According to the most recent NHANES data, more than 9 out of 10 US adults fail to meet the minimum intake for vitamin D, 8 out of 10 for vitamin E, and so many more nutrients are areas of concern. Even more alarming is that simply consuming enough nutrients, whether in food or supplements, does not guarantee that you are actually absorbing and using these nutrients. 

The big idea here is that gut health and your ability to absorb nutrients is even more important than just what we put into our mouths. The rest of the journey after putting food or supplements into our mouths involves the coordination of events like stomach acid, digestive enzymes, a gut lining with integrity, and a resilience microbiome.

Considering this big picture might help make your healing and nutrition status more predictable once you better understand what is involved in throwing roadblocks in our way. Let’s dive in.

Four Gut Health Factors that Affect Bioavailability

Before nutrients can be used by your cells, they have to survive a complex relay race through your digestive tract. From chewing to gut microbes to intestinal lining checkpoints, each step plays a critical role in transforming what you eat into what your body can actually use. Here’s four major functions to start:

1. Chewing, saliva, and stomach acid - Digestion begins in the mouth with chewing, while having enough stomach acid is important to help ideally break down proteins and release minerals for absorption.
2. Digestive enzymes and bile - The pancreas and liver/gallbladder play an additionally pivotal role in breaking down proteins, carbs, and fats so that fat-soluble vitamins A, D, E, & K can be absorbed. 
3. Microbiome interactions - Balance between friendly and potentially harmful bacteria is important to ensure inflammatory balance throughout the digestive tract and rest of the body.
4. Intestinal lining integrity and brush border absorption - Tight junctions between intestinal cells and nutrient transporters act like security gates. Only properly broken-down nutrients get through, and low stomach acid, bile, enzymes, or microbiome imbalances can leave too many doors closed or dysfunctional.

If even one of these functions are dysfunctional, even the cleanest diet and best supplements can become an expensive waste. Let’s dive into a few of these gut health functions in more detail.

Leaky Gut - Slowing Nutrient Absorption

A healthy intestinal lining is like a tightly zipped jacket. Stress, hidden or perceived, ultra‑processed foods, alcohol, or chronic infections can unzip those teeth, creating tiny gaps doctors call increased intestinal permeability, or leaky gut. 

Research shows that leaky gut raises low‑grade inflammation and correlates with lower blood levels of iron, zinc, and several B‑vitamins. Inflammation and stress can also shift function away from “rest and digest” causing nutrient uptake to stall.

The Microbiome and Nutrient Production Plus Absorption

Did you know that some of the good bacteria in your gut actually create nutrients that we need? This includes vitamin K2 and most of the B vitamins. In a way this function provides a nutritional safety net for us. 

Some species within the gut microbiome also produce important anti-inflammatory short-chain fatty acids (SCFAs) from the fiber that we eat. These important nutrients protect the integrity of the gut lining and contribute to the inflammation balance throughout the body. 

When the microbiome is imbalanced and gut lining impaired, this can result in less resilience to inflammation and poor mineral absorption, such as with iron and calcium.

Four Common Roadblocks that Negatively Affect Nutrient Absorption

Sometimes, your diet isn’t the issue. It's what’s getting in the way of your gut doing its job. Here are four frequently overlooked situations that quietly steal nutrients from your plate before they ever reach your bloodstream:

1. SIBO (Small Intestinal Bacterial Overgrowth)
   In a healthy gut, bacteria are mostly found in the large intestine. But in SIBO, bacteria creep into the small intestine where they don’t belong, and they compete with you for nutrients. These microbes can deactivate bile (needed to absorb fats and fat-soluble vitamins), leading to deficiencies in vitamins A, D, B12, and iron. Left unchecked, SIBO can trigger bloating, fatigue, and persistent nutrient gaps, no matter how clean your diet is.
2. Low Stomach Acid or Long-Term Antacid Use
   Stomach acid is essential for breaking down food, especially protein, and unlocking minerals like calcium, iron, and especially vitamin B12. But common acid-blocking medications (like PPIs) or age-related hypochlorhydria (low stomach acid) can reduce acid levels too much. The result is that you might be eating plenty but your body can’t access what it needs, leaving you low on key nutrients over time.
3. Pancreatic Enzyme Insufficiency
   Your pancreas releases enzymes that help digest proteins, fats, and carbs. If your enzyme output is low due to aging, chronic stress, or digestive disease, foods pass through your gut only partially digested. This especially affects absorption of fat-soluble vitamins like A, D, E, and K, as well as amino acids from protein.
4. Inflammatory or Autoimmune Gut Conditions
   Conditions like celiac disease or inflammatory bowel disease (IBD) can damage the finger-like villi that line your small intestine. Since these villi are responsible for absorbing nutrients, their erosion shortens the gut’s surface area—meaning less opportunity to take in folate, iron, zinc, and more. These deficiencies often persist even in people eating nutrient-dense foods.

