and “Heartburn” (Gastroesophageal Reflux)

Theisen, J., Nehra, D., Citron, D., Johansson, J., Hagen, J. A., Crookes, P. F., DeMeester, S. R., Bremner, C. G., DeMeester, T. R., & Peters, J. H. (2000). Suppression of gastric acid secretion in patients with gastroesophageal reflux disease results in gastric bacterial overgrowth and deconjugation of bile acids. Journal of gastrointestinal surgery: official journal of the Society for Surgery of the Alimentary Tract, 4(1), 50–54. https://doi.org/10.1016/s1091-255x(00)80032-3

Bile and Liver Health

Sun, R., Xu, C., Feng, B., Gao, X., & Liu, Z. (2021). Critical roles of bile acids in regulating intestinal mucosal immune responses. Therapeutic advances in gastroenterology, 14, 17562848211018098. https://doi.org/10.1177/17562848211018098
Vijayvargiya, P., Busciglio, I., Burton, D., Donato, L., Lueke, A., & Camilleri, M. (2018). Bile Acid Deficiency in a Subgroup of Patients With Irritable Bowel Syndrome With Constipation Based on Biomarkers in Serum and Fecal Samples. Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association, 16(4), 522–527. https://doi.org/10.1016/j.cgh.2017.06.039

Bile Salt Malabsorption and the Microbiome

Ridlon, J. M., Kang, D. J., Hylemon, P. B., & Bajaj, J. S. (2014). Bile acids and the gut microbiome. Current opinion in gastroenterology, 30(3), 332–338. https://doi.org/10.1097/MOG.0000000000000057
Sagar, N. M., Duboc, H., Kay, G. L., Alam, M. T., Wicaksono, A. N., Covington, J. A., Quince, C., Kokkorou, M., Svolos, V., Palmieri, L. J., Gerasimidis, K., Walters, J. R. F., & Arasaradnam, R. P. (2020). The pathophysiology of bile acid diarrhoea: differences in the colonic microbiome, metabolome and bile acids. Scientific reports, 10(1), 20436. https://doi.org/10.1038/s41598-020-77374-7
Guzior, D. V., & Quinn, R. A. (2021). Review: microbial transformations of human bile acids. Microbiome, 9(1), 140. https://doi.org/10.1186/s40168-021-01101-1

Helping Your Liver

Reduce Toxic Load

Bataller, R., Arab, J. P., & Shah, V. H. (2022). Alcohol-Associated Hepatitis. The New England journal of medicine, 387(26), 2436–2448. https://doi.org/10.1056/NEJMra2207599

Hepatoprotective Food

Iahtisham-Ul-Haq, Butt, M. S., Randhawa, M. A., & Shahid, M. (2019). Hepatoprotective effects of red beetroot-based beverages against CCl4 -induced hepatic stress in Sprague Dawley rats. Journal of food biochemistry, 43(12), e13057. https://doi.org/10.1111/jfbc.13057
Madrigal-Santillán, E., Madrigal-Bujaidar, E., Álvarez-González, I., Sumaya-Martínez, M. T., Gutiérrez-Salinas, J., Bautista, M., Morales-González, Á., García-Luna y González-Rubio, M., Aguilar-Faisal, J. L., & Morales-González, J. A. (2014). Review of natural products with hepatoprotective effects. World journal of gastroenterology, 20(40), 14787–14804. https://doi.org/10.3748/wjg.v20.i40.14787

Glutathione

Fidelus, R. K., & Tsan, M. F. (1987). Glutathione and lymphocyte activation: a function of ageing and auto-immune disease. Immunology, 61(4), 503–508. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1453448/
Perricone, C., De Carolis, C., & Perricone, R. (2009). Glutathione: a key player in autoimmunity. Autoimmunity reviews, 8(8), 697–701. https://doi.org/10.1016/j.autrev.2009.02.020
Hassan, M. Q., Hadi, R. A., Al-Rawi, Z. S., Padron, V. A., & Stohs, S. J. (2001). The glutathione defense system in the pathogenesis of rheumatoid arthritis. Journal of applied toxicology : JAT, 21(1), 69–73. https://doi.org/10.1002/jat.736

Other Tactics for Fixing SIBO and Normalizing Microbiome Distribution

Power of Herbs, Spices, and Other Foods to Control Microbial Growth

Dahl, S. M., Rolfe, V., Walton, G. E., & Gibson, G. R. (2023). Gut microbial modulation by culinary herbs and spices. Food chemistry, 409, 135286. https://doi.org/10.1016/j.foodchem.2022.135286

Spices to Avoid

Xiang, Q., Tang, X., Cui, S., Zhang, Q., Liu, X., Zhao, J., Zhang, H., Mao, B., & Chen, W. (2022). Capsaicin, the Spicy Ingredient of Chili Peppers: Effects on Gastrointestinal Tract and Composition of Gut Microbiota at Various Dosages. Foods (Basel, Switzerland), 11(5), 686. https://doi.org/10.3390/foods11050686
Kimball, E. S., Palmer, J. M., D’Andrea, M. R., Hornby, P. J., & Wade, P. R. (2005). Acute colitis induction by oil of mustard results in later development of an IBS-like accelerated upper GI transit in mice. American journal of physiology. Gastrointestinal and liver physiology, 288(6), G1266–G1273. https://doi.org/10.1152/ajpgi.00444.2004

Antimicrobial Herbs and Spices

Olivier, Rachel. (2013). Select herbals proposed as beneficial in the eradication of small intestinal bacterial overgrowth. The Original Internist, March 2013 20(1):30-38.
Delaquis, P. J., Stanich, K., Girard, B., & Mazza, G. (2002). Antimicrobial activity of individual and mixed fractions of dill, cilantro, coriander and eucalyptus essential oils. International journal of food microbiology, 74(1-2), 101–109. https://doi.org/10.1016/s0168-1605(01)00734-6
Han, J., Lin, H., & Huang, W. (2011). Modulating gut microbiota as an anti-diabetic mechanism of berberine. Medical science monitor : international medical journal of experimental and clinical research, 17(7), RA164–RA167. https://doi.org/10.12659/msm.881842
Joshi, P. V., Shirkhedkar, A. A., Prakash, K., & Maheshwari, V. L. (2011). Antidiarrheal activity, chemical and toxicity profile of Berberis aristata. Pharmaceutical biology, 49(1), 94–100. https://doi.org/10.3109/13880209.2010.500295
Arcila-Lozano, C. C., Loarca-Piña, G., Lecona-Uribe, S., & González de Mejía, E. (2004). El orégano: propiedades, composición y actividad biológica de sus componentes [Oregano: properties, composition and biological activity]. Archivos latinoamericanos de nutricion, 54(1), 100–111. https://pubmed.ncbi.nlm.nih.gov/15332363/
Saeed, S., & Tariq, P. (2009). Antibacterial activity of oregano (Origanum vulgare Linn.) against gram positive bacteria. Pakistan journal of pharmaceutical sciences, 22(4), 421–424. https://pubmed.ncbi.nlm.nih.gov/19783523/
Zarringhalam, M., Zaringhalam, J., Shadnoush, M., Safaeyan, F., & Tekieh, E. (2013). Inhibitory Effect of Black and Red Pepper and Thyme Extracts and Essential Oils on Enterohemorrhagic Escherichia coli and DNase Activity of Staphylococcus aureus. Iranian journal of pharmaceutical research : IJPR, 12(3), 363–369. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813290/
Esmaeili, D., Mobarez, A. M., & Tohidpour, A. (2012). Anti-helicobacter pylori activities of shoya powder and essential oils of thymus vulgaris and eucalyptus globulus. The open microbiology journal, 6, 65–69. https://doi.org/10.2174/1874285801206010065
Sahib A. S. (2013). Treatment of irritable bowel syndrome using a selected herbal combination of Iraqi folk medicines. Journal of ethnopharmacology, 148(3), 1008–1012. https://doi.org/10.1016/j.jep.2013.05.034
Ng, S. C., Lam, Y. T., Tsoi, K. K., Chan, F. K., Sung, J. J., & Wu, J. C. (2013). Systematic review: the efficacy of herbal therapy in inflammatory bowel disease. Alimentary pharmacology & therapeutics, 38(8), 854–863. https://doi.org/10.1111/apt.12464
Triantafyllidi, A., Xanthos, T., Papalois, A., & Triantafillidis, J. K. (2015). Herbal and plant therapy in patients with inflammatory bowel disease. Annals of gastroenterology, 28(2), 210–220. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4367210/
Omer, B., Krebs, S., Omer, H., & Noor, T. O. (2007). Steroid-sparing effect of wormwood (Artemisia absinthium) in Crohn’s disease: a double-blind placebo-controlled study. Phytomedicine : international journal of phytotherapy and phytopharmacology, 14(2-3), 87–95. https://doi.org/10.1016/j.phymed.2007.01.001
Chedid, V., Dhalla, S., Clarke, J. O., Roland, B. C., Dunbar, K. B., Koh, J., Justino, E., Tomakin, E., & Mullin, G. E. (2014). Herbal therapy is equivalent to rifaximin for the treatment of small intestinal bacterial overgrowth. Global advances in health and medicine, 3(3), 16–24. https://doi.org/10.7453/gahmj.2014.019
Anand, U., Jacobo-Herrera, N., Altemimi, A., & Lakhssassi, N. (2019). A Comprehensive Review on Medicinal Plants as Antimicrobial Therapeutics: Potential Avenues of Biocompatible Drug Discovery. Metabolites, 9(11), 258. https://doi.org/10.3390/metabo9110258

N-Acetylcysteine (NAC)

Walker, A. W., & Lawley, T. D. (2013). Therapeutic modulation of intestinal dysbiosis. Pharmacological research, 69(1), 75–86. https://doi.org/10.1016/j.phrs.2012.09.008
Dinicola, S., De Grazia, S., Carlomagno, G., & Pintucci, J. P. (2014). N-acetylcysteine as powerful molecule to destroy bacterial biofilms. A systematic review. European review for medical and pharmacological sciences, 18(19), 2942–2948. https://pubmed.ncbi.nlm.nih.gov/25339490/

Fungi: Mold and Yeast

Addressing the SIFO Problem

Lange J. H. (2004). Endotoxin as a factor for joint pain and rheumatoid arthritis. Clinical rheumatology, 23(6), 566–567. https://doi.org/10.1007/s10067-004-0947-y
Gray, M. R., Thrasher, J. D., Crago, R., Madison, R. A., Arnold, L., Campbell, A. W., & Vojdani, A. (2003). Mixed mold mycotoxicosis: immunological changes in humans following exposure in water-damaged buildings. Archives of environmental health, 58(7), 410–420. https://doi.org/10.1080/00039896.2003.11879142
Jahreis, S., Kuhn, S., Madaj, A. M., Bauer, M., & Polte, T. (2017). Mold metabolites drive rheumatoid arthritis in mice via promotion of IFN-gamma- and IL-17-producing T cells. Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association, 109(Pt 1), 405–413. https://doi.org/10.1016/j.fct.2017.09.027
Lieberman, A., & Curtis, L. (2020). Mold Exposure and Mitochondrial Antibodies. Alternative therapies in health and medicine, 26(6), 44–47.

Feeding Your Enemies

Sweet Does Not Equal Good

Sugar

Satokari R. (2020). High Intake of Sugar and the Balance between Pro- and Anti-Inflammatory Gut Bacteria. Nutrients, 12(5), 1348. https://doi.org/10.3390/nu12051348
Weissmann, Gerald. (2006). Is Sugar the Missing Link in RA?. Internal Medicine News. 39. 11. 10.1016/S1097-8690(06)74010-0.

