How Does Chronic Illness Affect Gut Health?

How Does Chronic Illness Affect Gut Health

When patients come to our clinic, we continuously assess their gut health regardless of the type of complex chronic illness they are being treated for. For many patients, this may seem like an odd request. What does gastrointestinal health have to do with Lyme disease, autoimmune, chronic fatigue, or any other chronic condition? From head to toe, gut health has everything to do with our body’s healing ability. Chronic illness can damage the gut in the following ways:

  1. Imbalance of harmful bacteria and a decrease of beneficial bacteria.
  2. Slow digestive motility
  3. Lead to chronic inflammation
  4. Cause intestinal permeability issues
  5. Increase the risk of cognitive health issues

Restoration Healthcare treats complex chronic illnesses, which can significantly impact gut health. Any severe disease, prescribed medications, or treatments can disrupt the balance of bacteria in the gut, leading to an overgrowth of harmful bacteria and a decrease in beneficial bacteria. This imbalance, known as dysbiosis, can result in digestive issues such as bloating, gas, and diarrhea. Chronic illness can also affect the motility of the digestive system, leading to slowed or irregular bowel movements. The most critical issue with a poorly functioning digestive system is inflammation.

Inflammation and Gut Health

The human body contains trillions of microorganisms; nearly 80% of the immune system resides in the human gut. A person’s intestinal tract is teeming with a vibrant gut microbiota that contains as many as one hundred trillion microorganisms, 1,000 species, and 7,000 strains of bacteria. Specific bacterial species can prevent or promote inflammation and play a significant role in supporting overall health.

Bacteria in the microbiota consist of three primary groups:

  1. Commensal bacteria are harmless bacteria that protect the immune system;
  2. Symbiotic bacteria are beneficial as they manage enzyme secretion and short-chain fatty acid production;
  3. Pathobiontic bacteria are harmful because they compete with other bacteria and vie for nutrients and necessary resources.

When pathobiontic bacteria become too abundant from antibiotics and medications, poor diet, and illness, they create an inflammatory-rich environment that triggers proinflammatory cytokines. Conditions like Crohn’s and inflammatory bowel disease (IBD) are linked to many proinflammatory cytokines. Ongoing studies show other metabolic disorders like obesity, fatty liver disease,  hypertension, kidney disease, depression, anxiety, and neurodegenerative diseases are linked to an abundance of proinflammatory cytokines.

Leaky Gut and Chronic Disease

When inflammation is persistent, it can damage the lining of the gut, which creates increased intestinal permeability, also known as leaky gut syndrome. Toxins and normally healthy undigested food particles enter the bloodstream through the open junctions, which may trigger an autoimmune response and lead to further inflammation.

According to research, the leakage can cause various health issues, including bloating and gas, cramps, fatigue, skin rashes, food allergies, sensitivities, and headaches. Other more severe conditions include autoimmune conditions, mood disorders and depression, Type 1 diabetes, Type 2 diabetes, IBD, and degenerative diseases like multiple sclerosis. Researchers are studying the possibility that many non-gastrointestinal related disorders may be associated with or exacerbated by leaky gut, including the following conditions:

Asthma and allergies

Parkinson’s disease,

Multiple sclerosis,



Eosinophilic esophagitis,



Chronic fatigue syndrome,

Non-alcoholic fatty liver disease (NAFLD),


Metabolic syndrome,

Rheumatoid arthritis

Central nervous system injury

Gut Permeability and the Brain

Another issue related to gut health and chronic illness is brain health. At our clinic, we frequently find that our patients experience gastrointestinal issues, brain fog, confusion, and frequent headaches as a symptom of their complex chronic illness. This is because the brain and gut are intimately connected through the gut-brain axis. It’s a complex bi-directional relationship meaning that injury to one end of the axis can negatively affect the other. Here is a scenario of how this may occur:

  1. Damage to the central nervous system through injury or illness can lead to disorders that affect the hypothalamic‐pituitary‐adrenal axis, autonomic nervous system, and enteric nervous system. These three systems are responsible for 1. signaling of the neural, endocrine, immune, and metabolic pathways, 2. involuntary physiologic processes, and 3. neural circuits for endocrine and immune function, respectively.
  2. The damage causes changes in the intestinal microenvironment, disrupting the immune system and altering intestinal bacteria.
  3. Ultimately, this increases intestinal permeability, i.e., leaky gut.
  4. Inflammatory agents produced by intestinal neurons, immune cells, and intestinal flora migrate through the intestinal barriers.
  5. When the breach occurs, it aggravates peripheral inflammation and the central nervous system causing central nervous system diseases and disorders.
  6. The bidirectional relationship between the gut and brain is why we examine a patient’s gut and brain health as standard practice for our patients.

Integrative Treatments for Leaky Gut

When our patients are treated for intestinal permeability or leaky gut, we use various treatments to heal the open junctions. When the gut is damaged, it interferes with nutrient and medication absorption, so most of our patients have regular Infusion-therapy sessions. Intravenous therapies bypass the gut, so when our physicians can prescribe suitable compounds for healing, the patient’s body readily absorbs what they need.

Other important aspects of healing the intestinal lining include dietary supplements, such as prebiotics and probiotics. Our physicians choose a symbiotic approach so that the prebiotics feed the probiotics to help restore the microbiota to a balanced state. An individual may need more specific vitamins and minerals because the body has not been absorbing adequate levels of nutrients.

Nutrition is always an essential aspect of care. Our patients work with their physicians to establish healthy eating habits abundant with polyphenols, fibers, and fermented foods that help heal the gut. We also emphasize stress management and mind-body techniques to heal the gut and the brain.

Some people may also have to avoid certain antagonizing foods because of food sensitivities and allergies that develop from inflammation and gut permeability issues. Our physician may also recommend avoiding gluten, sugars, and short-chain carbohydrates (sugars the intestines have trouble digesting).

Foods for a Healthy Gut

No matter one’s health status, there is food that can help improve gut health. None of these replace seeing a specialist if you believe you have a complex chronic illness, but eating a diet rich in prebiotic and probiotic foods is essential for gut health.

Probiotic foods are cultured and fermented foods that contain beneficial microorganisms. Prebiotics are non-digestible fibers that help feed probiotics and healthy gut bacteria. By maintaining a balance of probiotic and prebiotic foods, our bodies can maintain a healthy gastrointestinal system, immune and cardiovascular system, and central nervous system, which:

  1. Supports healthy blood sugar levels,
  2. Maintains normal blood lipids,
  3. Allows for healthy bowel motility,
  4. Balances beneficial gut bacteria,
  5. Reduces the risk for chronic diseases.

The following are essential foods to help balance healthy bacteria and prevent the overgrowth of damaging pathobiontic bacteria.

  • Yogurt  and kefir (non-dairy if your physician suggests),
  • Sauerkraut and pickled vegetables fermented by lactic acid bacteria (not vinegar),
  • Tempeh, fermented soybeans,
  • Kimchi or Korean fermented vegetables,
  • Miso from fermented soy,
  • Kombucha drinks (low sugar),
  • Dark leafy greens,
  • Artichokes,
  • Jerusalem Artichokes,
  • Chicory,
  • Asparagus,
  • Fennel,
  • Cabbage,
  • Seaweed,
  • Mushrooms,
  • Onions and garlic,
  • Apples,
  • Bananas,
  • Blueberries,
  • Nectarines,
  • Persimmons,
  • Watermelon,
  • Grapefruit,
  • Pomegranate,
  • Dried figs and dates

If you’re in or near Irvine, California, contact us for an initial consultation. Our medical director, Dr. Sunny Raleigh, is widely recognized by patients and referring physicians from across the country as among the top Chronic Illness doctors in the country.