A Functional Medicine Approach to Treating Depression

Dr. Kate Henry
A Functional Medicine Approach to Treating Depression

Depression affects up to 23% of the world’s population each year and is ranked among the top 5 leading causes of disability worldwide. Psychotherapy and pharmaceutical medications are the mainstay of traditional treatments for depression, but if these haven’t worked for you or a loved one, don’t give up! Functional medicine approaches to treating depression can significantly improve mood and focus on identifying the root cause of depression.


Signs & Symptoms of Depression

The National Institutes of Mental Health defines depression as “a period of at least two weeks of depressed mood or loss of interest in daily activities. As well as as problems with sleep, eating, energy, concentration, or self-worth.” This can show up differently for many people. For some, it looks like lying in bed and feeling like they no longer want to see friends or work. For others, it can look like eating more and finding themselves more tearful or irritable than normal. Depression also varies in severity and can be mild or debilitating. Thankfully, there are many effective ways to treat it, no matter how it shows up.

Possible Causes of Depression

Micronutrient Deficiencies

A number of nutrient deficiencies are linked with depression, including deficiencies in B vitamins like cobalamin (B12), folate (B9), pyridoxine (B6); minerals like zinc, selenium, magnesium, iodine, copper, and calcium; and other nutritional compounds like amino acids, antioxidants, vitamin D and omega 3’s. This list is not exhaustive. In fact, over 20 different nutrient deficiencies have been linked with depression!

If you’re like many, you may be thinking that it’s unlikely that you have a nutrient deficiency, particularly if you’re overweight or regularly consume enough total calories.

But research indicates that Americans are significantly deficient in many critical nutrients due to a nutrient-poor diet. For example, 90% of people with obesity are deficient in vitamin D - a nutrient that is directly linked with depression and seasonal affective disorder.

Hormone Disorders

Abnormalities in the hormone cortisol, thyroid hormone, estrogen, progesterone, testosterone, DHEA, and neurohormones like serotonin, dopamine, and norepinephrine are linked with depression.

Having hypothyroidism, for example, can lead to depression and other symptoms like weight gain, hair loss, fatigue, and bloating.

Minerals and Heavy Metals

Minerals (also known as metals) create electricity in the body. Our brains use electrical signals to communicate with our muscles, tissues, and organs and help release and transport neurotransmitters.

Having a mineral deficiency like iron-deficient anemia can absolutely result in a depressed mood. However, having too many metals or minerals is not a good thing either. Excessive levels of heavy metals like aluminum, lead, or mercury can cause depression, cognitive issues, and other mental health and brain-based disorders.

Food Allergies and Sensitivities

Food allergies that are mediated by IgE immunoglobulins and histamine reactions can cause depressed mood by altering blood flow to the brain. Similarly, IgG and IgA food sensitivities and food intolerances can impact mood. Celiac disease, for example, is an IgG / IgA immune intolerance to wheat that is linked with depression and other mood disorders.

Functional Medicine Labs to Find the Root Causes of Depression

Testing for Micronutrient Deficiencies

There are several ways to assess for nutrient deficiencies, including collect-at-home blood spot tests, blood draws, nutrient profiles that look at cell contents, and more. Even a standard CBC and CMP that your doctor runs every year at your check-up can detect some B vitamin and iron deficiencies.

Testing for Hormone Imbalances

Your practitioner can measure various hormones in the urine and blood, including progesterone, testosterone, DHEA, cortisol, estrogens, and more.

Testing for Heavy Metals

Practitioners can check hair, blood, and urine to detect heavy metal abnormalities. If findings are normal, but you still suspect you may have heavy metal toxicity, another option is a provocation challenge test. This type of test requires taking a small dose of a heavy metal chelator and then checking how much of that metal is excreted into the urine.

Testing for Food Sensitivities

When assessing food allergies and food sensitivities, there are many blood spot and blood draw collection kits that your practitioner can use to find the foods that you may be reacting to. An important point to note is - for food sensitivities - you actually have to have eaten the food in the last two weeks (preferably three days) for your body to make enough immunoglobulins to detect a reaction. Ask your practitioner for more information if you’re confused about this.

Functional Medicine Treatment for Depression

The treatment for your unique form of depression will determine your root cause. If you have a nutrient deficiency, your practitioner will help you design either a food-as medicine plan or prescribe a supplement to help replete you.

If your issue is hormonal, your clinician will prescribe hormone replacement or work to eliminate the barriers to normal hormone production using a combination of lifestyle, nutrients, herbs, and even pharmaceuticals.

