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Is Leaky Gut the Cause of Your Symptoms?

Functional medicine approach to Gut Health and Autoimmunity


Autoimmunity: A Case Study

Ulcerative colitis (UC) is an autoimmune related disease that causes inflammation and sores, called ulcers, in the lining of the rectum and colon. It is a chronic, autoimmune, relapsing, and remitting disorder that affects genetically susceptible individuals’ immune response to the world around them.

Case Presentation

A 36-year-old Indian female presented with a host of symptoms that have been plaguing her for the past 12 years. These include frequent abdominal pain, loose stools, gas, and bloating that come and go. She has also been suffering from recurrent sneezing and a runny nose throughout the year since her teenage years. The patient has been experiencing headaches on both sides of her forehead that are not affected by light but are relieved by painkillers. Additionally, she has difficulty sleeping and staying asleep, and she feels anxious.

Upon visiting her gastroenterologist, the patient was diagnosed with ulcerative colitis, a chronic inflammatory bowel disease that causes inflammation and ulcers in the digestive tract. She also has a family history of various medical conditions, including allergies, asthma, heart disease, diabetes, and hypertension.  From a functional medicine perspective, these conditions are considered her antecedent, meaning they are her predisposition to developing certain medical conditions.

The patient’s triggers are numerous and varied. They include being born via caesarean section, early weaning, surgery for a congenital heart defect under general anaesthesia, and antibiotic use. Other triggers are picky eating, an Indian vegetarian diet that is high in wheat and dairy (refined carbohydrates and low in fruits, vegetables, healthy fats, and protein), junk food during college, and binge drinking.

In addition, the patient has been exposed to numerous antibiotics and nonsteroidal anti-inflammatory drugs (NSAIDs) due to surgeries for CHD, recurrent flu, dysmenorrhoea, headaches, gastroenteritis, in vitro fertilisation (IVF), dilation and curettage (D&C) for miscarriage, and upper respiratory tract infections (URTIs).

Chief concerns

  1. Abdominal pain, gas, bloating, diarrhoea, blood in stool related to ulcerative colitis flares
  2. Sneezing & runny nose all over the year (allergic rhinitis)
  3. Headaches
  4. Stress, anxiety, irritability
  5. Disordered sleep pattern

History of Present illness

We discussed each one of the 3 major flares in her symptoms of abdominal pain, diarrhoea, bloody stools in the past 12 years in detail. This included symptoms, triggers, treatment plans at that time etc. 

She came to me in July 2018 just after having an upper respiratory tract infection and being prescribed 7 days of augmentin. She started having gas, bloating and 3-4 loose stools/ day. She got scared and started to look for ways to not to have a flare without medications. She has also felt low in energy after lunchtime. Also, recently she has suffered from brain fog.

Life History

  • Mother had a normal pregnancy, second child, brother 5 years older, born via LSCS as there was failure to progress.
  • No breastfeeding, so fed with formula. Early weaning at 4 months with rice.
  • Congenital heart defect.
  • Failure to gain weight.
  • Operation for the congenital heart defect.
  • A Sickly child with flu & fever, saw doctors who gave antibiotics & fever medication.
  • Childhood in a small agricultural town in India, she was not very happy as parents were in a dysfunctional marriage and used to fight in front of her.
  • Meals were mainly home-cooked, Indian vegetarian, wheat, dairy and rice-based. She was a picky eater so did not eat well at all.
  • She had menarche at the age of 13 and had to take NSAIDs every month since then for dysmenorrhoea. Her menses have normal flow with no clots and she doesn’t suffer from any other premenstrual symptoms. She has been checked by her gynaecologist who said that she doesn’t have any gynaecological problem.
  • She moved to Hostel in New Delhi at the age of 18, where she ate ready-made and Indian street (junk) food and did binge drinking during weekends. The exams were a stressful period and she started having abdominal episodes at that time. She also got gastroenteritis once and had to take a course of Norfloxacin for 7 days. 

  • She had allergic rhinitis and took antihistamines for it on a regular basis.
  • This lifestyle continued from graduation to post-graduation when she had the first severe flare in 2006 and the gastroenterologist in India diagnosed it as Ulcerative colitis. 
  • She got married after that and moved to Singapore. She had 2 children delivered by normal vaginal delivery, their pregnancies and delivery were uncomplicated. No history of accidents and injuries or getting medical treatment for any other health issue.

Social History

EducationBA 1998, MA 2000
EmploymentSchool Teacher- Full time work. Loves her work but feels stressed out when marking for exams.