Natural Sweeteners

Sheldon, M., Klyza, J., & Zimeri, A. M. (2019). Pesticide Contamination in Central Kentucky Urban Honey: A Pilot Study. Journal of Environmental Health, 82(1), 8–13. https://www.jstor.org/stable/26726953
Bezirtzoglou E, Voidarou C, Stavropoulou E, et al. Emerging antibiotic resistance in honey as a hazard for human health. J Bacteriol Mycol Open Access. 2016;2(1):6-12. DOI: 10.15406/jbmoa.2016.02.00012
A. Baggio , A. Gallina , C. Benetti & F. Mutinelli (2009) Residues of antibacterial drugs in honey from the Italian market, Food Additives & Contaminants: Part B, 2:1, 52-58, DOI: 10.1080/02652030902897721

Unnatural Sweeteners

Ruiz-Ojeda, F. J., Plaza-Díaz, J., Sáez-Lara, M. J., & Gil, A. (2019). Effects of Sweeteners on the Gut Microbiota: A Review of Experimental Studies and Clinical Trials. Advances in nutrition (Bethesda, Md.), 10(suppl_1), S31–S48. https://doi.org/10.1093/advances/nmy037
Shil, A., & Chichger, H. (2021). Artificial Sweeteners Negatively Regulate Pathogenic Characteristics of Two Model Gut Bacteria, E. coli and E. faecalis. International journal of molecular sciences, 22(10), 5228. https://doi.org/10.3390/ijms22105228
Suez, J., Korem, T., Zeevi, D., Zilberman-Schapira, G., Thaiss, C. A., Maza, O., Israeli, D., Zmora, N., Gilad, S., Weinberger, A., Kuperman, Y., Harmelin, A., Kolodkin-Gal, I., Shapiro, H., Halpern, Z., Segal, E., & Elinav, E. (2014). Artificial sweeteners induce glucose intolerance by altering the gut microbiota. Nature, 514(7521), 181–186. https://doi.org/10.1038/nature13793
Czarnecka, K., Pilarz, A., Rogut, A., Maj, P., Szymańska, J., Olejnik, Ł., & Szymański, P. (2021). Aspartame-True or False? Narrative Review of Safety Analysis of General Use in Products. Nutrients, 13(6), 1957. https://doi.org/10.3390/nu13061957
Chi, L., Bian, X., Gao, B., Tu, P., Lai, Y., Ru, H., & Lu, K. (2018). Effects of the Artificial Sweetener Neotame on the Gut Microbiome and Fecal Metabolites in Mice. Molecules (Basel, Switzerland), 23(2), 367. https://doi.org/10.3390/molecules23020367

Conquering Sugar Cravings

Good Options for Sweet Cravings

Pourmasoumi, M., Ghiasvand, R., Darvishi, L., Hadi, A., Bahreini, N., & Keshavarzpour, Z. (2019). Comparison and Assessment of Flixweed and Fig Effects on Irritable Bowel Syndrome with Predominant Constipation: A Single-Blind Randomized Clinical Trial. Explore (New York, N.Y.), 15(3), 198–205. https://doi.org/10.1016/j.explore.2018.09.003

Children’s Foods - Passing the Problem to the Next Generation

Allergy Statistics and Facts https://www.webmd.com/allergies/allergy-statistics
Zablotsky, B., Black, L. I., & Akinbami, L. J. (2023). Diagnosed Allergic Conditions in Children Aged 0-17 Years: United States, 2021. NCHS data brief, (459), 1–8. https://www.cdc.gov/nchs/data/databriefs/db459.pdf

Other Risks to Your Microbiome Health

Inflammation

Al Bander, Z., Nitert, M. D., Mousa, A., & Naderpoor, N. (2020). The Gut Microbiota and Inflammation: An Overview. International journal of environmental research and public health, 17(20), 7618. https://doi.org/10.3390/ijerph17207618

Antibiotics

Antibiotics Residues in Food

Franco, D. A., Webb, J., & Taylor, C. E. (1990). Antibiotic and Sulfonamide Residues in Meat: Implications for Human Health. Journal of food protection, 53(2), 178–185. https://doi.org/10.4315/0362-028X-53.2.178
Ramatla, T., Ngoma, L., Adetunji, M., & Mwanza, M. (2017). Evaluation of Antibiotic Residues in Raw Meat Using Different Analytical Methods. Antibiotics (Basel, Switzerland), 6(4), 34. https://doi.org/10.3390/antibiotics6040034
Price, L. B., Rogers, L., & Lo, K. (2022). Policy reforms for antibiotic use claims in livestock. Science (New York, N.Y.), 376(6589), 130–132. https://doi.org/10.1126/science.abj1823
Treiber, F. M., & Beranek-Knauer, H. (2021). Antimicrobial Residues in Food from Animal Origin-A Review of the Literature Focusing on Products Collected in Stores and Markets Worldwide. Antibiotics (Basel, Switzerland), 10(5), 534. https://doi.org/10.3390/antibiotics10050534
Van Boeckel, T. P., Brower, C., Gilbert, M., Grenfell, B. T., Levin, S. A., Robinson, T. P., Teillant, A., & Laxminarayan, R. (2015). Global trends in antimicrobial use in food animals. Proceedings of the National Academy of Sciences of the United States of America, 112(18), 5649–5654. https://doi.org/10.1073/pnas.1503141112

Antibiotics’ Effect on the Microbiota of Animal Products

White, D. G., Zhao, S., Sudler, R., Ayers, S., Friedman, S., Chen, S., McDermott, P. F., McDermott, S., Wagner, D. D., & Meng, J. (2001). The isolation of antibiotic-resistant salmonella from retail ground meats. The New England journal of medicine, 345(16), 1147–1154. https://doi.org/10.1056/NEJMoa010315
Manyi-Loh, C., Mamphweli, S., Meyer, E., & Okoh, A. (2018). Antibiotic Use in Agriculture and Its Consequential Resistance in Environmental Sources: Potential Public Health Implications. Molecules (Basel, Switzerland), 23(4), 795. https://doi.org/10.3390/molecules23040795
Butaye, P., Devriese, L. A., & Haesebrouck, F. (2003). Antimicrobial growth promoters used in animal feed: effects of less well known antibiotics on gram-positive bacteria. Clinical microbiology reviews, 16(2), 175–188. https://doi.org/10.1128/CMR.16.2.175-188.2003

Navigating Animal Products

Van Boeckel, T. P., Brower, C., Gilbert, M., Grenfell, B. T., Levin, S. A., Robinson, T. P., Teillant, A., & Laxminarayan, R. (2015). Global trends in antimicrobial use in food animals. Proceedings of the National Academy of Sciences of the United States of America, 112(18), 5649–5654. https://doi.org/10.1073/pnas.1503141112
Landers, T. F., Cohen, B., Wittum, T. E., & Larson, E. L. (2012). A review of antibiotic use in food animals: perspective, policy, and potential. Public health reports (Washington, D.C. : 1974), 127(1), 4–22. https://doi.org/10.1177/003335491212700103

Xue, B., Dai, K., Zhang, X., Wang, S., Li, C., Zhao, C., Yang, X., Xi, Z., Qiu, Z., Shen, Z., & Wang, J. (2020). Low-concentration of dichloroacetonitrile (DCAN) in drinking water perturbs the health-associated gut microbiome and metabolic profile in rats. Chemosphere, 258, 127067. https://doi.org/10.1016/j.chemosphere.2020.127067
Martino D. (2019). The Effects of Chlorinated Drinking Water on the Assembly of the Intestinal Microbiome. Challenges. 2019; 10(1):10. https://doi.org/10.3390/challe10010010

Reverse Osmosis and Remineralization

Kozisek, Frantisek. (2004). Health Risk from Drinking Demineralized Water. Rolling Revision of the WHO Guidelines for Drinking Water Quality. National Institute of Public Health Czech Republic.

Why Water Quality Matters

Guidelines for drinking-water quality: the fourth edition incorporating the first addendum. Geneva: World Health Organization; 2017. https://www.who.int/publications/i/item/9789241549950

Chemical Additives and Toxins in Our Food

Chemical Toxins in the Polluted World

Microplastics and Nanoplastics

Mason, S. A., Welch, V. G., & Neratko, J. (2018). Synthetic Polymer Contamination in Bottled Water. Frontiers in chemistry, 6, 407. https://doi.org/10.3389/fchem.2018.00407
Ge, Y., Yang, S., Zhang, T., Wan, X., Zhu, Y., Yang, F., Yin, L., Pu, Y., & Liang, G. (2023). The hepatotoxicity assessment of micro/nanoplastics: A preliminary study to apply the adverse outcome pathways. The Science of the total environment, 902, 165659. https://doi.org/10.1016/j.scitotenv.2023.165659

Fish Safety

Savoca, M. S., McInturf, A. G., & Hazen, E. L. (2021). Plastic ingestion by marine fish is widespread and increasing. Global change biology, 27(10), 2188–2199. https://doi.org/10.1111/gcb.15533

Heavy Metals and Chelation Foods

Potera C. (2007). U.S. rice serves up arsenic. Environmental health perspectives, 115(6), A296. https://doi.org/10.1289/ehp.115-a296
F. Bamonti et al. Metal chelation therapy in rheumatoid arthritis: a case report. Successful management of rheumatoid arthritis by metal chelation therapy. Biometals 2011 Dec;24(6):1093–1098.
T. Uchikawa et al. Chlorella suppresses methylmercury transfer to the fetus in pregnant mice. J Toxicol Sci 2011 Oct;36(5):675–680.
David B. Smith, William F. Cannon, Laurel G. Woodruff, Federico Solano, and Karl J. Ellefsen. (2014) Geochemical and Mineralogical Maps for Soils of the Conterminous United States. U.S. Department of the Interior. U.S. Geological Survey. https://pubs.usgs.gov/of/2014/1082/pdf/ofr2014-1082.pdf
Meharg, A. A., Williams, P. N., Adomako, E., Lawgali, Y. Y., Deacon, C., Villada, A., Cambell, R. C., Sun, G., Zhu, Y. G., Feldmann, J., Raab, A., Zhao, F. J., Islam, R., Hossain, S., & Yanai, J. (2009). Geographical variation in total and inorganic arsenic content of polished (white) rice. Environmental science & technology, 43(5), 1612–1617. https://doi.org/10.1021/es802612a
Sears M. E. (2013). Chelation: harnessing and enhancing heavy metal detoxification–a review. TheScientificWorldJournal, 2013, 219840. https://doi.org/10.1155/2013/219840

Alcohol

Zhang, X., Yasuda, K., Gilmore, R. A., Westmoreland, S. V., Platt, D. M., Miller, G. M., & Vallender, E. J. (2019). Alcohol-induced changes in the gut microbiome and metabolome of rhesus macaques. Psychopharmacology, 236(5), 1531–1544. https://doi.org/10.1007/s00213-019-05217-z
Ames, N. J., Barb, J. J., Schuebel, K., Mudra, S., Meeks, B. K., Tuason, R. T. S., Brooks, A. T., Kazmi, N., Yang, S., Ratteree, K., Diazgranados, N., Krumlauf, M., Wallen, G. R., & Goldman, D. (2020). Longitudinal gut microbiome changes in alcohol use disorder are influenced by abstinence and drinking quantity. Gut microbes, 11(6), 1608–1631. https://doi.org/10.1080/19490976.2020.1758010
Capurso, G., & Lahner, E. (2017). The interaction between smoking, alcohol and the gut microbiome. Best practice & research. Clinical gastroenterology, 31(5), 579–588. https://doi.org/10.1016/j.bpg.2017.10.006
Gabbard, S. L., Lacy, B. E., Levine, G. M., & Crowell, M. D. (2014). The impact of alcohol consumption and cholecystectomy on small intestinal bacterial overgrowth. Digestive diseases and sciences, 59(3), 638–644. https://doi.org/10.1007/s10620-013-2960-y

Food Additives: Hacking the Food

Concealing Poverty

Collins, J., Robinson, C., Danhof, H. et al. (2018). Dietary trehalose enhances virulence of epidemic Clostridium difficile. Nature 553, 291–294 (2018). https://doi.org/10.1038/nature25178
Lebelo, K., Malebo, N., Mochane, M. J., & Masinde, M. (2021). Chemical Contamination Pathways and the Food Safety Implications along the Various Stages of Food Production: A Review. International journal of environmental research and public health, 18(11), 5795. https://doi.org/10.3390/ijerph18115795
Naimi, S., Viennois, E., Gewirtz, A.T. et al. (2021). Direct impact of commonly used dietary emulsifiers on human gut microbiota. Microbiome 9, 66 (2021). https://doi.org/10.1186/s40168-020-00996-6
Lerner, A., & Matthias, T. (2020). Processed Food Additive Microbial Transglutaminase and Its Cross-Linked Gliadin Complexes Are Potential Public Health Concerns in Celiac Disease. International journal of molecular sciences, 21(3), 1127. https://doi.org/10.3390/ijms21031127
Baraldi, L. G., Martinez Steele, E., Canella, D. S., & Monteiro, C. A. (2018). Consumption of ultra-processed foods and associated sociodemographic factors in the USA between 2007 and 2012: evidence from a nationally representative cross-sectional study. BMJ open, 8(3), e020574. https://doi.org/10.1136/bmjopen-2017-020574

Key 2. Inflammation: Reduce

Intermittent Hormesis

Rattan S. I. (2008). Hormesis in aging. Ageing research reviews, 7(1), 63–78. https://doi.org/10.1016/j.arr.2007.03.002
Calabrese E. J. (2008). Hormesis and medicine. British journal of clinical pharmacology, 66(5), 594–617. https://doi.org/10.1111/j.1365-2125.2008.03243.x

Chronic Inflammation

Consequences of Chronic Inflammation

Abu-Shakra, M., & Shoenfeld, Y. (1991). Chronic infections and autoimmunity. Immunology series, 55, 285–313. https://pubmed.ncbi.nlm.nih.gov/1954289/
Arango MT, Shoenfeld Y, Cervera R, et al. (2013). Infection and autoimmune diseases. In: Anaya JM, Shoenfeld Y, Rojas-Villarraga A, et al., editors. Autoimmunity: From Bench to Bedside [Internet]. Bogota (Colombia): El Rosario University Press; 2013 Jul 18. Chapter 19. Available from: https://www.ncbi.nlm.nih.gov/books/NBK459437/

When You Change Your Own Genes

Detanico, T., St Clair, J. B., Aviszus, K., Kirchenbaum, G., Guo, W., & Wysocki, L. J. (2013). Somatic mutagenesis in autoimmunity. Autoimmunity, 46(2), 102–114. https://doi.org/10.3109/08916934.2012.757597
Dörner, T., Giesecke, C. & Lipsky, P.E. (2011). Mechanisms of B cell autoimmunity in SLE . Arthritis Res Ther 13, 243 (2011). https://doi.org/10.1186/ar3433
Nobel Prize. (2023, August 23). The Nobel Prize in Physiology or Medicine 1987. NobelPrize.org. https://www.nobelprize.org/prizes/medicine/1987/summary/