If you have a food allergy or sensitivity, your practitioner will work with you to properly eliminate all IgE mediated responses (allergies) and eliminate and reintroduce IgG mediated responses (sensitivities) while still ensuring that you get proper micronutrient needs. Some practitioners will refer out to Integrative Nutritionists.

Many people are curious if “natural medicine” can be used instead of pharmaceuticals to treat depression. For many people, the answer is yes. For others, natural medicine makes a great addition to their existing treatment plan. A great example is taking folic acid or folate with an SSRI to increase the effectiveness of the SSRI. Your unique plan will be a combination of whatever works best for you, whether it’s pharmaceuticals, meditation, food, sleep, or movement.


There are many root causes of depression that a functional medicine practitioner can help you detect, treat and heal. These include nutrient deficiencies, hormonal imbalances, food allergies and sensitivities, and many more.

A skilled practitioner can help you find your individual root cause and heal your depression naturally if you choose so that you can get back to feeling happy, healthy, and in love with your life.

*Special thanks to Dr. Kate Henry's naturopathic assistant, Lindsey Bevilacqua, for her help with this article.

Other Articles You May Be Interested In

Featured Bundles

No items found.


  1. Berthoud, Hans-Rudolf. “The Vagus Nerve, Food Intake and Obesity.” Regulatory Peptides, vol. 149, no. 1-3, Aug. 2008, pp. 15–25, www.ncbi.nlm.nih.gov/pmc/articles/PMC2597723/, 10.1016/j.regpep.2007.08.024. Accessed 10 Aug. 2021.
  2. “Blood Test: Tissue Transglutaminase IgA, IgG.” Rchsd.org, RCHSD, 2014, www.rchsd.org/health-articles/blood-test-tissue-transglutaminase-iga-igg/. Accessed 6 Jan. 2022.
  3. Browning, Kirsteen N., and R. Alberto Travagli. “Central Nervous System Control of Gastrointestinal Motility and Secretion and Modulation of Gastrointestinal Functions.” Comprehensive Physiology, 30 Sept. 2014, pp. 1339–1368, www.ncbi.nlm.nih.gov/pmc/articles/PMC4858318/, 10.1002/cphy.c130055. Accessed 10 Aug. 2021.
  4. Coppen, Alec, and John Bailey. “Enhancement of the Antidepressant Action of Fluoxetine by Folic Acid: A Randomised, Placebo Controlled Trial.” Journal of Affective Disorders, vol. 60, no. 2, Nov. 2000, pp. 121–130, pubmed.ncbi.nlm.nih.gov/10967371/, 10.1016/s0165-0327(00)00153-1. Accessed 6 Jan. 2022.
  5. Du, Jing, et al. “The Role of Nutrients in Protecting Mitochondrial Function and Neurotransmitter Signaling: Implications for the Treatment of Depression, PTSD, and Suicidal Behaviors.” Critical Reviews in Food Science and Nutrition, vol. 56, no. 15, 3 Nov. 2014, pp. 2560–2578, www.ncbi.nlm.nih.gov/pmc/articles/PMC4417658/, 10.1080/10408398.2013.876960. Accessed 6 Jan. 2022.
  6. Fernstrom, John D. “Effects of the Diet on Brain Neurotransmitters.” Metabolism, vol. 26, no. 2, Feb. 1977, pp. 207–223, pubmed.ncbi.nlm.nih.gov/13261/, 10.1016/0026-0495(77)90057-9. Accessed 17 Jan. 2021.
  7. Figueiredo, Bárbara, et al. “Breastfeeding and Postpartum Depression: State of the Art Review.” Jornal de Pediatria, vol. 89, no. 4, July 2013, pp. 332–338, www.sciencedirect.com/science/article/pii/S0021755713000892?via%3Dihub, 10.1016/j.jped.2012.12.002. Accessed 23 Mar. 2021.
  8. Glenn, Jordan M., et al. “Dietary Protein and Amino Acid Intake: Links to the Maintenance of Cognitive Health.” Nutrients, vol. 11, no. 6, 12 June 2019, p. 1315, www.ncbi.nlm.nih.gov/pmc/articles/PMC6627761/, 10.3390/nu11061315. Accessed 28 Oct. 2021. (Glenn et al.).
