Poor digestion and absorption

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‘You are what you eat’ is only partially true: ‘You are also what you absorb…’.Merino del Portillo, M., Clemente-Suárez, V.J., Ruisoto, P., Jimenez, M., Ramos-Campo, D.J., Beltran-Velasco, A.I., Martínez-Guardado, I., Rubio-Zarapuz, A., Navarro-Jiménez, E. and Tornero-Aguilera, J.F., 2024. Nutritional modulation of the gut–brain axis: a comprehensive review of dietary interventions in depression and anxiety management. Metabolites, 14(10), p.549. Merlo, G., Bachtel, G. and Sugden, S.G., 2024. Gut microbiota, nutrition, and mental health. Frontiers in Nutrition, 11, p.1337889.

Even if you have a very healthy diet, if you have gut issues, your digestion could be compromised, and you won’t absorb the nutrients you need, which can lead to imbalances in neurotransmitters and in hormones, leading to mental health symptoms.

Furthermore, issues with digestion can create bi-products which can cause mental health symptoms:

  • For instance, when a particular enzyme called DPP-IV, which helps break down gluten and casein, malfunctions, noxious peptides can be created in the gut and end up in the brain
  • Peptides are ‘morphine-like’ in nature, and wreak havoc with brain function just as heroin or a psychedelic drug wouldKean, J.D., Sarris, J. and Scholey, A., 2021. Casomorphins and gliadorphins have diverse systemic effects spanning gut, brain and internal organs. International Journal of Environmental Research and Public Health, 18(15), p.7911.

Possible mental health symptoms of poor digestion and absorption

Possible causes of poor digestion and absorption

A healthy gut is essential to digest and absorb the nutrients from your diet. Certain factors can disrupt optimal digestion and absorption of nutrients.

Stomach acid, also known as gastric acid or hydrochloric acid (HCl), is composed of hydrochloric acid (HCl), potassium chloride (KCl) and Sodium Chloride (NaCl). These components are essential for proper digestion and absorption of nutrients. They also help to keep the pH in the digestive system optimal, which is crucial for maintaining a correct balance of bacteria in our gut. Indeed, gastric acid has the ability to neutralise harmful bacteria, fungi  and other pathogens which may enter our digestive tract through intake of food, water or air.

Stomach acid is critical for triggering digestive enzymes, absorbing B12, B9 and vitamin C, managing microbes, and for immune health.

  • HCL is secreted by parietal cells in the stomach wall
  • When a person starts to eat, the stomach starts to produce HCL which helps start the digestion process
  • HCL is instrumental in the production of pepsin which digests protein, and which renders some minerals, such as calcium and iron, more absorbable
  • HCL helps to kill bacteria, viruses and parasites that enter with the food
  • HCL stimulates the secretion of pancreatic juices

Possible causes of low stomach acid

  • Long term stress and repeatedly stressful mealtimes
    • Short term stress can actually boost HCl, however chronic stress will reduce HCl production
  • Nutrient deficient diet and processed foods
    • Lack of sufficient minerals in the diet, excess carbohydrates, especially refined sugar, which deplete minerals
    • Zinc deficiency, Vitamin B deficiency, especially B1
  • Drinking iced water with meals, as very cold water blocks the production of HCl
  • Ageing
    • From our mid-30s onwards, the natural production of stomach acid starts to diminish. By the time we are in our late 40s or early 50s, most women and men produce less than half the stomach acid they did in their 20sVara-Luiz, F., Mendes, I., Palma, C., Mascarenhas, P., Simas, D., Gomes, P., Gonçalves, A., Simão, I., Teixeira, M., Lopes, S. et al., 2025. Age-related decline of gastric secretion: facts and controversies.
  • Antacid use, and some prescription drugs can suppress HCL production
  • Chronic illness
  • Candida

Low pancreatic enzymes can hamper digestion and absorption of nutrients, and coupled with leaky gut, can cause larger proteins to break past the mucosal barriers where they can then cause an inflammatory reaction.

Possible symptoms of low pancreatic enzyme secretion

  • Fatty stools (Steatorrhoea)
  • Bloating, discomfort, pain within one hour of eating
  • Reflux
  • Drowsiness after meals
  • Loss of appetite
  • Food allergies/sensitivities
  • Low zinc, B12 and folate absorption

Whitcomb, D.C., Buchner, A.M. and Forsmark, C.E., 2023. AGA clinical practice update on the epidemiology, evaluation, and management of exocrine pancreatic insufficiency: expert review. Gastroenterology, 165(5), pp.1292–1301. Alkaade, S. and Vareedayah, A.A., 2025. Exocrine pancreatic insufficiency.

Possible causes of low pancreatic enzymes

  • Genetic factors
  • Zinc deficiency
  • Toxins such as mercury, which inactivate these enzymesElbossaty, W.F., 2025. Mercury toxicity resulting from enzyme alterations: a minireview. BioMetals, 38, pp.1–14.

High cortisol levels signals digestion to stop, in favor of more important bodily functions involved in the fight or flight response:

  • Blood is diverted from the stomach to the muscles
  • The production of digestive enzymes and saliva are slowed
  • Intestinal contractions and absorption of nutrients are stoppedLeigh, S.-J., Uhlig, F., Wilmes, L., Sanchez-Diaz, P., Gheorghe, C.E., Goodson, M.S., Kelley-Loughnane, N., Hyland, N.P., Cryan, J.F. and Clarke, G., 2023. The impact of acute and chronic stress on gastrointestinal physiology and function: a microbiota–gut–brain axis perspective. The Journal of Physiology, 601(20), pp.4491–4538.
  • High cortisol depletes vitamins B1, B5, B6, B12, CB1, B6 and B12 which are important for stress tolerance
  • High cortisol depletes tyrosine
  • High cortisol depletes magnesiumPickering, G., Mazur, A., Trousselard, M., Bienkowski, P., Yaltsewa, N., Amessou, M., Noah, L. and Pouteau, E., 2020. Magnesium status and stress: the vicious circle concept revisited. Nutrients, 12(12), p.3672.

Leaky gut and inflammation can contribute to poor digestion and absorption of nutrients.

How leaky gut and inflammation can impact our mental health.

Gut dysbiosis and SIBO can contribute to poor digestion and absorption of nutrients.

How gut dysbiosis and SIBO can impact our mental health.