Immune Cells in the Intestine

Vighi, G., Marcucci, F., Sensi, L., Di Cara, G., & Frati, F. (2008). Allergy and the gastrointestinal system. Clinical and experimental immunology, 153 Suppl 1(Suppl 1), 3–6. https://doi.org/10.1111/j.1365-2249.2008.03713.x

Inflammation and Other DILL+ Factors

Walker, A. W., & Lawley, T. D. (2013). Therapeutic modulation of intestinal dysbiosis. Pharmacological research, 69(1), 75–86. https://doi.org/10.1016/j.phrs.2012.09.008
Shanahan F. (2000). Probiotics and inflammatory bowel disease: is there a scientific rationale?. Inflammatory bowel diseases, 6(2), 107–115. https://doi.org/10.1097/00054725-200005000-00007

Inflammatory Foods

Vojdani, A., Gushgari, L. R., & Vojdani, E. (2020). Interaction between food antigens and the immune system: Association with autoimmune disorders. Autoimmunity reviews, 19(3), 102459. https://doi.org/10.1016/j.autrev.2020.102459

Fats and Oils

Ergas, D., Eilat, E., Mendlovic, S., & Sthoeger, Z. M. (2002). n-3 fatty acids and the immune system in autoimmunity. The Israel Medical Association journal : IMAJ, 4(1), 34–38. https://pubmed.ncbi.nlm.nih.gov/11802309/
Molendi-Coste, O., Legry, V., & Leclercq, I. A. (2011). Why and How Meet n-3 PUFA Dietary Recommendations?. Gastroenterology research and practice, 2011, 364040. https://doi.org/10.1155/2011/364040
Yamashima, T., Ota, T., Mizukoshi, E., Nakamura, H., Yamamoto, Y., Kikuchi, M., Yamashita, T., & Kaneko, S. (2020). Intake of ω-6 Polyunsaturated Fatty Acid-Rich Vegetable Oils and Risk of Lifestyle Diseases. Advances in nutrition (Bethesda, Md.), 11(6), 1489–1509. https://doi.org/10.1093/advances/nmaa072
Fernandes G. (1994). Dietary lipids and risk of autoimmune disease. Clinical immunology and immunopathology, 72(2), 193–197. https://doi.org/10.1006/clin.1994.1129
Harbige L. S. (2003). Fatty acids, the immune response, and autoimmunity: a question of n-6 essentiality and the balance between n-6 and n-3. Lipids, 38(4), 323–341. https://doi.org/10.1007/s11745-003-1067-z
Harbige L. S. (1998). Dietary n-6 and n-3 fatty acids in immunity and autoimmune disease. The Proceedings of the Nutrition Society, 57(4), 555–562. https://doi.org/10.1079/pns19980081
Tortosa-Caparrós, E., Navas-Carrillo, D., Marín, F., & Orenes-Piñero, E. (2017). Anti-inflammatory effects of omega 3 and omega 6 polyunsaturated fatty acids in cardiovascular disease and metabolic syndrome. Critical reviews in food science and nutrition, 57(16), 3421–3429. https://doi.org/10.1080/10408398.2015.1126549
Rodríguez-García, C., Sánchez-Quesada, C., Algarra, I., & Gaforio, J. J. (2020). The High-Fat Diet Based on Extra-Virgin Olive Oil Causes Dysbiosis Linked to Colorectal Cancer Prevention. Nutrients, 12(6), 1705. https://doi.org/10.3390/nu12061705
Mboma, J., Leblanc, N., Angers, P., Rocher, A., Vigor, C., Oger, C., Reversat, G., Vercauteren, J., Galano, J. M., Durand, T., & Jacques, H. (2018). Effects of Cyclic Fatty Acid Monomers from Heated Vegetable Oil on Markers of Inflammation and Oxidative Stress in Male Wistar Rats. Journal of agricultural and food chemistry, 66(27), 7172–7180. https://doi.org/10.1021/acs.jafc.8b01836
Lauretti, E., & Praticò, D. (2017). Effect of canola oil consumption on memory, synapse and neuropathology in the triple transgenic mouse model of Alzheimer’s disease. Scientific reports, 7(1), 17134. https://doi.org/10.1038/s41598-017-17373-3

Trans Fats and Hydrogenated Oils

Okamura, T., Hashimoto, Y., Majima, S., Senmaru, T., Ushigome, E., Nakanishi, N., Asano, M., Yamazaki, M., Takakuwa, H., Hamaguchi, M., & Fukui, M. (2021). Trans Fatty Acid Intake Induces Intestinal Inflammation and Impaired Glucose Tolerance. Frontiers in immunology, 12, 669672. https://doi.org/10.3389/fimmu.2021.669672

Proteins and Animal Products

Characteristics of Various Protein-Rich Foods

Lerner, A., & Matthias, T. (2020). Processed Food Additive Microbial Transglutaminase and Its Cross-Linked Gliadin Complexes Are Potential Public Health Concerns in Celiac Disease. International journal of molecular sciences, 21(3), 1127. https://doi.org/10.3390/ijms21031127

Individual Food Reactions

Food sensitivity and allergies

Food Panel Tests

Bock S. A. (2010). AAAAI support of the EAACI Position Paper on IgG4. The Journal of allergy and clinical immunology, 125(6), 1410. https://doi.org/10.1016/j.jaci.2010.03.013
Carr, S., Chan, E., Lavine, E., & Moote, W. (2012). CSACI Position statement on the testing of food-specific IgG. Allergy, asthma, and clinical immunology : official journal of the Canadian Society of Allergy and Clinical Immunology, 8(1), 12. https://doi.org/10.1186/1710-1492-8-12

Elimination Diet and Autoimmune Protocol (AIP)

Konijeti, G. G., Kim, N., Lewis, J. D., Groven, S., Chandrasekaran, A., Grandhe, S., Diamant, C., Singh, E., Oliveira, G., Wang, X., Molparia, B., & Torkamani, A. (2017). Efficacy of the Autoimmune Protocol Diet for Inflammatory Bowel Disease. Inflammatory bowel diseases, 23(11), 2054–2060. https://doi.org/10.1097/MIB.0000000000001221
Chandrasekaran, A., Groven, S., Lewis, J. D., Levy, S. S., Diamant, C., Singh, E., & Konijeti, G. G. (2019). An Autoimmune Protocol Diet Improves Patient-Reported Quality of Life in Inflammatory Bowel Disease. Crohn’s & colitis 360, 1(3), otz019. https://doi.org/10.1093/crocol/otz019
Chandrasekaran, A., Molparia, B., Akhtar, E., Wang, X., Lewis, J. D., Chang, J. T., Oliveira, G., Torkamani, A., & Konijeti, G. G. (2019). The Autoimmune Protocol Diet Modifies Intestinal RNA Expression in Inflammatory Bowel Disease. Crohn’s & colitis 360, 1(3), otz016. https://doi.org/10.1093/crocol/otz016

Spices and Herbs to Reduce Inflammation

Peter, K. V. (Ed.). (2012). Handbook of herbs and spices (Vol. 1). Woodhead Publishing Series in Food Science, Technology and Nutrition (2nd ed.). Cambridge, England: Woodhead Publishing.
Jungbauer, A., & Medjakovic, S. (2012). Anti-inflammatory properties of culinary herbs and spices that ameliorate the effects of metabolic syndrome. Maturitas, 71(3), 227–239. https://doi.org/10.1016/j.maturitas.2011.12.009

Hot or Not

Xiang, Q., Tang, X., Cui, S., Zhang, Q., Liu, X., Zhao, J., Zhang, H., Mao, B., & Chen, W. (2022). Capsaicin, the Spicy Ingredient of Chili Peppers: Effects on Gastrointestinal Tract and Composition of Gut Microbiota at Various Dosages. Foods (Basel, Switzerland), 11(5), 686. https://doi.org/10.3390/foods11050686
Jensen-Jarolim, E., Gajdzik, L., Haberl, I., Kraft, D., Scheiner, O., & Graf, J. (1998). Hot spices influence permeability of human intestinal epithelial monolayers. The Journal of nutrition, 128(3), 577–581. https://doi.org/10.1093/jn/128.3.577

Supplements and Inflammation

Vitamin D

Fletcher, J., Cooper, S. C., Ghosh, S., & Hewison, M. (2019). The Role of Vitamin D in Inflammatory Bowel Disease: Mechanism to Management. Nutrients, 11(5), 1019. https://doi.org/10.3390/nu11051019
Cantorna, M. T., & Mahon, B. D. (2004). Mounting evidence for vitamin D as an environmental factor affecting autoimmune disease prevalence. Experimental biology and medicine (Maywood, N.J.), 229(11), 1136–1142. https://doi.org/10.1177/153537020422901108
Sean D Pitman, (2019). Beating Crohn’s: And Other Autoimmune Diseases.
Yang, C. Y., Leung, P. S., Adamopoulos, I. E., & Gershwin, M. E. (2013). The implication of vitamin D and autoimmunity: a comprehensive review. Clinical reviews in allergy & immunology, 45(2), 217–226. https://doi.org/10.1007/s12016-013-8361-3
van Ballegooijen, A. J., Pilz, S., Tomaschitz, A., Grübler, M. R., & Verheyen, N. (2017). The Synergistic Interplay between Vitamins D and K for Bone and Cardiovascular Health: A Narrative Review. International journal of endocrinology, 2017, 7454376. https://doi.org/10.1155/2017/7454376
Kostoglou-Athanassiou, I., Athanassiou, P., Lyraki, A., Raftakis, I., & Antoniadis, C. (2012). Vitamin D and rheumatoid arthritis. Therapeutic advances in endocrinology and metabolism, 3(6), 181–187. https://doi.org/10.1177/2042018812471070

Zinc

Sanna, A., Firinu, D., Zavattari, P., & Valera, P. (2018). Zinc Status and Autoimmunity: A Systematic Review and Meta-Analysis. Nutrients, 10(1), 68. https://doi.org/10.3390/nu10010068
Haase, H., & Rink, L. (2014). Multiple impacts of zinc on immune function. Metallomics : integrated biometal science, 6(7), 1175–1180. https://doi.org/10.1039/c3mt00353a
Kitabayashi, C., Fukada, T., Kanamoto, M., Ohashi, W., Hojyo, S., Atsumi, T., Ueda, N., Azuma, I., Hirota, H., Murakami, M., & Hirano, T. (2010). Zinc suppresses Th17 development via inhibition of STAT3 activation. International immunology, 22(5), 375–386. https://doi.org/10.1093/intimm/dxq017
Rosenkranz, E., Metz, C. H., Maywald, M., Hilgers, R. D., Weßels, I., Senff, T., Haase, H., Jäger, M., Ott, M., Aspinall, R., Plümäkers, B., & Rink, L. (2016). Zinc supplementation induces regulatory T cells by inhibition of Sirt-1 deacetylase in mixed lymphocyte cultures. Molecular nutrition & food research, 60(3), 661–671. https://doi.org/10.1002/mnfr.201500524
Hojyo, S., Miyai, T., Fujishiro, H., Kawamura, M., Yasuda, T., Hijikata, A., Bin, B. H., Irié, T., Tanaka, J., Atsumi, T., Murakami, M., Nakayama, M., Ohara, O., Himeno, S., Yoshida, H., Koseki, H., Ikawa, T., Mishima, K., & Fukada, T. (2014). Zinc transporter SLC39A10/ZIP10 controls humoral immunity by modulating B-cell receptor signal strength. Proceedings of the National Academy of Sciences of the United States of America, 111(32), 11786–11791. https://doi.org/10.1073/pnas.1323557111
Prasad A. S. (2000). Effects of zinc deficiency on Th1 and Th2 cytokine shifts. The Journal of infectious diseases, 182 Suppl 1, S62–S68. https://doi.org/10.1086/315916
Schubert, C., Guttek, K., Grüngreiff, K., Thielitz, A., Bühling, F., Reinhold, A., Brocke, S., & Reinhold, D. (2014). Oral zinc aspartate treats experimental autoimmune encephalomyelitis. Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine, 27(6), 1249–1262. https://doi.org/10.1007/s10534-014-9786-8

Gum and Teeth Health

Ogrendik M. (2013). Rheumatoid arthritis is an autoimmune disease caused by periodontal pathogens. International journal of general medicine, 6, 383–386. https://doi.org/10.2147/IJGM.S45929
Ogrendik M. (2009). Rheumatoid arthritis is linked to oral bacteria: etiological association. Modern rheumatology, 19(5), 453–456. https://doi.org/10.1007/s10165-009-0194-9
Kaur, G., Mohindra, K., & Singla, S. (2017). Autoimmunity-Basics and link with periodontal disease. Autoimmunity reviews, 16(1), 64–71. https://doi.org/10.1016/j.autrev.2016.09.013
Nesse, W., Dijkstra, P. U., Abbas, F., Spijkervet, F. K., Stijger, A., Tromp, J. A., van Dijk, J. L., & Vissink, A. (2010). Increased prevalence of cardiovascular and autoimmune diseases in periodontitis patients: a cross-sectional study. Journal of periodontology, 81(11), 1622–1628. https://doi.org/10.1902/jop.2010.100058