Family History

Family MemberHealth History
Maternal GrandfatherDied at 70, cause unknown
Maternal GrandmotherDied at 50 due to heart disease
Paternal GrandfatherDied at 85, cause unknown
Paternal GrandmotherDied at 90, cause unknown
MotherHas diabetes, hypertension
FatherHas allergic rhinitis, asthma
SonAllergic rhinitis, asthma

Birth History

LSCS, formula-fed, early weaning
Failure to gain weight
Congenital heart defect
Surgery for CHD

Personal History 

Sexual historyOnly one sexual partner- her husband
Religious / spiritual practicePrays regularly
PurposeHas sense of purpose and wants to be a good mother and wants to help her clients feel better

Physical Examination

Standing128/76 pulse 72 pulse ox 98%
Supine126/76 pulse 70 pulse ox 97%
Sidelying124/72 Pulse 70 96% Orthostatic BP, pulse and pulse ox stable with lying,standing and after running up/down the stairs
124/72 Pulse 70 96% Orthostatic BP, pulse and pulse ox stable with lying,standing and after running up/down the stairs124/72 Pulse 70 96% Orthostatic BP, pulse and pulse ox stable with lying,standing and after running up/down the stairs
GeneralWell appearing
PsychOriented X3, intact recent and remote memory, judgement and insight, looked anxious. Nails: white spots, no ridges, appear strong, doesn’t bite them
TongueWhite coated, no scalloping, fasciculations, creases seen
TeethGingivitis, has gum bleeding, no fillings, no sign of gum recession or periodontitis
SkinNormal, normal body hair distribution
HairDry and dull hair, no hair loss
EyesConjunctiva clear without pallor, EOM intact, PERRL
NoseNo external lesions, mucosa non-inflamed, septum and turbinates normal
MouthPharynx non-inflamed, no tonsillar hypertrophy or exudate, palate mobile,uvula midline. Good dentition. Oral mucosa moist and normal in appearance
NeckSupple, without lesions or adenopathy, thyroid non-enlarged and non-tender
HeartPMI nondisplaced, no thrills or lifts, regular rate, rhythm w/ normal S1 &S2, no S3 or S4 detected, no murmurs or gallops
ChestNormal respiratory effort, chest wall without deformities, lungs clear to auscultation. No wheezing noted
AbdomenNon-distended, bowel sounds normal, no tenderness, organomegaly, masses, bruits, or hernia, no cva tenderness
MusculoskeletalNormal gait and station. No deformity, swelling, pain, erythema, decreased range of motion or strength found in u/l extremities or spine Neuro: CN 2-12 normal. DTRs present/normal in upper and lower extremities

Putting together the pieces of the Jigsaw


This patient’s medical history is complex and multifaceted, with various factors potentially contributing to her symptoms. Having experience of working in the Department of Gastroenterology and General Medicine in a busy London hospital, based on her medical history and physical examination findings, I assessed that she might be suffering from increased intestinal permeability (Leaky Gut). 

Various exposures in her life (antibiotics, NSAIDs, chronic stress, allergenic foods, poor diet, alcohol, gastroenteritis) could have caused increased intestinal permeability, caused gut dysbiosis and caused maldigestion & malabsorption leading to the abdominal symptoms. This can also cause micronutrient deficiencies, immune dysregulation, inflammation, oxidative stress giving rise to ulcerative colitis, headaches and allergic rhinitis. 

Given her symptoms of anxiety, sleep issues, brain fog, low energy and the chronic stressors throughout her life she could be having adrenal stress and imbalance in her neurotransmitters.

Patient Goals

  1. To find the underlying root cause of abdominal symptoms (ulcerative colitis) and to not take medications for it.
  2. To help with headaches and not to rely on pain killers
  3. To help with the allergic rhinitis and not to take the anti-allergics
  4. To help manage stress and anxiety
  5. To improve sleep quality
  6. To feel healthy again and to be able to take good care of her young kids and perform her work well



1. 7-day diet and lifestyle diary

2. Maldigestion test 

3. Conventional Labs: 

  • a) Celiac panel (given she had been eating gluten)
  • b) Vitamin D3 
  • c) Thyroid panel: TSH, TT3, RT3, FT3, FT4, antibodies, and iodine level

4. Functional  Lab tests: 

 As she had financial restrictions, we decided to prioritise GI map test, Vitamin D, coeliac panel & basic thyroid function test which included TSH, FT3, FT4. 

