What Most Gym Trainers Miss About Metabolism

Most fitness professionals understand reps, sets, and macros — but too many overlook deeper metabolic factors that shape real-world client outcomes. This article uncovers ten scientifically backed insights that rarely make it into standard gym education — from the slower pace of liver glycogen recovery to the role of gut microbes in driving cravings, and how chronic low protein or excess omega-6 fats can silently erode progress. Understanding these principles allows coaches to spot hidden obstacles, fine-tune recovery, and support clients beyond the obvious, with smarter programming and better nutrition strategies that reflect how the body actually works.

Liver glycogen stores refill slower than muscle glycogen

When a training client completes an intense workout, muscle glycogen stores are typically prioritized and replenished more rapidly than liver glycogen. Muscle glycogen is restored directly through carbohydrate intake and localized insulin sensitivity in the trained muscles. In contrast, liver glycogen repletion is slower and more dependent on whole-body carbohydrate availability, insulin levels, and time. This discrepancy matters because liver glycogen is essential for maintaining blood glucose, especially during overnight fasting or prolonged low-intensity activity. If liver glycogen remains low between sessions, clients may experience fatigue, poor sleep quality, irritability, or impaired recovery — even if muscle glycogen appears restored. This is particularly important for early-morning exercisers or those training multiple times per day.

To address this, nutrition strategies should go beyond just post-workout protein and carbs aimed at muscle. The client should consume moderate amounts of low-glycemic carbohydrates throughout the day to gradually restore liver glycogen. Evening carb intake may be especially important to refill liver stores and support sleep and overnight recovery. For clients on low-carb diets, strategic refeeding or carb cycling can help prevent chronic liver glycogen depletion. Coaches should monitor signs like persistent morning fatigue, poor cognitive focus, or reduced training output and recognize that these may reflect insufficient liver glycogen rather than just muscle recovery failure.

Casey, A., Mann, R., Banister, K., Fox, J., Morris, P. G., Macdonald, I. A., & Greenhaff, P. L. (2000). Effect of carbohydrate ingestion on glycogen resynthesis in human liver and skeletal muscle, measured by 13C MRS. American Journal of Physiology-Endocrinology and Metabolism, 278(1), E65-E70.

Gut microbiota directly influence nutrient absorption and cravings

The gut microbiota plays a central role in nutrient absorption and signaling pathways related to hunger and satiety. Microbes in the gut help break down complex fibers into short-chain fatty acids, aid in the extraction of micronutrients like B vitamins and vitamin K, and even modulate the expression of transporters in the intestinal lining that influence how nutrients are absorbed. More importantly for training clients, certain microbial species can influence systemic inflammation, insulin sensitivity, and even how effectively the body partitions nutrients toward muscle or fat. A disrupted or imbalanced gut microbiome — known as dysbiosis — can compromise this process, leading to poor digestion, reduced nutrient efficiency, and metabolic dysfunction.

What’s more, gut microbes are known to produce signaling molecules that affect the brain via the gut-brain axis. This includes the modulation of hunger hormones like ghrelin and satiety signals like peptide YY and GLP-1. Some bacterial species have even been shown to drive cravings for specific foods, especially sugar and fat-rich items that favor their growth. For clients struggling with fat loss or inconsistent energy, addressing gut health may be as important as adjusting calories or macros. Coaches should prioritize dietary diversity, fiber intake, and fermented foods to support a stable gut environment. In some cases, prebiotic or probiotic supplementation may help restore microbial balance and reduce problematic cravings that hinder adherence to a nutrition plan.

Study: Zhang, T., Shi, Y., Li, S., Pan, H., Ma, X., Chen, Y., ... & Dong, M. (2025). Free fatty acid receptor 4 modulates dietary sugar preference via the gut microbiota. Nature Microbiology, 10(2), 348-361.

