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Q; We eat a well balanced diet but still we won't sometimes get the desired results of eating a healthy diet. Why is this? 

Krishna: 

I recently posted an article 

not-all-fruits-and-vegetables-are-equal-when-it-comes-to-heart-health

This article says not all fruits and vegetables are equal when it comes to heart health and it clearly explains why.  

Conditions where the gut cannot absorb nutrients are collectively referred to as malabsorption syndromes. These occur when damage, inflammation, or a lack of digestive enzymes prevents the small intestine from transferring vitamins, minerals, and calories into the bloodstream. 
Common conditions that lead to poor nutrient absorption include:
Celiac Disease: An autoimmune reaction to gluten that damages the villi—the tiny, finger-like projections in the small intestine responsible for absorbing nutrients. 
Inflammatory Bowel Disease (IBD): Conditions like Crohn's disease and Ulcerative Colitis cause chronic inflammation of the bowel wall, severely impairing the gut's ability to absorb nutrients. 
Pancreatic Insufficiency: Diseases like cystic fibrosis or chronic pancreatitis reduce the amount of digestive enzymes produced, making it impossible to break down and absorb fats and fat-soluble vitamins. 
Small Intestinal Bacterial Overgrowth (SIBO): An abnormal increase in bacteria in the small intestine that consumes and interferes with the absorption of nutrients. 
Short Bowel Syndrome: Occurs when a large portion of the small intestine is surgically removed due to disease or injury, reducing the surface area available for absorption. 
Lactose Intolerance: A deficiency in the enzyme lactase, which causes an inability to digest lactose, leading to discomfort and poor absorption of related nutrients. 
Infections and Parasites: Bacterial, viral, or parasitic infections (such as Whipple's disease) can damage the intestinal lining and cause malabsorption. 
If you are experiencing symptoms like chronic diarrhea, unintentional weight loss, or persistent fatigue, it is best to consult a medical professional. 

There are several compounds in the foods we eat classified as anti-nutrients. Examples include:

Glucosinolates and goitrogens in cruciferous vegetables (broccoli, Brussels sprouts, cabbage, kale)—can prevent the absorption of iodine, which may then interfere with thyroid function and cause goiter. Those already with an iodine deficiency or a condition called hypothyroidism are most susceptible.
Lectins in legumes (beans, peanuts, soybeans), whole grains—can interfere with the absorption of calcium, iron, phosphorus, and zinc.
Oxalates in green leafy vegetables, tea, beans, nuts, beets—can bind to calcium and prevent it from being absorbed.
Phytates (phytic acid) in whole grains, seeds, legumes, some nuts—can decrease the absorption of iron, zinc, magnesium, and calcium.
Saponins in legumes, whole grains—can interfere with normal nutrient absorption.
Tannins in tea, coffee, legumes—can decrease iron absorption.

Though certain foods may contain residual amounts of anti-nutrients after processing and cooking, the health benefits of eating these foods outweigh any potential negative  negative nutritional effects. Eating a variety of nutritious foods daily and avoiding eating large amounts of a single food at one meal can help to offset minor losses in nutrient absorption caused by anti-nutrients.

Anti-nutrients may also exert health benefits. Phytates, for example, have been found to lower cholesterol, slow digestion, and prevent sharp rises in blood sugar.  Many anti-nutrients have antioxident and anticancer actions, so avoiding them entirely is not recommended.

Your overall benefits of eating a healthy diet will depend on your own biochemistry, health, microbes in your gut and their interaction with the food you eat,   the way you cook/process the foods before eating, and interactions of foods you consume in one go. 

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