I referred her to a health coach who can provide her with the tools to make nutritional and lifestyle changes which will help make her journey easier. I also referred her to a mindfulness practitioner who can teach her the mindfulness breathing techniques to help with stress and sleep. She agreed with the two referrals.

Lifestyle Interventions

Sleep & relaxation- Discussed the importance of a good night sleep. Sleep can affect all nodes of the functional medicine matrix. A good night’s sleep is healing and it affects mood & energy levels and I passed a sleep hygiene leaflet to her to read and follow. I also discussed with her the importance of relaxation to help with the stress hormone and neurotransmitters and asked her to discuss with her husband for ways he can help her in finding time for relaxation. I discussed her case with our health coach and mindfulness practitioner who will give her tools and resources to make these changes easier.

Nutrition & Hydration

Started her on a special diet. I discussed with her the importance of removing potential allergenic foods to help with the increased intestinal permeability. We discussed the removal of commonly sensitive foods. This was a huge lifestyle change for her, but she was willing to give it a try as she did not want to go through another flare of ulcerative colitis.  We also discussed increasing fruits & vegetables in her diet which are known to be helpful in Ulcerative colitis. We also discussed removing wine as alcohol causes increased intestinal permeability. She was on board to try the dietary changes with the help of a health coach.

Exercise & Movement

To increase walks to 4-5 times per week or add in 20 minutes yoga 3 times a day. Asked her to discuss with her husband to share workload related to kids and house chores so that she can get time to exercise. Exercise helps with balancing the adrenal gland and is known to be helpful in inflammatory bowel disease.


Discussed with her the importance of managing stressors as it can affect sleep, mood and gut health. So balancing adrenal stress hormones is very useful. I passed her the mindfulness breathing leaflet. And also referred her to a mindfulness practitioner.


Confide with husband and share workload with him. Spend more time with friends`like going for a walk together. Communicate more with parents to help improve relationships.


Mindfulness practitioner for mindfulness breathing to help with stress and insomnia

Functional medicine health coach- to provide with tools and resources to help her follow the prescribed diet.

Other Interventions

In her first visit, I explained to her the importance of good quality supplements which are FDA approved GMP certified, which are third party checked for purity, free from heavy metals and excipients. I asked her to change her current supplements to:

  1. OmegaAvail 3gm (Designs for Health)- 2 soft gel two times a day after a meal

Her mainly vegetarian diet seems to be lacking polyunsaturated fat and Omega 3 are well researched to be useful in reducing inflammation in Ulcerative Colitis

It has EPA (Eicosapentaenoic Acid) 662  + DHA (Docosahexaenoic Acid) 250mg

This clinical grade omega 3 is derived from Sustainably sourced Marine Stewardship Council (MSC)‑certified wild Alaskan fish oils. It’s Molecularly distilled and filtered to ensure purity and to maximize the removal of metals, pesticides, PCBs, and other contaminants.

  1. Therbiotic complete 1 capsule after a meal

Her history suggested that she could be having gut dysbiosis so probiotics will increase the amount of beneficial bacteria. Asked her to start the Klaire Lab probiotic after the stool sample is taken.

It’s a Probiotic Blend (25 Billion CFU) in a base of Inulin 280mg / This probiotic has InTactic® technology so that none of the good bacteria die in stomach acid. I explained to her that most of the probiotics on the market do not have InTactic® technology.


Follow Up #1:  3 weeks after the Initial Visit


Abdominal pain, bloating, gas & headache were the same, though anxiety, sleep, sneezing and runny nose were slightly better. She managed to follow the  diet reasonably well with the help of the health coach. She took her supplements regularly. She also tried to follow lifestyle intervention as far as possible.  


Normal BP, underweight, well supported by her family  


Wt: 46kg (same as first visit)

BP: 126/ 72, pulse 72, MSQ – 52 

Laboratory Findings:

GI map Stool analysis report

Klebsiella pneumoniae 4+

Adequate beneficial bacteria

Candida lusitaniae- 1+

No parasites

Digestion & Absorption marker in the normal range

Lactoferrin- 108 high (Normal- less than 7.3 microg/ml)

Calprotectin- 483 high ( Normal- less than 50 microg/g)

Lysozyme- 763 (Normal- less than 600 ng/ml)

White Blood cells- Moderately high

Secretory IgA- 378 (Normal 51-204 mg/dl)

Valerate- 0.1 low (0.8-7%)

Rest of the SCFA- in normal range

ph- 5.4 low (6-7.8)


Blood panel

25 (OH) Vitamin D- 20

Zinc- low 0.4 mcg/ml (normal range is 0.66 to 1.10 mcg/mL)

Coeliac panel- normal

TSH, FT3, FT4- within normal limit


Overall Summary & Recommendations

She was suffering from a vicious cycle of maldigestion, malabsorption, gut dysbiosis, inflammation and immune dysregulation, possible sympathetic drive & adrenal stress, all of this leading to micronutrient deficiencies, mitochondrial dysfunction and her symptoms.