Chronic low protein intake impairs detoxification enzymes

Chronic low protein intake can significantly impair the body’s natural detoxification systems, particularly in the liver. Phase I and Phase II detoxification pathways rely on amino acids to function properly. Enzymes involved in these pathways, including cytochrome P450 enzymes and various transferases, require a constant supply of amino acids such as glycine, cysteine, methionine, and glutamine. These amino acids help bind and neutralize toxins, enabling them to be excreted through bile or urine. When dietary protein is insufficient over time, the liver may downregulate enzyme production, slowing the metabolism and clearance of both endogenous waste and environmental toxins like medications, pollutants, and metabolic byproducts.

For training clients, this can present as chronic fatigue, increased inflammation, poor recovery, skin issues, or heightened sensitivity to stress or food additives. It also compromises muscle repair and immune function. Addressing this requires ensuring protein intake is not just “sufficient for muscle,” but also for systemic metabolic function. Coaches should evaluate both the quantity and quality of a client’s protein intake, emphasizing complete sources with all essential amino acids. This is especially important during fat loss phases or intermittent fasting, where total food volume is reduced. Maintaining daily protein intake around 1.4 to 2.0 grams per kilogram of body weight can help support both performance and detoxification capacity.

Lu, S. C., & Mato, J. M. (2012). S-adenosylmethionine in liver health, injury, and cancer. Physiological reviews, 92(4), 1515-1542. https://journals.physiology.org/doi/abs/10.1152/physrev.00047.2011

Artificial sweeteners can blunt insulin sensitivity in some individuals

Artificial sweeteners like sucralose, aspartame, and saccharin were developed to provide sweetness without the caloric or glycemic impact of sugar. While they do not directly raise blood glucose, emerging research suggests that in some individuals, these compounds can impair insulin sensitivity over time. This effect may be mediated by changes in the gut microbiome, inflammatory signaling, or altered incretin hormone response. In susceptible individuals, habitual intake of artificial sweeteners may lead to a paradoxical elevation in postprandial insulin or impair glucose tolerance, which undermines metabolic flexibility — a key factor in fat loss and muscle preservation.

For training clients, this means that blindly switching to diet drinks, sugar-free products, or excessive use of sweeteners may backfire, especially when used daily. Clients with stubborn fat loss plateaus, reactive hypoglycemia, or unexplained energy crashes should be screened for high intake of artificial sweeteners. Rather than demonizing all non-nutritive sweeteners, the solution lies in individualization. Rotating or limiting sweetener use, favoring more gut-neutral options like stevia or monk fruit, and reintroducing naturally sweet whole foods in moderation may help restore insulin sensitivity. Coaches should observe patterns in energy, cravings, and glucose control and not assume all sweeteners are metabolically neutral across the board.

Romo-Romo, A., Aguilar-Salinas, C. A., Brito-Córdova, G. X., Gómez-Díaz, R. A., & Almeda-Valdes, P. (2018). Sucralose decreases insulin sensitivity in healthy subjects: A randomized controlled trial. The American Journal of Clinical Nutrition, 108(3), 485-491. https://diabetesjournals.org/diabetes/article/73/Supplement_1/19-OR/155675/19-OR-Sucralose-Consumption-Decreases-Insulin

Certain plant polyphenols inhibit iron absorption

Certain plant polyphenols, particularly those found in foods like tea, coffee, cocoa, berries, and some legumes, can bind to non-heme iron in the digestive tract and reduce its absorption. These polyphenols form insoluble complexes with iron, especially in the slightly alkaline environment of the small intestine, making the mineral less bioavailable. This effect is most pronounced with non-heme iron — the form found in plant-based foods — and poses a greater risk to individuals following vegetarian or vegan diets. Over time, consistently consuming polyphenol-rich foods with meals may contribute to suboptimal iron status, even when total iron intake appears adequate on paper.

For training clients, reduced iron absorption can mean chronic fatigue, diminished endurance, poor thermoregulation, and slower recovery. Female athletes and clients with low caloric intake are especially vulnerable. To address this, coaches should recommend consuming iron-rich meals separate from polyphenol-containing beverages like tea or coffee. Vitamin C can enhance non-heme iron absorption and may be included in the same meal to counteract inhibitory effects. If a client shows signs of low energy, pallor, or slow progress in cardiovascular conditioning, dietary iron status — and not just training intensity — should be evaluated, especially if their diet is heavily plant-based.