  9. Hidese, Shinsuke, et al. “Association between Iron-Deficiency Anemia and Depression: A Web-Based Japanese Investigation.” Psychiatry and Clinical Neurosciences, vol. 72, no. 7, 9 May 2018, pp. 513–521, pubmed.ncbi.nlm.nih.gov/29603506/, 10.1111/pcn.12656. Accessed 6 Jan. 2022.
  10. Ilchmann-Diounou, Hanna, and Sandrine Menard. “Psychological Stress, Intestinal Barrier Dysfunctions, and Autoimmune Disorders: An Overview.” Frontiers in Immunology, vol. 11, 25 Aug. 2020, pubmed.ncbi.nlm.nih.gov/32983091/, 10.3389/fimmu.2020.01823. Accessed 10 Aug. 2021.
  11. Jamilian, Mehri, et al. “The Effects of Probiotic and Selenium Co-Supplementation on Parameters of Mental Health, Hormonal Profiles, and Biomarkers of Inflammation and Oxidative Stress in Women with Polycystic Ovary Syndrome.” Journal of Ovarian Research, vol. 11, no. 1, 14 Sept. 2018, www.ncbi.nlm.nih.gov/pmc/articles/PMC6137747/, 10.1186/s13048-018-0457-1. Accessed 6 Jan. 2022. Overall, the co-administration of probiotic and selenium for 12 weeks to women with PCOS had beneficial effects on mental health parameters, serum total testosterone, hirsutism, hs-CRP, TAC, GSH and MDA levels.
  12. Kreutz, Johanna M., et al. “Narrative Review: Nutrient Deficiencies in Adults and Children with Treated and Untreated Celiac Disease.” Nutrients, vol. 12, no. 2, 15 Feb. 2020, p. 500, www.ncbi.nlm.nih.gov/pmc/articles/PMC7071237/#B110-nutrients-12-00500, 10.3390/nu12020500. Accessed 10 Aug. 2021.
  13. Liu, Tao, et al. “A Meta-Analysis of Oxidative Stress Markers in Depression.” PLOS ONE, vol. 10, no. 10, 7 Oct. 2015, p. e0138904, pubmed.ncbi.nlm.nih.gov/26445247/?from_term=cholesterol+depression&from_pos=4, 10.1371/journal.pone.0138904. Accessed 8 May 2020.
  14. “Major Depression.” National Institute of Mental Health (NIMH), 2019, www.nimh.nih.gov/health/statistics/major-depression. Accessed 6 Jan. 2022.
  15. Mizuguchi, Yuki, et al. “Prediction of Response to Medical Therapy by Serum Soluble (Pro)Renin Receptor Levels in Graves’ Disease.” PLOS ONE, vol. 13, no. 4, 5 Apr. 2018, p. e0195464, www.ncbi.nlm.nih.gov/pmc/articles/PMC5886569/, 10.1371/journal.pone.0195464. Accessed 24 Aug. 2021.
  16. Murray, Christopher, et al. BURDEN of DISEASE a Comprehensive Assessment of Mortality and Disability from Diseases, Injuries, and Risk Factors in 1990 and Projected to 2020 EDITED by :I’ I 1ffW.
  17. Murray, Christopher J L, et al. The Global Burden of Disease. 1 : A Comprehensive Assessment of Mortalityand Disability from Diseases, Injuries, and Risk Factors in 1990 and Projected to 2020 : (Uden Titel). Cambridge, Mass., Published By The Harvard School Of Public Health Onbehalf Of The World Health Organization And The World Bank, 1996, digitallibrary.un.org/record/195443?ln=en. Accessed 6 Jan. 2022.
  18. NIDDK. “Celiac Disease Tests.” National Institute of Diabetes and Digestive and Kidney Diseases, 6 Jan. 2022, www.niddk.nih.gov/health-information/professionals/clinical-tools-patient-management/digestive-diseases/celiac-disease-health-care-professionals. Accessed 6 Jan. 2022.
  19. “NIH Human Microbiome Project Defines Normal Bacterial Makeup of the Body.” National Institutes of Health (NIH), 31 Aug. 2015, www.nih.gov/news-events/news-releases/nih-human-microbiome-project-defines-normal-bacterial-makeup-body. Accessed 10 Aug. 2021.
  20. “Office of Dietary Supplements - Folate.” Nih.gov, 2016, ods.od.nih.gov/factsheets/Folate-HealthProfessional/. Accessed 6 Jan. 2022.
  21. “Office of Dietary Supplements - Iodine.” Nih.gov, 2019, ods.od.nih.gov/factsheets/Iodine-HealthProfessional/. Accessed 6 Jan. 2022.
  22. “Office of Dietary Supplements - Iron.” Nih.gov, 2015, ods.od.nih.gov/factsheets/Iron-HealthProfessional/. Accessed 6 Jan. 2022.
  23. “Office of Dietary Supplements - Omega-3 Fatty Acids.” Nih.gov, 2015, ods.od.nih.gov/factsheets/Omega3FattyAcids-HealthProfessional/. Accessed 6 Jan. 2022.