These were the imbalances found as per the FUNCTIONAL MEDICINE MATRIX:

In her first visit, I explained to her the importance of good quality supplements which are FDA approved GMP certified, which are third party checked for purity, free from heavy metals and excipients. I asked her to change her current supplements to:

    • Digestion/Absorption – Maldigestion  and malabsorption.
    • Intestinal permeability – leaky gut – no evidence of coeliac
    • Gut microbiome –  bacterial dysbiosis & mild candida in large intestine 
    • Immune modulation/Infection/ Inflammation – high inflammation, yeast and  dysbiotic bacteria – no parasites, sIgA low
      Nervous system – sympathetic overdrive.
  1. IMMUNE & INFLAMMATION  – Imbalanced immune system due to gut dysbiosis, increased intestinal permeability, food sensitivities and micronutrient deficiencies. Working on all these factors and adding in Saccharomyces boulardii will help with secretory IgA and reducing inflammation
  2. COMMUNICATION & TRANSPORTATION – Cortisol levels are possibly high with a tired and wired pattern. Melatonin levels could be low too given the sleep disturbances. Mindful breathing will help, but consider doing the adrenal function test.  
  3. ENERGY – Chances of oxidative stress and micronutrient deficiencies given the previous imbalanced diet and malabsorption.
  4. NUTRIENTS  – Low Vitamin D, low zinc as per the blood test. Add Vitamin D and zinc and if required later we can do Nutreval to know more about micronutrient deficiencies.
  5. DETOXIFICATION – Toxins/ Biotransformation- no known exposure, but something to consider testing for in the future if progress isn’t made.

She had 5 more follow up sessions with me, once every month and we worked through all these imbalances one by one using detailed Functional medicine protocol.

Current Status


The patient’s goal was to find out the underlying root cause of her abdominal symptoms (ulcerative colitis). We succeeded in doing that by a detailed history, examination and functional testing and found that she had gut dysbiosis, increased intestinal permeability, inflammation and adrenal stress. She hasn’t had to take any medications for it for the last 18 months.

She wanted to cure headaches and we were able to do it by taking care of the mitochondrial, gut and adrenal health.

She was fed up with having allergies and we succeeded in removing them by removing the triggers for her sneezing and her runny nose. We worked  improving gut health and the immune system.

Her anxiety is gone and sleep is much better and we worked on it by putting on many lifestyle interventions and balancing her adrenal hormones and neurotransmitters.

She feels healthy now and is able to take good care of her kids and is performing very well in her work.

The patient’s ulcerative colitis is in remission for the past 18 months now. She was able to introduce most of the food back in her diet except for a few. There is currently no need for follow up as she feels well now. I have explained to her that if she feels any of her symptoms back again, we should look into SIBO and toxic load for her as we did not explore these further. All her goals are met and she emails me yearly to update me about her condition and has been doing very well.

Frequently Asked Questions

What are Autoimmune Conditions and what causes them?

Autoimmune conditions are disorders where the immune system mistakenly attacks healthy cells in the body. This can lead to a wide range of symptoms and affect various body parts. Common autoimmune diseases include Rheumatoid arthritis, Psoriasis, Lupus, Thyroid diseases, and Type 1 diabetes. Symptoms of autoimmune diseases can vary but often include fatigue, joint pain and swelling, skin problems, abdominal pain or digestive issues, recurring fever, and swollen glands. Factors like genetics, environmental triggers, ethnicity, and certain medications can contribute to the development of autoimmune diseases. 

Can functional medicine doctors help with autoimmune disease?

Functional medicine doctors can indeed help with autoimmune diseases by taking a personalized, holistic approach to identify and address the root causes of the condition. Unlike conventional medicine that often focuses on symptom management and reducing immune system activity, functional medicine aims to restore health by understanding why illness occurs. In my experience, gut health plays a significant role in autoimmune diseases. Comprehensive gut tests check for gut infections and intestinal permeability. By addressing underlying mechanisms causing autoimmunity, functional medicine can potentially prevent and even reverse autoimmune disorders.

Dr Menka Gupta


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