Key 3. Leaky gut: Repair

Constant Repair

Mu, Q., Kirby, J., Reilly, C. M., & Luo, X. M. (2017). Leaky Gut As a Danger Signal for Autoimmune Diseases. Frontiers in immunology, 8, 598. https://doi.org/10.3389/fimmu.2017.00598
Milo, R., & Phillips, R. (2015). Cell biology by the numbers. CRC Press.
Park, J. H., Kotani, T., Konno, T., Setiawan, J., Kitamura, Y., Imada, S., Usui, Y., Hatano, N., Shinohara, M., Saito, Y., Murata, Y., & Matozaki, T. (2016). Promotion of Intestinal Epithelial Cell Turnover by Commensal Bacteria: Role of Short-Chain Fatty Acids. PloS one, 11(5), e0156334. https://doi.org/10.1371/journal.pone.0156334
Williams, J. M., Duckworth, C. A., Burkitt, M. D., Watson, A. J., Campbell, B. J., & Pritchard, D. M. (2015). Epithelial cell shedding and barrier function: a matter of life and death at the small intestinal villus tip. Veterinary pathology, 52(3), 445–455. https://doi.org/10.1177/0300985814559404

Unhealthy Epithelium and Increased Intestinal Permeability

Lerner, A., & Matthias, T. (2015). Changes in intestinal tight junction permeability associated with industrial food additives explain the rising incidence of autoimmune disease. Autoimmunity reviews, 14(6), 479–489. https://doi.org/10.1016/j.autrev.2015.01.009

Gut Lining and Other DILL+ Factors

Morris, G., Berk, M., Carvalho, A. F., Caso, J. R., Sanz, Y., & Maes, M. (2016). The Role of Microbiota and Intestinal Permeability in the Pathophysiology of Autoimmune and Neuroimmune Processes with an Emphasis on Inflammatory Bowel Disease Type 1 Diabetes and Chronic Fatigue Syndrome. Current pharmaceutical design, 22(40), 6058–6075. https://doi.org/10.2174/1381612822666160914182822
Salguero, M. V., Al-Obaide, M. A. I., Singh, R., Siepmann, T., & Vasylyeva, T. L. (2019). Dysbiosis of Gram-negative gut microbiota and the associated serum lipopolysaccharide exacerbates inflammation in type 2 diabetic patients with chronic kidney disease. Experimental and therapeutic medicine, 18(5), 3461–3469. https://doi.org/10.3892/etm.2019.7943
Xi, Y., Yan, J., Li, M., Ying, S., & Shi, Z. (2019). Gut microbiota dysbiosis increases the risk of visceral gout in goslings through translocation of gut-derived lipopolysaccharide. Poultry science, 98(11), 5361–5373. https://doi.org/10.3382/ps/pez357
Belančić A. (2020). Gut microbiome dysbiosis and endotoxemia - Additional pathophysiological explanation for increased COVID-19 severity in obesity. Obesity medicine, 20, 100302. https://doi.org/10.1016/j.obmed.2020.100302
Pastor Rojo, O., López San Román, A., Albéniz Arbizu, E., de la Hera Martínez, A., Ripoll Sevillano, E., & Albillos Martínez, A. (2007). Serum lipopolysaccharide-binding protein in endotoxemic patients with inflammatory bowel disease. Inflammatory bowel diseases, 13(3), 269–277. https://doi.org/10.1002/ibd.20019
Bischoff, S.C., Barbara, G., Buurman, W. et al. Intestinal permeability – a new target for disease prevention and therapy. BMC Gastroenterol 14, 189 (2014). https://doi.org/10.1186/s12876-014-0189-7

Eliminate Obstacles

Obstacle #4: Harmful Food Ingredients

Gluten

Elkan, A. C., Sjöberg, B., Kolsrud, B., Ringertz, B., Hafström, I., & Frostegård, J. (2008). Gluten-free vegan diet induces decreased LDL and oxidized LDL levels and raised atheroprotective natural antibodies against phosphorylcholine in patients with rheumatoid arthritis: a randomized study. Arthritis research & therapy, 10(2), R34. https://doi.org/10.1186/ar2388
Hafström, I., Ringertz, B., Spångberg, A., von Zweigbergk, L., Brannemark, S., Nylander, I., Rönnelid, J., Laasonen, L., & Klareskog, L. (2001). A vegan diet free of gluten improves the signs and symptoms of rheumatoid arthritis: the effects on arthritis correlate with a reduction in antibodies to food antigens. Rheumatology (Oxford, England), 40(10), 1175–1179. https://doi.org/10.1093/rheumatology/40.10.1175
Sander, G. R., Cummins, A. G., Henshall, T., & Powell, B. C. (2005). Rapid disruption of intestinal barrier function by gliadin involves altered expression of apical junctional proteins. FEBS letters, 579(21), 4851–4855. https://doi.org/10.1016/j.febslet.2005.07.066
Hollon, J., Puppa, E. L., Greenwald, B., Goldberg, E., Guerrerio, A., & Fasano, A. (2015). Effect of gliadin on permeability of intestinal biopsy explants from celiac disease patients and patients with non-celiac gluten sensitivity. Nutrients, 7(3), 1565–1576. https://doi.org/10.3390/nu7031565
Neyrinck, A. M., Van Hée, V. F., Piront, N., De Backer, F., Toussaint, O., Cani, P. D., & Delzenne, N. M. (2012). Wheat-derived arabinoxylan oligosaccharides with prebiotic effect increase satietogenic gut peptides and reduce metabolic endotoxemia in diet-induced obese mice. Nutrition & diabetes, 2(1), e28. https://doi.org/10.1038/nutd.2011.24
Tojo, R., Suárez, A., Clemente, M. G., de los Reyes-Gavilán, C. G., Margolles, A., Gueimonde, M., & Ruas-Madiedo, P. (2014). Intestinal microbiota in health and disease: role of bifidobacteria in gut homeostasis. World journal of gastroenterology, 20(41), 15163–15176. https://doi.org/10.3748/wjg.v20.i41.15163

Saturated Fats and Excessive Omega-6 Oils

Rohr, M. W., Narasimhulu, C. A., Rudeski-Rohr, T. A., & Parthasarathy, S. (2020). Negative Effects of a High-Fat Diet on Intestinal Permeability: A Review. Advances in nutrition (Bethesda, Md.), 11(1), 77–91. https://doi.org/10.1093/advances/nmz061
Usami, M., Komurasaki, T., Hanada, A., Kinoshita, K., & Ohata, A. (2003). Effect of gamma-linolenic acid or docosahexaenoic acid on tight junction permeability in intestinal monolayer cells and their mechanism by protein kinase C activation and/or eicosanoid formation. Nutrition (Burbank, Los Angeles County, Calif.), 19(2), 150–156. https://doi.org/10.1016/s0899-9007(02)00927-9
Usami, M., Muraki, K., Iwamoto, M., Ohata, A., Matsushita, E., & Miki, A. (2001). Effect of eicosapentaenoic acid (EPA) on tight junction permeability in intestinal monolayer cells. Clinical nutrition (Edinburgh, Scotland), 20(4), 351–359. https://doi.org/10.1054/clnu.2001.0430
John, S., Luben, R., Shrestha, S. S., Welch, A., Khaw, K. T., & Hart, A. R. (2010). Dietary n-3 polyunsaturated fatty acids and the aetiology of ulcerative colitis: a UK prospective cohort study. European journal of gastroenterology & hepatology, 22(5), 602–606. https://doi.org/10.1097/MEG.0b013e3283352d05
Willemsen, L. E., Koetsier, M. A., Balvers, M., Beermann, C., Stahl, B., & van Tol, E. A. (2008). Polyunsaturated fatty acids support epithelial barrier integrity and reduce IL-4 mediated permeability in vitro. European journal of nutrition, 47(4), 183–191. https://doi.org/10.1007/s00394-008-0712-0
Uchiyama, K., Nakamura, M., Odahara, S., Koido, S., Katahira, K., Shiraishi, H., Ohkusa, T., Fujise, K., & Tajiri, H. (2010). N-3 polyunsaturated fatty acid diet therapy for patients with inflammatory bowel disease. Inflammatory bowel diseases, 16(10), 1696–1707. https://doi.org/10.1002/ibd.21251
Scoville, E. A., Allaman, M. M., Adams, D. W., Motley, A. K., Peyton, S. C., Ferguson, S. L., Horst, S. N., Williams, C. S., Beaulieu, D. B., Schwartz, D. A., Wilson, K. T., & Coburn, L. A. (2019). Serum Polyunsaturated Fatty Acids Correlate with Serum Cytokines and Clinical Disease Activity in Crohn’s Disease. Scientific reports, 9(1), 2882. https://doi.org/10.1038/s41598-019-39232-z

Excessive Saponins and Lectins

Johnson, I. T., Gee, J. M., Price, K., Curl, C., & Fenwick, G. R. (1986). Influence of saponins on gut permeability and active nutrient transport in vitro. The Journal of nutrition, 116(11), 2270–2277. https://doi.org/10.1093/jn/116.11.2270

Alcohol

Bode, C., & Bode, J. C. (2003). Effect of alcohol consumption on the gut. Best practice & research. Clinical gastroenterology, 17(4), 575–592. https://doi.org/10.1016/s1521-6918(03)00034-9
Draper, L. R., Gyure, L. A., Hall, J. G., & Robertson, D. (1983). Effect of alcohol on the integrity of the intestinal epithelium. Gut, 24(5), 399–404. https://doi.org/10.1136/gut.24.5.399
Bishehsari, F., Magno, E., Swanson, G., Desai, V., Voigt, R. M., Forsyth, C. B., & Keshavarzian, A. (2015). Alcohol and gut-derived inflammation. Alcohol Research & Clinical Reviews, 38(2), 121-132. https://arcr.niaaa.nih.gov/volume/38/2/alcohol-and-gut-derived-inflammation
Calleja-Conde, J., Echeverry-Alzate, V., Bühler, K. M., Durán-González, P., Morales-García, J. Á., Segovia-Rodríguez, L., Rodríguez de Fonseca, F., Giné, E., & López-Moreno, J. A. (2021). The Immune System through the Lens of Alcohol Intake and Gut Microbiota. International journal of molecular sciences, 22(14), 7485. https://doi.org/10.3390/ijms22147485
Purohit, V., Bode, J. C., Bode, C., Brenner, D. A., Choudhry, M. A., Hamilton, F., Kang, Y. J., Keshavarzian, A., Rao, R., Sartor, R. B., Swanson, C., & Turner, J. R. (2008). Alcohol, intestinal bacterial growth, intestinal permeability to endotoxin, and medical consequences: summary of a symposium. Alcohol (Fayetteville, N.Y.), 42(5), 349–361. https://doi.org/10.1016/j.alcohol.2008.03.131

Obstacle #5: Medication

NSAIDs

Montenegro, L., Losurdo, G., Licinio, R., Zamparella, M., Giorgio, F., Ierardi, E., Di Leo, A., & Principi, M. (2014). Non steroidal anti-inflammatory drug induced damage on lower gastro-intestinal tract: is there an involvement of microbiota?. Current drug safety, 9(3), 196–204. https://doi.org/10.2174/1574886309666140424143852
Marlicz, W., Loniewski, I., Grimes, D. S., & Quigley, E. M. (2014). Nonsteroidal anti-inflammatory drugs, proton pump inhibitors, and gastrointestinal injury: contrasting interactions in the stomach and small intestine. Mayo Clinic proceedings, 89(12), 1699–1709. https://doi.org/10.1016/j.mayocp.2014.07.015
Pavlidis, P., & Bjarnason, I. (2015). Aspirin Induced Adverse Effects on the Small and Large Intestine. Current pharmaceutical design, 21(35), 5089–5093. https://doi.org/10.2174/1381612821666150915110058
Odenwald, M. A., & Turner, J. R. (2013). Intestinal permeability defects: is it time to treat?. Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association, 11(9), 1075–1083. https://doi.org/10.1016/j.cgh.2013.07.001
Weber, C. R., Raleigh, D. R., Su, L., Shen, L., Sullivan, E. A., Wang, Y., & Turner, J. R. (2010). Epithelial myosin light chain kinase activation induces mucosal interleukin-13 expression to alter tight junction ion selectivity. The Journal of biological chemistry, 285(16), 12037–12046. https://doi.org/10.1074/jbc.M109.064808
Bjarnason, I., & Takeuchi, K. (2009). Intestinal permeability in the pathogenesis of NSAID-induced enteropathy. Journal of gastroenterology, 44 Suppl 19, 23–29. https://doi.org/10.1007/s00535-008-2266-6
Bjarnason, I., & Takeuchi, K. (2009). Intestinal permeability in the pathogenesis of NSAID-induced enteropathy. Journal of gastroenterology, 44 Suppl 19, 23–29. https://doi.org/10.1007/s00535-008-2266-6
Timpe Behnen E. Ask the Expert: Which NSAIDs are Most Selective for COX-1 and COX-2?. Pract Pain Manag. 2013;13(7).

Obstacle #7: Insufficient Mastication

Rodrigues Neves, C., Buskermolen, J., Roffel, S., Waaijman, T., Thon, M., Veerman, E., & Gibbs, S. (2019). Human saliva stimulates skin and oral wound healing in vitro. Journal of tissue engineering and regenerative medicine, 13(6), 1079–1092. https://doi.org/10.1002/term.2865
Keswani, S. G., Balaji, S., Le, L. D., Leung, A., Parvadia, J. K., Frischer, J., Yamano, S., Taichman, N., & Crombleholme, T. M. (2013). Role of salivary vascular endothelial growth factor (VEGF) in palatal mucosal wound healing. Wound repair and regeneration : official publication of the Wound Healing Society [and] the European Tissue Repair Society, 21(4), 554–562. https://doi.org/10.1111/wrr.12065

Obstacle #9: Chilled Food and Drinks

Liu JQ, Hu TY, Diao KY, Yu D, Song YN, Mo LH, Yang G, Liu ZQ, Liu ZG, Yang PC. Cold stress promotes IL-33 expression in intestinal epithelial cells to facilitate food allergy development. Cytokine. 2020 Dec;136:155295. doi: 10.1016/j.cyto.2020.155295. Epub 2020 Sep 22. PMID: 32977238.