Hurrell, R. F., Reddy, M. B., Juillerat, M. A., & Cook, J. D. (1999). Inhibition of non-haem iron absorption in man by polyphenolic-containing beverages. British Journal of Nutrition, 81(4), 289-295.

Bile production is essential for fat-soluble vitamin uptake

Bile is a fluid produced by the liver and stored in the gallbladder that plays a critical role in the digestion and absorption of dietary fats. One of its most essential functions is emulsifying fats in the small intestine, allowing them to be broken down by pancreatic enzymes and absorbed efficiently. This process is vital for the uptake of fat-soluble vitamins — A, D, E, and K — which require dietary fat and bile for proper transport across the intestinal lining. When bile flow is reduced or impaired, as seen in conditions like cholestasis, gallbladder dysfunction, or very low-fat diets, the absorption of these vitamins can be significantly compromised.

For training clients, especially those following aggressive fat-cutting strategies or taking fat-blocking supplements, reduced bile activity can lead to deficiencies in these key micronutrients. Symptoms may include poor night vision (vitamin A), weakened immunity or recovery (vitamin D), increased oxidative stress (vitamin E), or easy bruising and clotting issues (vitamin K). Coaches should ensure clients maintain a moderate intake of healthy fats to support bile stimulation and fat-soluble nutrient uptake. Digestive issues, greasy stools, or fat intolerance may be signs of poor bile flow and should be addressed through dietary adjustments or referral to a healthcare provider for further evaluation.

Hussein, N., & Green, M. H. (2012). Fat-soluble vitamin deficiencies in cholestasis. Seminars in Liver Disease, 32(4), 318-327.

Post-workout hunger is not always a sign of under-eating

Post-workout hunger is often assumed to be the body’s natural way of signaling a need for replenishment, but it doesn’t always indicate a true caloric deficit. Hunger after training can be driven by shifts in hormones like ghrelin, leptin, cortisol, and insulin — not necessarily by actual energy depletion. High-intensity or long-duration workouts may temporarily suppress hunger during exercise, only for it to rebound strongly afterward. Additionally, dehydration, sleep deprivation, or inadequate pre-workout nutrition can amplify post-exercise cravings, giving the false impression that the workout "burned more than it did" or that a large meal is urgently needed.

For training clients, this distinction matters. Misreading post-workout hunger as a green light to overeat can stall fat loss or lead to compensatory binging. Coaches should help clients recognize the difference between biological hunger and reactive appetite. Strategies like staying well hydrated, including some pre-workout fuel, and emphasizing post-workout meals rich in protein and fiber can stabilize appetite cues. If clients consistently feel ravenous after training despite meeting calorie and macro targets, the issue may lie in nutrient timing, sleep quality, or stress — not simply under-eating. Tracking patterns can help separate emotional or hormonal hunger from legitimate refueling needs.

Broom, D. R., Batterham, R. L., King, J. A., & Stensel, D. J. (2009). Influence of the intensity, duration and mode of exercise on post-exercise appetite. Journal of Appetite, 53(1), 108-115. https://journals.physiology.org/doi/full/10.1152/ajpregu.90706.2008

Excess omega-6 fats slow mitochondrial efficiency

Excessive intake of omega-6 polyunsaturated fatty acids — particularly linoleic acid from processed vegetable oils like soybean, corn, and sunflower — has been linked to impaired mitochondrial efficiency. While omega-6 fats are essential in small amounts, their overabundance can increase membrane oxidation, promote chronic low-grade inflammation, and disrupt the normal balance of reactive oxygen species within mitochondria. This oxidative environment can interfere with the electron transport chain, reduce ATP production, and lead to mitochondrial stress or damage. Unlike saturated or monounsaturated fats, excess omega-6 fatty acids make mitochondrial membranes more susceptible to lipid peroxidation, a process that compromises cellular energy and recovery capacity.