  24. “Office of Dietary Supplements - Potassium.” Nih.gov, 2017, ods.od.nih.gov/factsheets/Potassium-HealthProfessional/. Accessed 23 Mar. 2021.
  25. “Office of Dietary Supplements - Selenium.” Nih.gov, 2020, ods.od.nih.gov/factsheets/Selenium-HealthProfessional/. Accessed 6 Jan. 2022.
  26. “Office of Dietary Supplements - Vitamin B12.” Nih.gov, 2013, ods.od.nih.gov/factsheets/VitaminB12-HealthProfessional/. Accessed 6 Jan. 2022.
  27. “Office of Dietary Supplements - Vitamin E.” Nih.gov, 2017, ods.od.nih.gov/factsheets/VitaminE-HealthProfessional/. Accessed 27 July 2021.
  28. Roberts, Seren Haf, et al. “Folate Augmentation of Treatment – Evaluation for Depression (FolATED): Protocol of a Randomised Controlled Trial.” BMC Psychiatry, vol. 7, no. 1, 15 Nov. 2007, www.ncbi.nlm.nih.gov/pmc/articles/PMC2238748/, 10.1186/1471-244x-7-65. Accessed 6 Jan. 2022. In addition, there is evidence to suggest that folate deficiency, (e.g., as may be produced by inflammatory disorders or anticonvulsant drug treatment [19]), may aggravate depression or impair response to treatment.
  29. Sangle, Prerna, et al. “Vitamin B12 Supplementation: Preventing Onset and Improving Prognosis of Depression.” Cureus, 26 Oct. 2020, www.ncbi.nlm.nih.gov/pmc/articles/PMC7688056/, 10.7759/cureus.11169. Accessed 6 Jan. 2022. The study showed lesser scores on the Mini-Mental Status Exam (MMSE) and higher depression scores among patients with lower plasma levels of Vitamin B12 [25].
  30. TSUJITA, Natsuki, et al. “Effect of Tryptophan, Vitamin B6, and Nicotinamide-Containing Supplement Loading between Meals on Mood and Autonomic Nervous System Activity in Young Adults with Subclinical Depression: A Randomized, Double-Blind, and Placebo-Controlled Study.” Journal of Nutritional Science and Vitaminology, vol. 65, no. 6, 31 Dec. 2019, pp. 507–514, 10.3177/jnsv.65.507. First sentence of discussion.
  31. Vargas, Heber Odebrecht, et al. “Oxidative Stress and Inflammatory Markers Are Associated with Depression and Nicotine Dependence.” Neuroscience Letters, vol. 544, June 2013, pp. 136–140, pubmed.ncbi.nlm.nih.gov/23583694/, 10.1016/j.neulet.2013.03.059. Accessed 3 Nov. 2021.
  32. Via, Michael. “The Malnutrition of Obesity: Micronutrient Deficiencies That Promote Diabetes.” ISRN Endocrinology, vol. 2012, 15 Mar. 2012, pp. 1–8, www.ncbi.nlm.nih.gov/pmc/articles/PMC3313629/#:~:text=Despite%20excessive%20dietary%20consumption%2C%20obese,diabetes%20in%20the%20obese%20population., 10.5402/2012/103472. Accessed 6 Jan. 2022.
  33. Wolters, Maike, et al. “Effects of N-3 Polyunsaturated Fatty Acid Supplementation in the Prevention and Treatment of Depressive Disorders—a Systematic Review and Meta-Analysis.” Nutrients, vol. 13, no. 4, 25 Mar. 2021, p. 1070, pubmed.ncbi.nlm.nih.gov/33806078/, 10.3390/nu13041070. Accessed 21 Sept. 2021.
  34. World. “Depression.” Who.int, World Health Organization: WHO, 13 Sept. 2021, www.who.int/news-room/fact-sheets/detail/depression. Accessed 6 Jan. 2022.
Dr. Kate Henry
Dr. Kate Henry is a naturopathic doctor with advanced training in mind-body medicine and functional approaches in psychiatry. Her study of nutrition, botanicals, and lifestyle medicine has enabled her to offer unique expertise and out-of-the-box solutions for chronic and stubborn health issues, including SIBO, PCOS, depression, anxiety, POTS, and more.
Order from 20+ labs in 20 seconds (DUTCH, GPL, Genova & More!)
We make ordering quick and painless — and best of all, it's free for practitioners.
Return to Magazine

Join our mailing list

Thank you! Your submission has been received!
Oops! Something went wrong while submitting the form.