Actively Repair

Nutrition For the Gut Epithelium

Butyrate and Other SCFA (Short Chain Fatty Acids)

Schulthess, J., Pandey, S., Capitani, M., Rue-Albrecht, K. C., Arnold, I., Franchini, F., Chomka, A., Ilott, N. E., Johnston, D. G. W., Pires, E., McCullagh, J., Sansom, S. N., Arancibia-Cárcamo, C. V., Uhlig, H. H., & Powrie, F. (2019). The Short Chain Fatty Acid Butyrate Imprints an Antimicrobial Program in Macrophages. Immunity, 50(2), 432–445.e7. https://doi.org/10.1016/j.immuni.2018.12.018
Chen, J., & Vitetta, L. (2020). Butyrate in Inflammatory Bowel Disease Therapy. Gastroenterology, 158(5), 1511. https://doi.org/10.1053/j.gastro.2019.08.064
Richards, J. L., Yap, Y. A., McLeod, K. H., Mackay, C. R., & Mariño, E. (2016). Dietary metabolites and the gut microbiota: an alternative approach to control inflammatory and autoimmune diseases. Clinical & translational immunology, 5(5), e82. https://doi.org/10.1038/cti.2016.29
Tan, J., McKenzie, C., Potamitis, M., Thorburn, A. N., Mackay, C. R., & Macia, L. (2014). The role of short-chain fatty acids in health and disease. Advances in immunology, 121, 91–119. https://doi.org/10.1016/B978-0-12-800100-4.00003-9

Resistant Starch

Liljeberg Elmståhl H. (2002). Resistant starch content in a selection of starchy foods on the Swedish market. European journal of clinical nutrition, 56(6), 500–505. https://doi.org/10.1038/sj.ejcn.1601338
Patterson, M. A., Maiya, M., & Stewart, M. L. (2020). Resistant Starch Content in Foods Commonly Consumed in the United States: A Narrative Review. Journal of the Academy of Nutrition and Dietetics, 120(2), 230–244. https://doi.org/10.1016/j.jand.2019.10.019
Topping, D. L., & Clifton, P. M. (2001). Short-chain fatty acids and human colonic function: roles of resistant starch and nonstarch polysaccharides. Physiological reviews, 81(3), 1031–1064. https://doi.org/10.1152/physrev.2001.81.3.1031

Acetate and Lactate

Duncan, S. H., Holtrop, G., Lobley, G. E., Calder, A. G., Stewart, C. S., & Flint, H. J. (2004). Contribution of acetate to butyrate formation by human faecal bacteria. The British journal of nutrition, 91(6), 915–923. https://doi.org/10.1079/BJN20041150
Budak, N. H., Aykin, E., Seydim, A. C., Greene, A. K., & Guzel-Seydim, Z. B. (2014). Functional properties of vinegar. Journal of food science, 79(5), R757–R764. https://doi.org/10.1111/1750-3841.12434

Naturally Fermented Foods

Shimizu, H., Masujima, Y., Ushiroda, C., Mizushima, R., Taira, S., Ohue-Kitano, R., & Kimura, I. (2019). Dietary short-chain fatty acid intake improves the hepatic metabolic condition via FFAR3. Scientific reports, 9(1), 16574. https://doi.org/10.1038/s41598-019-53242-x
Montel, M. C., Buchin, S., Mallet, A., Delbes-Paus, C., Vuitton, D. A., Desmasures, N., & Berthier, F. (2014). Traditional cheeses: rich and diverse microbiota with associated benefits. International journal of food microbiology, 177, 136–154. https://doi.org/10.1016/j.ijfoodmicro.2014.02.019
Madsen, K. L., Doyle, J. S., Jewell, L. D., Tavernini, M. M., & Fedorak, R. N. (1999). Lactobacillus species prevents colitis in interleukin 10 gene-deficient mice. Gastroenterology, 116(5), 1107–1114. https://doi.org/10.1016/s0016-5085(99)70013-2

Other Nutrients

Sulphur and Methylsulfonylmethane (MSM)

University of Pennsylvania. (2015, August 11). Study details ‘rotten egg’ gas’ role in autoimmune disease. ScienceDaily. November 1, 2023 https://www.sciencedaily.com/releases/2015/08/150811171508.htm

Glutamine

Rao, R., & Samak, G. (2012). Role of Glutamine in Protection of Intestinal Epithelial Tight Junctions. Journal of epithelial biology & pharmacology, 5(Suppl 1-M7), 47–54. https://doi.org/10.2174/1875044301205010047
Shu, X. L., Yu, T. T., Kang, K., & Zhao, J. (2016). Effects of glutamine on markers of intestinal inflammatory response and mucosal permeability in abdominal surgery patients: A meta-analysis. Experimental and therapeutic medicine, 12(6), 3499–3506. https://doi.org/10.3892/etm.2016.3799
Zuhl, M. N., Lanphere, K. R., Kravitz, L., Mermier, C. M., Schneider, S., Dokladny, K., & Moseley, P. L. (2014). Effects of oral glutamine supplementation on exercise-induced gastrointestinal permeability and tight junction protein expression. Journal of applied physiology (Bethesda, Md. : 1985), 116(2), 183–191. https://doi.org/10.1152/japplphysiol.00646.2013
Coëffier, M., Marion-Letellier, R., & Déchelotte, P. (2010). Potential for amino acids supplementation during inflammatory bowel diseases. Inflammatory bowel diseases, 16(3), 518–524. https://doi.org/10.1002/ibd.21017

Quercetin

Suzuki, T., & Hara, H. (2009). Quercetin enhances intestinal barrier function through the assembly of zonula [corrected] occludens-2, occludin, and claudin-1 and the expression of claudin-4 in Caco-2 cells. The Journal of nutrition, 139(5), 965–974. https://doi.org/10.3945/jn.108.100867

Sea-buckthorn

Shi, J., Wang, L., Lu, Y., Ji, Y., Wang, Y., Dong, K., Kong, X., & Sun, W. (2017). Protective effects of seabuckthorn pulp and seed oils against radiation-induced acute intestinal injury. Journal of radiation research, 58(1), 24–32. https://doi.org/10.1093/jrr/rrw069
Ganju, L., Padwad, Y., Singh, R., Karan, D., Chanda, S., Chopra, M. K., Bhatnagar, P., Kashyap, R., & Sawhney, R. C. (2005). Anti-inflammatory activity of Seabuckthorn (Hippophae rhamnoides) leaves. International immunopharmacology, 5(12), 1675–1684. https://doi.org/10.1016/j.intimp.2005.03.017
Erkkola, Risto & Yang, Baoru. (2003). Sea buckthorn oils: Towards healthy mucous membranes. Agro Food Industry Hi-Tech. 14. 53-57.
Zielińska, A., & Nowak, I. (2017). Abundance of active ingredients in sea-buckthorn oil. Lipids in health and disease, 16(1), 95. https://doi.org/10.1186/s12944-017-0469-7

Flaxseed

Xu, ZhenXia & Chen, Wenchao & Deng, Qianchun & Huang, Qingde & Wang, Xu & Yang, Chen & Huang, Fenghong. (2020). Flaxseed oligosaccharides alleviate DSS-induced colitis through modulation of gut microbiota and repair of intestinal barrier in mice. Food & Function. 11. 10.1039/D0FO01105C.

Bone Broth

Mar-Solís, L. M., Soto-Domínguez, A., Rodríguez-Tovar, L. E., Rodríguez-Rocha, H., García-García, A., Aguirre-Arzola, V. E., Zamora-Ávila, D. E., Garza-Arredondo, A. J., & Castillo-Velázquez, U. (2021). Analysis of the Anti-Inflammatory Capacity of Bone Broth in a Murine Model of Ulcerative Colitis. Medicina (Kaunas, Lithuania), 57(11), 1138. https://doi.org/10.3390/medicina57111138

Zinc

Chai, F., Truong-Tran, A. Q., Evdokiou, A., Young, G. P., & Zalewski, P. D. (2000). Intracellular zinc depletion induces caspase activation and p21 Waf1/Cip1 cleavage in human epithelial cell lines. The Journal of infectious diseases, 182 Suppl 1, S85–S92. https://doi.org/10.1086/315914
Virgili, F., Canali, R., Figus, E., Vignolini, F., Nobili, F., & Mengheri, E. (1999). Intestinal damage induced by zinc deficiency is associated with enhanced CuZn superoxide dismutase activity in rats: effect of dexamethasone or thyroxine treatment. Free radical biology & medicine, 26(9-10), 1194–1201. https://doi.org/10.1016/s0891-5849(98)00307-4
Roy, S. K., Behrens, R. H., Haider, R., Akramuzzaman, S. M., Mahalanabis, D., Wahed, M. A., & Tomkins, A. M. (1992). Impact of zinc supplementation on intestinal permeability in Bangladeshi children with acute diarrhoea and persistent diarrhoea syndrome. Journal of pediatric gastroenterology and nutrition, 15(3), 289–296. https://doi.org/10.1097/00005176-199210000-00010
Sachdev, H. P., Mittal, N. K., Mittal, S. K., & Yadav, H. S. (1988). A controlled trial on utility of oral zinc supplementation in acute dehydrating diarrhea in infants. Journal of pediatric gastroenterology and nutrition, 7(6), 877–881. https://doi.org/10.1097/00005176-198811000-00015
Hambidge K. M. (1992). Zinc and diarrhea. Acta paediatrica (Oslo, Norway : 1992). Supplement, 381, 82–86. https://doi.org/10.1111/j.1651-2227.1992.tb12377.x
Arcasoy, A., Akar, N., Ors, U., Delilbasi, L., & Karayalcin, S. (1990). Ultrastructural changes in the mucosa of the small intestine in patients with geophagia (Prasad’s syndrome). Journal of pediatric gastroenterology and nutrition, 11(2), 279–282. https://doi.org/10.1097/00005176-199008000-00022

Vitamins

Guerreiro, C. S., Calado, Â., Sousa, J., & Fonseca, J. E. (2018). Diet, Microbiota, and Gut Permeability-The Unknown Triad in Rheumatoid Arthritis. Frontiers in medicine, 5, 349. https://doi.org/10.3389/fmed.2018.00349
Gordon, B. L., Galati, J. S., Yang, S., Longman, R. S., Lukin, D., Scherl, E. J., & Battat, R. (2022). Prevalence and factors associated with vitamin C deficiency in inflammatory bowel disease. World journal of gastroenterology, 28(33), 4834–4845. https://doi.org/10.3748/wjg.v28.i33.4834
Cevikel, M. H., Tuncyurek, P., Ceylan, F., Meteoglu, I., Kozaci, D., & Boylu, S. (2008). Supplementation with high-dose ascorbic acid improves intestinal anastomotic healing. European surgical research. Europaische chirurgische Forschung. Recherches chirurgicales europeennes, 40(1), 29–33. https://doi.org/10.1159/000108622
Schoultz, I., McKay, C. M., Graepel, R., Phan, V. C., Wang, A., Söderholm, J., & McKay, D. M. (2012). Indomethacin-induced translocation of bacteria across enteric epithelia is reactive oxygen species-dependent and reduced by vitamin C. American journal of physiology. Gastrointestinal and liver physiology, 303(5), G536–G545. https://doi.org/10.1152/ajpgi.00125.2012
Pham, V. T., Fehlbaum, S., Seifert, N., Richard, N., Bruins, M. J., Sybesma, W., Rehman, A., & Steinert, R. E. (2021). Effects of colon-targeted vitamins on the composition and metabolic activity of the human gut microbiome- a pilot study. Gut microbes, 13(1), 1–20. https://doi.org/10.1080/19490976.2021.1875774
Xu, C., Sun, R., Qiao, X., Xu, C., Shang, X., Niu, W., & Chao, Y. (2014). Effect of vitamin e supplementation on intestinal barrier function in rats exposed to high altitude hypoxia environment. The Korean journal of physiology & pharmacology : official journal of the Korean Physiological Society and the Korean Society of Pharmacology, 18(4), 313–320. https://doi.org/10.4196/kjpp.2014.18.4.313
Liu, F., Cottrell, J. J., Furness, J. B., Rivera, L. R., Kelly, F. W., Wijesiriwardana, U., Pustovit, R. V., Fothergill, L. J., Bravo, D. M., Celi, P., Leury, B. J., Gabler, N. K., & Dunshea, F. R. (2016). Selenium and vitamin E together improve intestinal epithelial barrier function and alleviate oxidative stress in heat-stressed pigs. Experimental physiology, 101(7), 801–810. https://doi.org/10.1113/EP085746
Warden, R. A., Noltorp, R. S., Francis, J. L., Dunkley, P. R., & O’Loughlin, E. V. (1997). Vitamin A deficiency exacerbates methotrexate-induced jejunal injury in rats. The Journal of nutrition, 127(5), 770–776. https://doi.org/10.1093/jn/127.5.770
Ulitsky, A., Ananthakrishnan, A. N., Naik, A., Skaros, S., Zadvornova, Y., Binion, D. G., & Issa, M. (2011). Vitamin D deficiency in patients with inflammatory bowel disease: association with disease activity and quality of life. JPEN. Journal of parenteral and enteral nutrition, 35(3), 308–316. https://doi.org/10.1177/0148607110381267
Kong, J., Zhang, Z., Musch, M. W., Ning, G., Sun, J., Hart, J., Bissonnette, M., & Li, Y. C. (2008). Novel role of the vitamin D receptor in maintaining the integrity of the intestinal mucosal barrier. American journal of physiology. Gastrointestinal and liver physiology, 294(1), G208–G216. https://doi.org/10.1152/ajpgi.00398.2007
Liu, K. Y., Nakatsu, C. H., Jones-Hall, Y., Kozik, A., & Jiang, Q. (2021). Vitamin E alpha- and gamma-tocopherol mitigate colitis, protect intestinal barrier function and modulate the gut microbiota in mice. Free radical biology & medicine, 163, 180–189. https://doi.org/10.1016/j.freeradbiomed.2020.12.017