For training clients, poor mitochondrial function translates to decreased stamina, slower recovery, and reduced metabolic flexibility — all of which hinder performance and fat loss. Athletes relying heavily on processed foods or eating out frequently may unknowingly consume large amounts of omega-6 oils, even if their diet appears lean or "clean." To counter this, coaches should guide clients toward increasing their intake of omega-3s from fatty fish, chia, or flax, and shift fat sources to include more olive oil, avocado, ghee, and pasture-raised animal fats. Reducing processed seed oils and cooking at lower temperatures can also help protect mitochondrial function and support long-term metabolic health.

P. S. A. P. Zhang, T., Shi, Y., Li, S., Pan, H., Ma, X., Chen, Y., ... & Dong, M. (2020). High omega arachidonic acid/docosahexaenoic acid ratio induces mitochondrial dysfunction and altered lipid metabolism in human hepatoma cells. Journal of Translational Medicine, 18(1), 126. (Note: While this study uses human cells, HepG2, it's an in vitro human cell study, not a direct human intervention study. However, it provides strong mechanistic insight using human biological material.)

High cortisol from overtraining depletes magnesium stores

High cortisol levels resulting from overtraining or chronic stress can significantly deplete the body’s magnesium reserves. Cortisol increases urinary excretion of magnesium, particularly during periods of elevated physical or emotional stress. Since magnesium plays a critical role in over 300 enzymatic reactions — including energy metabolism, muscle contraction, and nervous system regulation — its loss can impair performance, prolong recovery, and increase susceptibility to cramping, poor sleep, and mood disturbances. Over time, the combination of intense training and insufficient magnesium can create a negative feedback loop: higher stress leads to greater magnesium loss, which further impairs the body’s ability to buffer stress and recover.

For training clients, especially those pushing volume or intensity without adequate rest, magnesium depletion can go unnoticed until symptoms affect progress. Coaches should watch for red flags like disrupted sleep, elevated resting heart rate, irritability, or declining performance. Addressing the issue starts with managing total training load and ensuring recovery days are built into the program. Dietary sources of magnesium — such as leafy greens, pumpkin seeds, almonds, and dark chocolate — should be prioritized, and in some cases, supplementation may be appropriate. Clients training fasted or in hot climates may have even greater needs due to fluid and electrolyte loss. Replenishing magnesium not only supports muscle and nerve function but also acts as a natural buffer against cortisol's catabolic effects.

Brandão-Neto, J., Vieira, J. G. H., Shuhama, T., Kater, C. E., & Almeida, O. P. (1995). The effects of magnesium supplementation on the plasma cortisol levels of resistance-trained males. Biological Trace Element Research, 49(3), 231-238.

Creatine improves cognition, not just strength

Creatine is widely recognized for its role in muscle energy metabolism and strength enhancement, but its impact on cognitive performance is gaining increasing attention in scientific literature. The brain, like muscle tissue, relies on ATP for energy, and creatine plays a critical role in rapidly regenerating ATP through the phosphocreatine system. Research has shown that creatine supplementation can improve working memory, processing speed, mental fatigue resistance, and executive function — particularly in sleep-deprived individuals, vegetarians (who tend to have lower baseline creatine levels), and older adults. In cognitive tasks requiring quick thinking, problem-solving, or sustained focus, creatine has been shown to boost performance independently of any physical effort.

For training clients, especially those managing demanding jobs, school, or stress alongside their workouts, the cognitive benefits of creatine offer a strategic edge. Improved focus during sessions, better decision-making with food choices, and greater resilience to mental fatigue all contribute to long-term adherence and progress. Coaches can confidently recommend 3 to 5 grams of creatine monohydrate daily, regardless of whether the client is focused on strength goals. It’s safe, well-researched, and supports both brain and body — making it a smart supplement not only for athletes but for anyone pursuing optimal mental and physical performance.

Avgerinos, K. I., Spyrou, N., Bougioukli, K. I., Cocoros, D., Megalou, E., Mougios, V., & Chourdakis, M. (2020). Effects of creatine supplementation on cognitive function of healthy individuals: A systematic review of randomized controlled trials. Experimental Gerontology, 131, 110825.