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Functional Medicine for Gut Health

Your gut, or GI (gastrointestinal) tract, breaks down food so your body can use it, and it is home to trillions of bacteria. Digestive symptoms such as heartburn, bloating and constipation are common, and they can have many different causes. At Avicenna Functional Medicine, our team works alongside your primary care doctor or gastroenterologist (a GI doctor), looking at factors that may contribute, and we do not replace your doctor or your prescribed treatment.1, 3, 5, 7

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Medically reviewed by Fawad Ahmed, MD on · Last updated

Man standing in his kitchen after a meal with a hand on his stomach, looking uncomfortable, for a page on gut health

What is gut health?

Gut health involves your digestive tract and the bacteria that live in it. Working together with your nerves, hormones and blood, they digest the food and drinks you have each day.1

Your digestive tract is a long, twisting tube that runs from your mouth to your anus. Food passes through the mouth, the esophagus (the tube that carries food to your stomach), the stomach, the small intestine and the large intestine. Your liver, pancreas and gallbladder are also part of the digestive system.1

Digestion breaks food into parts small enough for your body to absorb and use for energy, growth and cell repair. Your stomach mixes food with stomach acid and other digestive juices. Your small intestine absorbs most of the nutrients in your food. Your large intestine absorbs water and turns waste into stool.1

Nerves and hormones help control digestion. Signals travel within your gut and back and forth between your gut and your brain.1

Your microbiome is the collection of microbes, such as bacteria, fungi and viruses, and their genes, that naturally live on and inside your body. Each body site, such as the gut, skin and mouth, has its own community of microbes.2

One study estimated that an adult body holds about 38 trillion bacteria, roughly as many as the body's own cells. The vast majority of these bacteria live in the colon, which is part of the large intestine.3, 2, 1

Microbes help protect you against germs, help your immune system develop, and help you digest food to make energy. In the large intestine, bacteria help break down the nutrients that are left and make vitamin K. Your core microbiome forms in the first years of life, but it can change over time with diet, medicines and things in your environment.2, 1

Research has linked an imbalance in the gut microbiome to a broad range of conditions, both in and outside the gut. But there is no agreed way yet to tell when a gut microbiome is out of balance. An international consensus of 69 experts from 18 countries noted that a common definition of dysbiosis (an imbalance in the gut microbiome) is not available, so it can't yet be used in medical care. More research is needed.4

Diagram of the digestive tract for gut health, from mouth to large intestine, showing what each part does and where most gut bacteria liveMouth: chewingstarts digestionEsophagus:carries food downSmall intestine:absorbs mostnutrientsStomach: mixesfood with acidLarge intestine:forms stoolMost gutbacteria livehere
Food travels from the mouth down the esophagus to the stomach, which mixes it with acid. The small intestine absorbs most nutrients, and the large intestine, where most gut bacteria live, absorbs water and forms stool.1, 3

Common digestive symptoms

Digestive symptoms such as heartburn, indigestion, bloating and constipation are common. Almost everyone has belly pain at some point, and most of the time it is not serious. But how bad pain feels does not always show how serious its cause is.5, 7

Many people think they need to have a bowel movement every day, but this is not correct. If you have three bowel movements each week and feel well, you are healthy.5

Common digestive symptoms include:5

  • Heartburn: a burning feeling in your chest or throat when stomach acid moves up into your food pipe5
  • Indigestion: feeling full too soon during a meal, feeling uncomfortably full after a meal, or burning or pain in your upper belly5, 6
  • Gas, burping and bloating (a feeling of fullness in the upper belly)5
  • Belly pain or cramps5, 7
  • Nausea (the feeling that you need to vomit) and vomiting5, 6
  • Constipation: straining, passing small, hard stools, or feeling that your bowels haven't fully emptied5
  • Diarrhea: loose or watery stools5

How digestive problems are diagnosed and treated

Many different conditions can cause belly pain and other digestive symptoms. Less serious causes of belly pain include constipation, irritable bowel syndrome (IBS), food allergies or intolerances (such as lactose intolerance), food poisoning and stomach flu. Other possible causes include ulcers, inflammation of the gallbladder, inflammatory bowel disease and reflux (GERD).7, 5

If you have digestive symptoms often, or if they are severe, a primary care doctor or GI doctor can help find out what is causing them and how to treat them.5

Your provider will do a physical exam and ask about your symptoms and medical history. Your symptoms, where you feel pain and when it happens help your provider find the cause. They may also ask what makes it worse, such as eating, stress or lying down, and what medicines you take.7

Tests that may be done include blood, urine and stool tests, a CT scan, or an ultrasound of the belly. Others are an upper endoscopy, in which a tube is passed through the mouth into the esophagus, stomach and upper small intestine, and a colonoscopy, in which a tube is passed through the rectum into the colon.7

Some common digestive problems are disorders of gut-brain interaction. These are related to problems with how the brain and gut work together. They are not diseases, but groups of symptoms that occur together. Most long-lasting indigestion is diagnosed as one of these, called functional dyspepsia. IBS is another example.6, 5

Don't take any medicine for belly pain without talking to your provider first.7

How our care fits alongside your primary care doctor or gastroenterologist

Avicenna Functional Medicine does not replace your primary care doctor or gastroenterologist, or the treatment they prescribe. Our role is to add to your care, not to take its place.