Water-Fasting

Remely, M., Hippe, B., Geretschlaeger, I., Stegmayer, S., Hoefinger, I., & Haslberger, A. (2015). Increased gut microbiota diversity and abundance of Faecalibacterium prausnitzii and Akkermansia after fasting: a pilot study. Wiener klinische Wochenschrift, 127(9-10), 394–398. https://doi.org/10.1007/s00508-015-0755-1
Özkul, C., Yalınay, M., & Karakan, T. (2019). Islamic fasting leads to an increased abundance of Akkermansia muciniphila and Bacteroides fragilis group: A preliminary study on intermittent fasting. The Turkish journal of gastroenterology : the official journal of Turkish Society of Gastroenterology, 30(12), 1030–1035. https://doi.org/10.5152/tjg.2019.19185
Cignarella, F., Cantoni, C., Ghezzi, L., Salter, A., Dorsett, Y., Chen, L., Phillips, D., Weinstock, G. M., Fontana, L., Cross, A. H., Zhou, Y., & Piccio, L. (2018). Intermittent Fasting Confers Protection in CNS Autoimmunity by Altering the Gut Microbiota. Cell metabolism, 27(6), 1222–1235.e6. https://doi.org/10.1016/j.cmet.2018.05.006
Paoli, A., Tinsley, G., Bianco, A., & Moro, T. (2019). The Influence of Meal Frequency and Timing on Health in Humans: The Role of Fasting. Nutrients, 11(4), 719. https://doi.org/10.3390/nu11040719
Fuhrman, J., Sarter, B., & Calabro, D. J. (2002). Brief case reports of medically supervised, water-only fasting associated with remission of autoimmune disease. Alternative therapies in health and medicine, 8(4), 112–111. <https://pubmed.ncbi.nlm.nih.gov/12126162/
Hafström, I., Ringertz, B., Gyllenhammar, H., Palmblad, J., & Harms-Ringdahl, M. (1988). Effects of fasting on disease activity, neutrophil function, fatty acid composition, and leukotriene biosynthesis in patients with rheumatoid arthritis. Arthritis and rheumatism, 31(5), 585–592. https://doi.org/10.1002/art.1780310502
Sundqvist, T., Lindström, F., Magnusson, K. E., Sköldstam, L., Stjernström, I., & Tagesson, C. (1982). Influence of fasting on intestinal permeability and disease activity in patients with rheumatoid arthritis. Scandinavian journal of rheumatology, 11(1), 33–38. https://doi.org/10.3109/03009748209098111

Elemental and Semi-Elemental Diets

Andoh, A., Inoue, R., Kawada, Y., Morishima, S., Inatomi, O., Ohno, M., Bamba, S., Nishida, A., Kawahara, M., & Naito, Y. (2019). Elemental diet induces alterations of the gut microbial community in mice. Journal of clinical biochemistry and nutrition, 65(2), 118–124. https://doi.org/10.3164/jcbn.19-8
Podas, T., Nightingale, J. M., Oldham, R., Roy, S., Sheehan, N. J., & Mayberry, J. F. (2007). Is rheumatoid arthritis a disease that starts in the intestine? A pilot study comparing an elemental diet with oral prednisolone. Postgraduate medical journal, 83(976), 128–131. https://doi.org/10.1136/pgmj.2006.050245
Kanazawa, M., & Fukudo, S. (2006). Effects of fasting therapy on irritable bowel syndrome. International journal of behavioral medicine, 13(3), 214–220. https://doi.org/10.1207/s15327558ijbm1303_4
Tavakkoli, H., Haghdani, S., Emami, M. H., Adilipour, H., Tavakkoli, M., & Tavakkoli, M. (2008). Ramadan fasting and inflammatory bowel disease. Indian journal of gastroenterology : official journal of the Indian Society of Gastroenterology, 27(6), 239–241. https://pubmed.ncbi.nlm.nih.gov/19405258/
Rajendran, N., & Kumar, D. (2010). Role of diet in the management of inflammatory bowel disease. World journal of gastroenterology, 16(12), 1442–1448. https://doi.org/10.3748/wjg.v16.i12.1442
Heuschkel, R. B., Menache, C. C., Megerian, J. T., & Baird, A. E. (2000). Enteral nutrition and corticosteroids in the treatment of acute Crohn’s disease in children. Journal of pediatric gastroenterology and nutrition, 31(1), 8–15. https://doi.org/10.1097/00005176-200007000-00005
Borrelli, O., Cordischi, L., Cirulli, M., Paganelli, M., Labalestra, V., Uccini, S., Russo, P. M., & Cucchiara, S. (2006). Polymeric diet alone versus corticosteroids in the treatment of active pediatric Crohn’s disease: a randomized controlled open-label trial. Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association, 4(6), 744–753. https://doi.org/10.1016/j.cgh.2006.03.010
Berni Canani, R., Terrin, G., Borrelli, O., Romano, M. T., Manguso, F., Coruzzo, A., D’Armiento, F., Romeo, E. F., & Cucchiara, S. (2006). Short- and long-term therapeutic efficacy of nutritional therapy and corticosteroids in paediatric Crohn’s disease. Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver, 38(6), 381–387. https://doi.org/10.1016/j.dld.2005.10.005
Pitman, S. D. (2019). Beating Crohn’s: And Other Autoimmune Diseases.

Key 4. Lazy gut: Reawaken

Gut Motility: Speedy or Sluggish

Bowel Transit Time

Siegel, R. L., Fedewa, S. A., Anderson, W. F., Miller, K. D., Ma, J., Rosenberg, P. S., & Jemal, A. (2017). Colorectal Cancer Incidence Patterns in the United States, 1974-2013. Journal of the National Cancer Institute, 109(8), djw322. https://doi.org/10.1093/jnci/djw322
Rebecca L. Siegel, Ahmedin Jemal, Elizabeth M. Ward; (2009). Increase in Incidence of Colorectal Cancer Among Young Men and Women in the United States. Cancer Epidemiol Biomarkers Prev 1 June 2009; 18 (6): 1695–1698. https://doi.org/10.1158/1055-9965.EPI-09-0186

Gut Motility and Other DILL+ Factors

Effect on the Microbiome - River vs Swamps

Asnicar, F., Leeming, E. R., Dimidi, E., Mazidi, M., Franks, P. W., Al Khatib, H., Valdes, A. M., Davies, R., Bakker, E., Francis, L., Chan, A., Gibson, R., Hadjigeorgiou, G., Wolf, J., Spector, T. D., Segata, N., & Berry, S. E. (2021). Blue poo: impact of gut transit time on the gut microbiome using a novel marker. Gut, 70(9), 1665–1674. https://doi.org/10.1136/gutjnl-2020-323877
Liu L. W. (2011). Chronic constipation: current treatment options. Canadian journal of gastroenterology = Journal canadien de gastroenterologie, 25 Suppl B(Suppl B), 22B–28B. Caenepeel, P., Janssens, J., Vantrappen, G. et al. Interdigestive myoelectric complex in germ-free rats. Digest Dis Sci 34, 1180–1184 (1989). https://doi.org/10.1007/BF01537265

Inflammation

Damage to Interstitial Cells of Cajal (ICC)

He, C. L., Soffer, E. E., Ferris, C. D., Walsh, R. M., Szurszewski, J. H., & Farrugia, G. (2001). Loss of interstitial cells of cajal and inhibitory innervation in insulin-dependent diabetes. Gastroenterology, 121(2), 427–434. https://doi.org/10.1053/gast.2001.26264
Vieira Frez, F. C., Martins Colombo Perles, J. V., Robert Linden, D., Gibbons, S. J., Amilcar Martins, H., Almeida Brito Romualdo, D., de Souza, S. R., Daion Piovezana Bossolani, G., & Zanoni, J. N. (2017). Restoration of density of interstitial cells of Cajal in the jejunum of diabetic rats after quercetin supplementation. Revista espanola de enfermedades digestivas, 109(3), 190–195. https://doi.org/10.17235/reed.2016.4338/2016

Physical Activities for Optimal Bowel Transit

Strengthening the Core and Abdominal Muscles

Song, B. K., Han, D., Brellenthin, A. G., & Kim, Y. S. (2021). Effects of core strengthening exercise on colon transit time in young adult women. Journal of exercise science and fitness, 19(3), 158–165. https://doi.org/10.1016/j.jesf.2021.02.001

Your Food and Gut Motility

The Fiber Paradox: Why Eat What You Can’t Digest

O’Keefe S. J. (2019). The association between dietary fibre deficiency and high-income lifestyle-associated diseases: Burkitt’s hypothesis revisited. The lancet. Gastroenterology & hepatology, 4(12), 984–996. https://doi.org/10.1016/S2468-1253(19)30257-2
Kjeldsen-Kragh, J., Haugen, M., Borchgrevink, C. F., & Førre, O. (1994). Vegetarian diet for patients with rheumatoid arthritis–status: two years after introduction of the diet. Clinical rheumatology, 13(3), 475–482. https://doi.org/10.1007/BF02242946
Hafström, I., Ringertz, B., Spångberg, A., von Zweigbergk, L., Brannemark, S., Nylander, I., Rönnelid, J., Laasonen, L., & Klareskog, L. (2001). A vegan diet free of gluten improves the signs and symptoms of rheumatoid arthritis: the effects on arthritis correlate with a reduction in antibodies to food antigens. Rheumatology (Oxford, England), 40(10), 1175–1179. https://doi.org/10.1093/rheumatology/40.10.1175
McDougall, J., Bruce, B., Spiller, G., Westerdahl, J., & McDougall, M. (2002). Effects of a very low-fat, vegan diet in subjects with rheumatoid arthritis. Journal of alternative and complementary medicine (New York, N.Y.), 8(1), 71–75. https://doi.org/10.1089/107555302753507195
Holscher H. D. (2017). Dietary fiber and prebiotics and the gastrointestinal microbiota. Gut microbes, 8(2), 172–184. https://doi.org/10.1080/19490976.2017.1290756

Prokinetic and Laxative Foods

Alexandrovich, I., Rakovitskaya, O., Kolmo, E., Sidorova, T., & Shushunov, S. (2003). The effect of fennel (Foeniculum Vulgare) seed oil emulsion in infantile colic: a randomized, placebo-controlled study. Alternative therapies in health and medicine, 9(4), 58–61. https://pubmed.ncbi.nlm.nih.gov/12868253/

Bile and Gut Motility

Ticho, A. L., Malhotra, P., Dudeja, P. K., Gill, R. K., & Alrefai, W. A. (2019). Bile Acid Receptors and Gastrointestinal Functions. Liver research, 3(1), 31–39. https://doi.org/10.1016/j.livres.2019.01.001

Careful With Laxatives

Liu L. W. (2011). Chronic constipation: current treatment options. Canadian journal of gastroenterology = Journal canadien de gastroenterologie, 25 Suppl B(Suppl B), 22B–28B.

