Nutrient deficiencies are a lack of proper essential nutrients (nutrients the body needs to function but does not make on its own) and can occur when the body is not properly absorbing nutrients or when a poor diet does not offer the nutrients necessary for the body to function optimally.

Common causes of nutrient deficiencies in those suffering from digestive disorders are the Standard American Diet (SAD), which is a diet high in fat, salt, sugar, and calories, and very low in nutrients, and digestive diseases such as celiac disease and leaky gut syndrome.

Some of the most common nutrient deficiencies associated with a poor diet and/or digestive conditions that include deficiencies in:

  • Iron
  • Vitamin D
  • B vitamin complex
  • Calcium
  • Vitamin A


Symptoms of a nutrient deficiency can vary widely, but most often include:

  • Hair loss
  • Skin problems
  • Weakness and fatigue
  • Depression
  • Constipation
  • Poor concentration
  • Joint pain, tingling, or numbness
  • Bloating
  • Feeling faint or dizzy
  • Oily stools that float (can be a sign of fat malabsorption from problems with the pancreas, liver, or gallbladder)

Nutrient deficiencies can have many causes ranging from poor nutrient absorption due to a disease or condition, to a diet lacking variety, color, and nutrient density. The most common causes of nutrient deficiencies in those suffering from digestive problems include:

  • Poor diet
  • Pancreatic disorders
  • Celiac disease
  • Leaky gut: Poor absorption of nutrients often develops as a result of damage to the villi (the finger-like projections in the small intestine responsible for absorbing nutrients), resulting in deficiencies and malnutrition even if you’re eating a relatively healthy diet.
  • Sugar: Because sugary foods often replace more nutritious ones and because sugar is devoid of the important nutrients your body needs to function well, overconsumption can lead to nutrient deficiencies
  • Dysbiosis (specifically SIBO): Gut bacteria may affect absorption of nutrients or consume them themselves
  • Parasitic infections: Parasites can consume nutrients before the gut is able to absorb them, leading to nutrient deficiencies


Nutrient deficiencies are also associated with thyroid disorder, because they can lead to thyroid dysfunction. Deficiencies as a result of a suboptimal diet, iodine deficiency, low levels of selenium in the soil, fluorinated water, and eating too many processed soy products are all implications that may lead to thyroid disorder.

If you suspect you have a nutrient deficiency, based on symptoms, your health history, or a poor diet, it is important to have your nutrient levels checked. Many nutritional deficiencies go undiagnosed because our bodies become accustomed to the chronic symptoms indicative of deficiencies, such as fatigue, bloating, weakness, depression, constipation, skin problems, and hair loss. To properly diagnose most nutrient deficiencies, a blood test is administered and serum levels are measured.

Diet & Promoting a Healthy Microbiome

The best treatment options for nutrient deficiencies are eating a nutrient-dense diet, to ensure you are getting the nutrients you need, and promoting a healthy microbiome, to ensure your body is absorbing the nutrients you are putting into it.

Eating a diet rich in fiber, variety, and color, and focusing on deeply pigmented fruits and vegetables, are some of the best ways to heal nutrient deficiencies, ensure proper nutrient consumption, and optimize nutrient absorption and a healthy gut. Focus on brightly-colored produce— crimson strawberries, bright orange peppers, sunny yellow lemons, deep green spinach—which contain the essential vitamins and minerals needed to enhance digestion and keep your microbiome healthy.

Increasing your consumption of these healthy and vibrantly colored plant foods will also help crowd out sugar and other empty calorie foods in your diet. Although eliminating sugar is recommended, sometimes focusing on increasing your consumption of nutrient dense plant foods is more effective in reducing and eliminating sugar in the diet.

If your nutrient deficiencies are due to a digestive disease or condition such as leaky gut, dysbiosis, parasitic infection, or celiac disease, taking a robust probiotic in addition to eating a healthful diet, is recommended to aid in repopulating your gut bacteria.

Multivitamin/Multi-mineral Supplements

Supplements, such as a multivitamin/multi-minerals, or a single nutrient supplement like calcium, is often administered to those suffering from nutrient deficiencies. Unfortunately, this is not the best method of therapy, as studies show that the body does not metabolize synthetic and/or extracted nutrients in the same way as nutrients consumed in whole foods.

Eating a fiber-rich, nutrient dense diet and living the lifestyle Dr. Chutkan outlines in her books Gutbliss and The Microbiome Solution is the best way to ensure adequate nutrition and nutrient absorption.