In a functional medicine visit, we look at factors that may contribute to digestive symptoms, such as eating habits, trigger foods, food intolerances, past gut infections, medicines, stress, sleep and the gut microbiome, alongside the care you already receive.

Research links several of these factors to digestive symptoms. Spicy foods, caffeine and lying down too soon after eating can make heartburn worse. Long-lasting diarrhea can be caused by food intolerances, infections and sometimes certain medicines. Some medicines, such as certain antibiotics, may cause indigestion, and anxiety and depression may play a role in functional dyspepsia.5, 6

Your gut microbiome can change with diet and medicines. But because there is no agreed definition yet of an imbalanced gut microbiome, any testing we suggest is one piece of information, not a diagnosis. It does not replace the tests your doctor uses.2, 4

Please do not stop or change any prescribed medication without talking to the doctor who prescribed it.

What to expect at Avicenna

All visits are by telehealth, for patients located in Florida and Texas. We are a cash-pay practice, and we accept HSA and FSA. Care usually follows these steps:

  • A free, 30-minute discovery call to talk about your health and whether our approach is a good fit for you
  • A full intake visit with our health coach, under clinician supervision, covering your history, symptoms, current treatment and goals
  • Testing chosen for you, where it is likely to be useful
  • A personalized plan, with follow-up visits to review how you are doing and adjust the plan as needed

When to get urgent care

Some digestive symptoms can be a sign of a more serious condition. If you have indigestion, see a doctor right away if you also have any of these: trouble swallowing or pain when you swallow, frequent vomiting, bloody vomit, black stools that look like tar, severe and constant belly pain, bloating or swelling in your belly that lasts a long time, yellowing of your eyes or skin, weight loss without trying or loss of appetite, pain in your chest, jaw, neck or arm, or shortness of breath.6

Contact your provider if you have belly discomfort that lasts 1 week or longer, bloating that lasts more than 2 days, diarrhea for more than 5 days, or a fever over 100°F (37.7°C) with belly pain. Also contact them if you have a poor appetite that goes on for a long time, weight loss you can't explain, or you can't keep down any food or liquids.7

Get medical help right away or call 911 if you are vomiting blood or have blood in your stool (especially if it is bright red, maroon or dark, tarry black), or if you are unable to pass stool, especially if you are also vomiting. Do the same if you have sudden, sharp belly pain, a belly that is rigid and hard to the touch, or pain in or between your shoulder blades with nausea.7

Telehealth visits with our team are not for emergencies. Call 911 right away if you have warning signs of a medical emergency, such as:8

  • Chest pain or pressure that lasts two minutes or more8
  • Trouble breathing or shortness of breath8
  • Sudden confusion, unusual behavior or trouble waking up8
  • Fainting or passing out8
  • Sudden dizziness, weakness or changes in vision8
  • Being unable to speak8
  • Severe belly pain, or sudden severe pain anywhere in the body8
  • Coughing up or vomiting blood8
  • Thoughts of suicide or of harming someone else (you can also call or text 988)8

Who you’ll work with

Our Chief Medical Officer, Dr. Fawad Ahmed, and Co-Founder Sonia Mirza, APRN, FNP-BC, develop the practice’s treatment protocols. Your care is overseen by a clinician licensed in the state where you are at the time of your visit: in Florida, Dr. Ahmed or Sonia Mirza; in Texas, Sonia Mirza. Visits are with our health coach, who helps you put your plan into practice under that clinician’s supervision. Meet the team

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Sources

The small numbers on this page link to the source that backs each fact:

  1. NIDDK: Your digestive system & how it works. https://www.niddk.nih.gov/health-information/digestive-diseases/digestive-system-how-it-works
  2. NIEHS: Microbiome. https://www.niehs.nih.gov/health/topics/science/microbiome
  3. Sender R, Fuchs S, Milo R. Revised estimates for the number of human and bacteria cells in the body. PLoS Biol. 2016. https://pmc.ncbi.nlm.nih.gov/articles/PMC4991899/
  4. Porcari S, et al. International consensus statement on microbiome testing in clinical practice. Lancet Gastroenterol Hepatol. 2025 (repository copy). https://edepot.wur.nl/685103
  5. American College of Gastroenterology: Gastrointestinal (GI) symptoms overview. https://gi.org/topics/common-gi-symptoms/
  6. NIDDK: Symptoms & causes of indigestion. https://www.niddk.nih.gov/health-information/digestive-diseases/indigestion-dyspepsia/symptoms-causes
  7. MedlinePlus: Abdominal pain. https://medlineplus.gov/ency/article/003120.htm
  8. MedlinePlus: Recognizing medical emergencies. https://medlineplus.gov/ency/article/001927.htm

This page is general information, not medical advice, and it doesn’t create a patient relationship. See our Medical Disclaimer. In an emergency, call 911.

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* Our approach complements not replaces conventional medical care. Always consult your physician or qualified healthcare provider before making changes to medications, treatment, or care plan. Read our full Medical Disclaimer.