Key 5. Factors Beyond Digestive Health: Recondition

The Hygiene Paradox: When Too Clean Becomes Too Much

Hygiene Hypothesis and “Old Friends” Effect

Kondrashova, A., Seiskari, T., Ilonen, J., Knip, M., & Hyöty, H. (2013). The ‘Hygiene hypothesis’ and the sharp gradient in the incidence of autoimmune and allergic diseases between Russian Karelia and Finland. APMIS : acta pathologica, microbiologica, et immunologica Scandinavica, 121(6), 478–493. https://doi.org/10.1111/apm.12023
Haahtela, T., Laatikainen, T., Alenius, H., Auvinen, P., Fyhrquist, N., Hanski, I., von Hertzen, L., Jousilahti, P., Kosunen, T. U., Markelova, O., Mäkelä, M. J., Pantelejev, V., Uhanov, M., Zilber, E., & Vartiainen, E. (2015). Hunt for the origin of allergy - comparing the Finnish and Russian Karelia. Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology, 45(5), 891–901. https://doi.org/10.1111/cea.12527
Kondrashova, A., Reunanen, A., Romanov, A., Karvonen, A., Viskari, H., Vesikari, T., Ilonen, J., Knip, M., & Hyöty, H. (2005). A six-fold gradient in the incidence of type 1 diabetes at the eastern border of Finland. Annals of medicine, 37(1), 67–72. https://doi.org/10.1080/07853890410018952

Skin Microbiome and T-Lymphocytes

Ostrov, B. E., & Amsterdam, D. (2017). Immunomodulatory interplay of the microbiome and therapy of rheumatic diseases. Immunological investigations, 46(8), 769–792. https://doi.org/10.1080/08820139.2017.1373828
Clark R. A. (2010). Skin-resident T cells: the ups and downs of on site immunity. The Journal of investigative dermatology, 130(2), 362-370. https://doi.org/10.1038/jid.2009.247

Spend More Time and Eat Outdoors

Roslund, M. I., Puhakka, R., Grönroos, M., Nurminen, N., Oikarinen, S., Gazali, A. M., Cinek, O., Kramná, L., Siter, N., Vari, H. K., Soininen, L., Parajuli, A., Rajaniemi, J., Kinnunen, T., Laitinen, O. H., Hyöty, H., Sinkkonen, A., & ADELE research group (2020). Biodiversity intervention enhances immune regulation and health-associated commensal microbiota among daycare children. Science advances, 6(42), eaba2578. https://doi.org/10.1126/sciadv.aba2578

Non-Organic Agriculture

Meyer, A., Sandler, D. P., Beane Freeman, L. E., Hofmann, J. N., & Parks, C. G. (2017). Pesticide Exposure and Risk of Rheumatoid Arthritis among Licensed Male Pesticide Applicators in the Agricultural Health Study. Environmental health perspectives, 125(7), 077010. https://doi.org/10.1289/EHP1013
Parks, C. G., Hoppin, J. A., De Roos, A. J., Costenbader, K. H., Alavanja, M. C., & Sandler, D. P. (2016). Rheumatoid Arthritis in Agricultural Health Study Spouses: Associations with Pesticides and Other Farm Exposures. Environmental health perspectives, 124(11), 1728–1734. https://doi.org/10.1289/EHP129

Environment and Climate: Where You Live Matters

Microclimate: Small Changes Without the Big Move

Sick House

Luosujärvi, R. A., Husman, T. M., Seuri, M., Pietikäinen, M. A., Pollari, P., Pelkonen, J., Hujakka, H. T., Kaipiainen-Seppänen, O. A., & Aho, K. (2003). Joint symptoms and diseases associated with moisture damage in a health center. Clinical rheumatology, 22(6), 381–385. https://doi.org/10.1007/s10067-003-0753-y
Pizzorno J. (2016). Is Mold Toxicity Really a Problem for Our Patients? Part I-Respiratory Conditions. Integrative medicine (Encinitas, Calif.), 15(2), 6–10.
Tuuminen T. (2020). The Roles of Autoimmunity and Biotoxicosis in Sick Building Syndrome as a “Starting Point” for Irreversible Dampness and Mold Hypersensitivity Syndrome. Antibodies (Basel, Switzerland), 9(2), 26. https://doi.org/10.3390/antib9020026

Hormones. Why Do Females Experience More Autoimmune Conditions?

Moulton V. R. (2018). Sex Hormones in Acquired Immunity and Autoimmune Disease. Frontiers in immunology, 9, 2279. https://doi.org/10.3389/fimmu.2018.02279

Testosterone

MInguez-Alarcón, L., Chavarro, J. E., Mendiola, J., Roca, M., Tanrikut, C., Vioque, J., Jørgensen, N., & Torres-Cantero, A. M. (2017). Fatty acid intake in relation to reproductive hormones and testicular volume among young healthy men. Asian journal of andrology, 19(2), 184–190. https://doi.org/10.4103/1008-682X.190323
Lokeshwar, S. D., Patel, P., Fantus, R. J., Halpern, J., Chang, C., Kargi, A. Y., & Ramasamy, R. (2021). Decline in Serum Testosterone Levels Among Adolescent and Young Adult Men in the USA. European urology focus, 7(4), 886–889. https://doi.org/10.1016/j.euf.2020.02.006 Patel, Premal; Fantus, Richard; Lokeshwar*, Soum; Halpern, Joshua; Chang, Cecilia; Kargi, Atil; Ramasamy, Ranjith (2020). MP78-01 TRENDS IN SERUM TESTOSTERONE LEVELS AMONG ADOLESCENT AND YOUNG ADULT MEN IN THE UNITED STATES, Journal of Urology: April 2020 - Volume 203 - Issue Supplement 4 https://doi.org/10.1097/JU.0000000000000964.01

Xenoestrogens

Cecilia Chighizola and Pier Luigi Meroni. (2012). The role of environmental estrogens and autoimmunity. Autoimmun Rev 2012;11:A493–A501.
Smith, D.B., Cannon, W.F., Woodruff, L.G., Solano, Federico, and Ellefsen, K.J., 2014, Geochemical and mineralogical maps for soils of the conterminous United States: U.S. Geological Survey Open-File Report 2014–1082, 386 p., http://dx.doi.org/10.3133/ofr20141082
Kuhnle, G. G., Dell’Aquila, C., Aspinall, S. M., Runswick, S. A., Mulligan, A. A., & Bingham, S. A. (2008). Phytoestrogen content of foods of animal origin: dairy products, eggs, meat, fish, and seafood. Journal of agricultural and food chemistry, 56(21), 10099–10104. https://doi.org/10.1021/jf801344x
Kuhnle, Gunter & Dell’Aquila, Caterina & Aspinall, Sue & Runswick, Shirley & Joosen, Annemiek & Mulligan, Angela & Bingham, Sheila. (2009). Phytoestrogen content of fruits and vegetables commonly consumed in the UK based on LC–MS and 13C-labelled standards. Food Chemistry. 116. 542-554. 10.1016/j.foodchem.2009.03.002.

Physical Exercises

Timing

Costa, R. J. S., Snipe, R. M. J., Kitic, C. M., & Gibson, P. R. (2017). Systematic review: exercise-induced gastrointestinal syndrome-implications for health and intestinal disease. Alimentary pharmacology & therapeutics, 46(3), 246–265. https://doi.org/10.1111/apt.14157

Exercises for Healthy Testosterone Levels

Nickmilder, M., & Bernard, A. (2011). Associations between testicular hormones at adolescence and attendance at chlorinated swimming pools during childhood. International journal of andrology, 34(5 Pt 2), e446–e458. https://doi.org/10.1111/j.1365-2605.2011.01174.x
Tyndall, G.L., Kobe, R.W. & Houmard, J.A. Cortisol, testosterone, and insulin action during intense swimming training in humans. Europ. J. Appl. Physiol. 73, 61–65 (1996). https://doi.org/10.1007/BF00262810
Cumming, D. C., Wall, S. R., Quinney, H. A., & Belcastro, A. N. (1987). Decrease in serum testosterone levels with maximal intensity swimming exercise in trained male and female swimmers. Endocrine research, 13(1), 31–41. https://doi.org/10.1080/07435808709023660

Enhancing Limbs’ Capillary Circulation: A Simple Exercise

Venslauskas, M., Ostaševičius, V., & Marozas, V. (2013). Limb’s Vibrations Exercise Monitoring with MEMS Accelerometer to Identify Influence of Cardiovascular System. Vibroengineering. Vibroengineering Procedia. September 2013. Volume 1. ISSN 2345-0533 https://www.extrica.com/article/10759/pdf
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Cardio Training

Clarke, S. F., Murphy, E. F., O’Sullivan, O., Lucey, A. J., Humphreys, M., Hogan, A., Hayes, P., O’Reilly, M., Jeffery, I. B., Wood-Martin, R., Kerins, D. M., Quigley, E., Ross, R. P., O’Toole, P. W., Molloy, M. G., Falvey, E., Shanahan, F., & Cotter, P. D. (2014). Exercise and associated dietary extremes impact on gut microbial diversity. Gut, 63(12), 1913–1920. https://doi.org/10.1136/gutjnl-2013-306541
Rao, R., & Samak, G. (2012). Role of Glutamine in Protection of Intestinal Epithelial Tight Junctions. Journal of epithelial biology & pharmacology, 5(Suppl 1-M7), 47–54. https://doi.org/10.2174/1875044301205010047

Sleep and Circadian Rhythms

Sleep’s Role in Combating Chronic Illness

Poroyko, V. A., Carreras, A., Khalyfa, A., Khalyfa, A. A., Leone, V., Peris, E., Almendros, I., Gileles-Hillel, A., Qiao, Z., Hubert, N., Farré, R., Chang, E. B., & Gozal, D. (2016). Chronic Sleep Disruption Alters Gut Microbiota, Induces Systemic and Adipose Tissue Inflammation and Insulin Resistance in Mice. Scientific reports, 6, 35405. https://doi.org/10.1038/srep35405
Wilson, R. G., Stevens, B. W., Guo, A. Y., Russell, C. N., Thornton, A., Cohen, M. A., Sturgeon, H. C., Giallourakis, C., Khalili, H., Nguyen, D. D., Yajnik, V., Sauk, J., & Ananthakrishnan, A. N. (2015). High C-Reactive Protein Is Associated with Poor Sleep Quality Independent of Nocturnal Symptoms in Patients with Inflammatory Bowel Disease. Digestive diseases and sciences, 60(7), 2136–2143. https://doi.org/10.1007/s10620-015-3580-5
Swanson, G. R., Burgess, H. J., & Keshavarzian, A. (2011). Sleep disturbances and inflammatory bowel disease: a potential trigger for disease flare?. Expert review of clinical immunology, 7(1), 29–36. https://doi.org/10.1586/eci.10.83

Circadian Rhythms

Hsiao, Y. H., Chen, Y. T., Tseng, C. M., Wu, L. A., Lin, W. C., Su, V. Y., Perng, D. W., Chang, S. C., Chen, Y. M., Chen, T. J., Lee, Y. C., & Chou, K. T. (2015). Sleep disorders and increased risk of autoimmune diseases in individuals without sleep apnea. Sleep, 38(4), 581–586. https://doi.org/10.5665/sleep.4574
Kim, H. I., Jung, S. A., Choi, J. Y., Kim, S. E., Jung, H. K., Shim, K. N., & Yoo, K. (2013). Impact of shiftwork on irritable bowel syndrome and functional dyspepsia. Journal of Korean medical science, 28(3), 431–437. https://doi.org/10.3346/jkms.2013.28.3.431
Nojkov, B., Rubenstein, J. H., Chey, W. D., & Hoogerwerf, W. A. (2010). The impact of rotating shift work on the prevalence of irritable bowel syndrome in nurses. The American journal of gastroenterology, 105(4), 842–847. https://doi.org/10.1038/ajg.2010.48
Swanson, G. R., Burgess, H. J., & Keshavarzian, A. (2011). Sleep disturbances and inflammatory bowel disease: a potential trigger for disease flare?. Expert review of clinical immunology, 7(1), 29–36. https://doi.org/10.1586/eci.10.83
Murakami, M., & Tognini, P. (2020). The Circadian Clock as an Essential Molecular Link Between Host Physiology and Microorganisms. Frontiers in cellular and infection microbiology, 9, 469. https://doi.org/10.3389/fcimb.2019.00469
Martchenko, A., Martchenko, S. E., Biancolin, A. D., & Brubaker, P. L. (2020). Circadian Rhythms and the Gastrointestinal Tract: Relationship to Metabolism and Gut Hormones. Endocrinology, 161(12), bqaa167. https://doi.org/10.1210/endocr/bqaa167
Voigt, R. M., Forsyth, C. B., Green, S. J., Engen, P. A., & Keshavarzian, A. (2016). Circadian Rhythm and the Gut Microbiome. International review of neurobiology, 131, 193–205. https://doi.org/10.1016/bs.irn.2016.07.002
Frazier, K., & Chang, E. B. (2020). Intersection of the Gut Microbiome and Circadian Rhythms in Metabolism. Trends in endocrinology and metabolism: TEM, 31(1), 25–36. https://doi.org/10.1016/j.tem.2019.08.013
Gombert, M., Carrasco-Luna, J., Pin-Arboledas, G., & Codoñer-Franch, P. (2019). The connection of circadian rhythm to inflammatory bowel disease. Translational research : the journal of laboratory and clinical medicine, 206, 107–118. https://doi.org/10.1016/j.trsl.2018.12.001
Besedovsky, L., Lange, T., & Born, J. (2012). Sleep and immune function. Pflugers Archiv : European journal of physiology, 463(1), 121–137. https://doi.org/10.1007/s00424-011-1044-0
Awuah, W. A., Huang, H., Kalmanovich, J., Mehta, A., Mikhailova, T., Ng, J. C., Abdul-Rahman, T., Adebusoye, F. T., Tan, J. K., Kamanousa, K., Ferreira, T., Roy, S., Kundu, M., Yarlagadda, R., Mukerjee, N., Alexiou, A., & Papadakis, M. (2023). Circadian rhythm in systemic autoimmune conditions: Potential of chrono-immunology in clinical practice: A narrative review. Medicine, 102(32), e34614. https://doi.org/10.1097/MD.0000000000034614
AMHSI Research Team, Milken Research Team, Roitblat, Y., Burger, J., Vaiman, M., Nehuliaieva, L., Buchris, N., & Shterenshis, M. (2021). Owls and larks do not exist: COVID-19 quarantine sleep habits. Sleep medicine, 77, 177-183. https://doi.org/10.1016/j.sleep.2020.09.003
Carvalho, F. G., Hidalgo, M. P., & Levandovski, R. (2014). Differences in circadian patterns between rural and urban populations: an epidemiological study in countryside. Chronobiology international, 31(3), 442-449. https://doi.org/10.3109/07420528.2013.846350

Melatonin: Friend or Foe?