If you’re struggling with “mystery” nutrient deficiencies, it’s worth looking beyond diet alone. Identifying and treating these root-cause disruptions often restores absorption far more effectively than simply taking higher doses of supplements.

Sneaky Signs You’re Not Absorbing Nutrients Effectively

You might be eating all the “right” foods and still feel off. When absorption is compromised, subtle signs often show up long before anything abnormal appears in basic labs. Here are some common red flags to watch for:

• Cracks at the corners of your mouth – Often tied to riboflavin (B2) or iron deficiency, even with the right diet.
• Restless legs at night – May signal low iron or magnesium, especially if paired with fatigue or poor sleep quality.
• Pale, floating, or hard-to-flush stools – A classic clue that fats (and fat-soluble vitamins A, D, E, and K) are not being properly digested and absorbed.
• Chronically low vitamin D – Even with sunshine and supplements, poor bile flow or gut inflammation can block absorption of this important nutrient.
• Brittle nails, shedding hair, or bumpy skin on the back of the arms – These can point to low zinc, essential fatty acids, or vitamin A status.
• Lingering fatigue, even with a decent sleep – Sometimes it’s not energy input that’s the problem—it’s your cells not getting the nutrient fuel they need.

If two or more of these resonate with you, your body might be whispering, “I’m not absorbing well.” That’s your cue to dig deeper, not just with more supplements, but with advanced testing and root-cause insight.

Labs That Can Turn Symptoms Into Data

If you’re experiencing nagging symptoms despite a nutrient-rich diet and a shelf full of supplements, it might be time to look under the hood. Functional lab testing helps move us from guesswork to precision. With such tests, you can pinpoint where absorption is breaking down, which nutrients are lacking, and whether deeper gut dysfunction is at play.

• Standard & specialized blood panels – Markers like ferritin (iron storage), 25‑OH‑D (vitamin D), methylmalonic acid (B12 status), and homocysteine (linked to B12, B6, and folate needs) give a snapshot of nutrient levels in the bloodstream and how well they’re being utilized.
• Advanced functional stool testing – These advanced panels assess pancreatic enzyme output, markers of gut inflammation (like calprotectin), immune function (sIgA), and the balance of beneficial vs. harmful microbes. It’s one of the most direct ways to assess gut health.
• Organic Acids Test (OAT) – This urine-based test detects the byproducts that reflect microbial overgrowth, mitochondrial function, and nutrient cofactor needs, especially B-vitamins. It’s great for picking up issues before they show up in blood work.
• Breath testing for SIBO – Measures levels of hydrogen, methane, and hydrogen sulfide gas produced by bacteria in the small intestine. Elevated levels can reveal bacterial overgrowth that may be disrupting fat absorption and triggering symptoms like bloating, fatigue, or even low vitamin D or B12.

These tests help connect the dots between how you feel and what your body is actually doing, so you can make informed decisions and stop flying blind.

Five Science‑Backed Ways to Boost Real‑World Bioavailability

1. Chew at least 20 times per bite. Simple, free, and increases protein digestibility.
2. Nutrient pairings: Vitamin C triples plant‑iron absorption and fat unlocks vitamins A, D, E, & K absorption.
3. Feed the bugs: Aim for ≥ 15 g/day prebiotic fiber. SCFA production can raise calcium uptake from 10% to 30%.
4. Targeted probiotics, prebiotics, & digestive enzymes: A balanced microbiome and good digestive strength supports nutrient absorption. Consider daily support such as with Cielo Daily’s Horizon.
5. Prioritize sleep & stress care:Less than 7 hours of sleep per night is tied to higher inadequacy of vitamins A, C, D, E, K, and magnesium.

Key Takeaways

A balanced plate only matters if you can break it down, absorb it across a resilient gut wall, and let friendly microbes play their part. If you focus on fortifying your digestive function, (including enough acid, enzymes, barrier integrity, and a resilient microbiome), your multivitamin becomes insurance, not a daily rescue.

For more down-to-earth wellness content, stay connected with us and check out our related blog post on Bioavailability 101! Follow Cielo Daily and Dr. Kenny Mitelstadt on Instagram for regular content that helps you sift through the wellness noise out there!