Watad, A., Azrielant, S., Bragazzi, N. L., Sharif, K., David, P., Katz, I., Aljadeff, G., Quaresma, M., Tanay, G., Adawi, M., Amital, H., & Shoenfeld, Y. (2017). Seasonality and autoimmune diseases: The contribution of the four seasons to the mosaic of autoimmunity. Journal of autoimmunity, 82, 13-30. https://doi.org/10.1016/j.jaut.2017.06.001
Ghareghani, M., Zibara, K., & Rivest, S. (2023). Melatonin and vitamin D, two sides of the same coin, better to land on its edge to improve multiple sclerosis. Proceedings of the National Academy of Sciences of the United States of America, 120(14), e2219334120. https://doi.org/10.1073/pnas.2219334120
Lin G-J, Huang S-H, Chen S-J, Wang C-H, Chang D-M, Sytwu H-K. Modulation by Melatonin of the Pathogenesis of Inflammatory Autoimmune Diseases. International Journal of Molecular Sciences. 2013; 14(6):11742-11766. https://doi.org/10.3390/ijms140611742
Siah, K. T., Wong, R. K., & Ho, K. Y. (2014). Melatonin for the treatment of irritable bowel syndrome. World journal of gastroenterology, 20(10), 2492–2498. https://doi.org/10.3748/wjg.v20.i10.2492
Swanson, G. R., Gorenz, A., Shaikh, M., Desai, V., Forsyth, C., Fogg, L., Burgess, H. J., & Keshavarzian, A. (2015). Decreased melatonin secretion is associated with increased intestinal permeability and marker of endotoxemia in alcoholics. American journal of physiology. Gastrointestinal and liver physiology, 308(12), G1004–G1011. https://doi.org/10.1152/ajpgi.00002.2015
Chen, S. J., Huang, S. H., Chen, J. W., Wang, K. C., Yang, Y. R., Liu, P. F., Lin, G. J., & Sytwu, H. K. (2016). Melatonin enhances interleukin-10 expression and suppresses chemotaxis to inhibit inflammation in situ and reduce the severity of experimental autoimmune encephalomyelitis. International immunopharmacology, 31, 169–177. https://doi.org/10.1016/j.intimp.2015.12.020
https://www.sciencedirect.com/science/article/abs/pii/S1359610119300449
Zhao, C. N., Wang, P., Mao, Y. M., Dan, Y. L., Wu, Q., Li, X. M., Wang, D. G., Davis, C., Hu, W., & Pan, H. F. (2019). Potential role of melatonin in autoimmune diseases. Cytokine & growth factor reviews, 48, 1–10. https://doi.org/10.1016/j.cytogfr.2019.07.002

Snoring and Sleep Apnea: Hidden Threats to Brain Health

Phillips, B. G., Wang, Y., Ambati, S., Ma, P., & Meagher, R. B. (2020). Airways therapy of obstructive sleep apnea dramatically improves aberrant levels of soluble cytokines involved in autoimmune disease. Clinical immunology (Orlando, Fla.), 221, 108601. https://doi.org/10.1016/j.clim.2020.108601
Mirrakhimov A. E. (2013). Obstructive sleep apnea and autoimmune rheumatic disease: is there any link?. Inflammation & allergy drug targets, 12(5), 362-367. https://doi.org/10.2174/18715281113129990051
Kang, J. H., & Lin, H. C. (2012). Obstructive sleep apnea and the risk of autoimmune diseases: a longitudinal population-based study. Sleep medicine, 13(6), 583–588. https://doi.org/10.1016/j.sleep.2012.03.002

Oropharyngeal Exercises

Rueda, J. R., Mugueta-Aguinaga, I., Vilaró, J., & Rueda-Etxebarria, M. (2020). Myofunctional therapy (oropharyngeal exercises) for obstructive sleep apnoea. The Cochrane database of systematic reviews, 11(11), CD013449. https://doi.org/10.1002/14651858.CD013449.pub2

Your Digestive System Also Wants To Sleep

Martchenko, A., Martchenko, S. E., Biancolin, A. D., & Brubaker, P. L. (2020). Circadian Rhythms and the Gastrointestinal Tract: Relationship to Metabolism and Gut Hormones. Endocrinology, 161(12), bqaa167. https://doi.org/10.1210/endocr/bqaa167
Vaughn, Brad & Rotolo, Sean & Roth, Heidi. (2014). Circadian rhythm and sleep influences on digestive physiology and disorders. ChronoPhysiology and Therapy. 2014. 67. 10.2147/CPT.S44806.
Duboc, H., Coffin, B., & Siproudhis, L. (2020). Disruption of Circadian Rhythms and Gut Motility: An Overview of Underlying Mechanisms and Associated Pathologies. Journal of clinical gastroenterology, 54(5), 405–414. https://doi.org/10.1097/MCG.0000000000001333
Vaughn B, Rotolo S, Roth H. (2014). Circadian rhythm and sleep influences on digestive physiology and disorders. ChronoPhysiology and Therapy. 2014;4:67-77

https://doi.org/10.2147/CPT.S44806

Scheving L. A. (2000). Biological clocks and the digestive system. Gastroenterology, 119(2), 536–549. https://doi.org/10.1053/gast.2000.9305

Hydrotherapy and Temperature Contrast

Contrast Showers: A Practice You Can Start Today

Buijze, G. A., Sierevelt, I. N., van der Heijden, B. C., Dijkgraaf, M. G., & Frings-Dresen, M. H. (2016). The Effect of Cold Showering on Health and Work: A Randomized Controlled Trial. PloS one, 11(9), e0161749. https://doi.org/10.1371/journal.pone.0161749

Sauna and Steam Room

Crinnion W. J. (2011). Sauna as a valuable clinical tool for cardiovascular, autoimmune, toxicant- induced and other chronic health problems. Alternative medicine review : a journal of clinical therapeutic, 16(3), 215–225.
Oosterveld, F. G., Rasker, J. J., Floors, M., Landkroon, R., van Rennes, B., Zwijnenberg, J., van de Laar, M. A., & Koel, G. J. (2009). Infrared sauna in patients with rheumatoid arthritis and ankylosing spondylitis. A pilot study showing good tolerance, short-term improvement of pain and stiffness, and a trend towards long-term beneficial effects. Clinical rheumatology, 28(1), 29–34. https://doi.org/10.1007/s10067-008-0977-y
Eversden, L., Maggs, F., Nightingale, P., & Jobanputra, P. (2007). A pragmatic randomised controlled trial of hydrotherapy and land exercises on overall well being and quality of life in rheumatoid arthritis. BMC musculoskeletal disorders, 8, 23. https://doi.org/10.1186/1471-2474-8-23
Mahlouji, M., Alizadeh Vaghasloo, M., Dadmehr, M., Rezaeizadeh, H., Nazem, E., & Tajadini, H. (2020). Sweating as a Preventive Care and Treatment Strategy in Traditional Persian Medicine. Galen medical journal, 9, e2003. https://doi.org/10.31661/gmj.v9i0.2003

Oral Health and Other Autoimmune Triggers

Chronic Inflammation in Your Body

Rashid, T., & Ebringer, A. (2012). Autoimmunity in Rheumatic Diseases Is Induced by Microbial Infections via Crossreactivity or Molecular Mimicry. Autoimmune diseases, 2012, 539282. https://doi.org/10.1155/2012/539282
Balandraud, N., Roudier, J., & Roudier, C. (2004). Epstein-Barr virus and rheumatoid arthritis. Autoimmunity reviews, 3(5), 362–367. https://doi.org/10.1016/j.autrev.2004.02.002
Larsen, M., Sauce, D., Deback, C., Arnaud, L., Mathian, A., Miyara, M., Boutolleau, D., Parizot, C., Dorgham, K., Papagno, L., Appay, V., Amoura, Z., & Gorochov, G. (2011). Exhausted cytotoxic control of Epstein-Barr virus in human lupus. PLoS pathogens, 7(10), e1002328. https://doi.org/10.1371/journal.ppat.1002328
Poole, B. D., Scofield, R. H., Harley, J. B., & James, J. A. (2006). Epstein-Barr virus and molecular mimicry in systemic lupus erythematosus. Autoimmunity, 39(1), 63–70. https://doi.org/10.1080/08916930500484849
Pender M. P. (2012). CD8+ T-Cell Deficiency, Epstein-Barr Virus Infection, Vitamin D Deficiency, and Steps to Autoimmunity: A Unifying Hypothesis. Autoimmune diseases, 2012, 189096. https://doi.org/10.1155/2012/189096
Toussirot, E., & Roudier, J. (2008). Epstein-Barr virus in autoimmune diseases. Best practice & research. Clinical rheumatology, 22(5), 883–896. https://doi.org/10.1016/j.berh.2008.09.007

Oral Microbiome, Gums, and Teeth

Chronic Gum Inflammation and Dental Pockets

Mercado, F. B., Marshall, R. I., Klestov, A. C., & Bartold, P. M. (2001). Relationship between rheumatoid arthritis and periodontitis. Journal of periodontology, 72(6), 779-787. https://doi.org/10.1902/jop.2001.72.6.779
Routsias, J. G., Goules, J. D., Goules, A., Charalampakis, G., & Pikazis, D. (2011). Autopathogenic correlation of periodontitis and rheumatoid arthritis. Rheumatology (Oxford, England), 50(7), 1189-1193. https://doi.org/10.1093/rheumatology/ker090

Oral Microbiome

Loyola-Rodriguez, J. P., Martinez-Martinez, R. E., Abud-Mendoza, C., Patiño-Marin, N., & Seymour, G. J. (2010). Rheumatoid arthritis and the role of oral bacteria. Journal of oral microbiology, 2, 10.3402/jom.v2i0.5784. https://doi.org/10.3402/jom.v2i0.5784
Olsen, I., & Yamazaki, K. (2019). Can oral bacteria affect the microbiome of the gut?. Journal of oral microbiology, 11(1), 1586422. https://doi.org/10.1080/20002297.2019.1586422

Autoimmunity Unlocked

5 Keys to Transform Microbiome, Immune, and Digestive Health and Reclaim Your Life. A 5R+ Holistic System Encyclopedia with Tactics for Rheumatoid Arthritis, Lupus, and Crohn’s.

Appendix 2: References and Additional Reading

Hope in the Face of the Incurable

Immune System - The Good, the Bad, and the Ugly

The Ugly: An Ailing Immune System

Diseases Related to Immune System Disorders

The Immune System and Cancer - An Inconspicuous Link

Autoimmune Diseases - A Modern Epidemic

Immune Illness On the Rise

The Good: The Holistic Way to Restore the Immune System

DILL+: Locks and Vicious Cycles

Key 1. Dysbiosis: Repopulate the Microbiome

The Last Discovered Organ That Reshapes Our Understanding of Health

Microbial Forces Within Us

A Busy, Adaptable Organ

Dimension 1: Microbiome Composition

Variety - Farmland vs Forest

Actively Repopulate

Building a Healthy Community

Probiotics

Fermented Vegetables and Pickles

Fermented Dairy

Cheese

Fecal Microbial Transplantation: Success or Temporary Fix?

Feeding your Allies

Prebiotics

Dead or Alive - Enzymes in Your Food

Frozen, Dried, Salted - Preserving Raw Produce

Polyphenols: The Colorful Path to a Diverse Microbiome

Vitamin K

The Myth of Healthy Toppings on Junk Food

Food Diversity

Dimension 2: Microbiome Distribution

SIBO, IBS, IBD, Ulcers: Many Faces of Microbiome Maldistribution

Small Intestinal Bacterial Overgrowth (SIBO)

Below the Waterline: Subclinical SIBO

Ulcers and Helicobacter pylori

Healthy Digestion to Fix Microbiota Distribution

Don’t Rush the Reactor

Surgical Procedures to Avoid

Stomach Acid

Acid - The Protective Firewall

Antacids and “Heartburn” (Gastroesophageal Reflux)

Bile and Liver Health

Bile Salt Malabsorption and the Microbiome

Helping Your Liver

Reduce Toxic Load

Hepatoprotective Food

Glutathione

Other Tactics for Fixing SIBO and Normalizing Microbiome Distribution

Power of Herbs, Spices, and Other Foods to Control Microbial Growth

Spices to Avoid

Antimicrobial Herbs and Spices

N-Acetylcysteine (NAC)

Fungi: Mold and Yeast

Addressing the SIFO Problem

Feeding Your Enemies

Sweet Does Not Equal Good

Sugar

Natural Sweeteners

Unnatural Sweeteners

Conquering Sugar Cravings

Good Options for Sweet Cravings

Children’s Foods - Passing the Problem to the Next Generation

Other Risks to Your Microbiome Health

Inflammation

Antibiotics

Antibiotics Residues in Food

Antibiotics’ Effect on the Microbiota of Animal Products

Navigating Animal Products

Chlorine and Related Compounds in Water

Reverse Osmosis and Remineralization

Why Water Quality Matters

Chemical Additives and Toxins in Our Food

Chemical Toxins in the Polluted World

Microplastics and Nanoplastics

Fish Safety

Heavy Metals and Chelation Foods

Alcohol