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What actually makes food nourishing - quality, sourcing and the things diets miss

A doctor's evidence-based guide to what genuinely makes food nourishing, covering food quality, water, vegetables, grains, legumes and animal foods, and why how food is grown, processed and prepared matters as much as what you eat.

Dr Shehan Wijesingha · · Reading time ~ 18 minutes

In this article

Key takeaways

  • Most people are not short of calories. They are short of nourishment. How food is grown, processed and prepared matters as much as what you eat.
  • Start with water. Choose water that is both clean and mineralised, filtered of contaminants with minerals retained or restored.
  • Make vegetables and fruit the core of the plate. Eat a wide variety, and the deeper and more varied the colour, the better.
  • Eat grains and legumes whole and well prepared. Soaking beans before cooking improves digestibility, and true whole-grain bread beats refined.
  • With meat and fish, sourcing decides the value. Favour organic, grass-fed or pasture-raised animal foods and smaller wild-caught fish, and limit processed meat.
  • This is a foundation, not a personalised plan. Personalisation builds on these fundamentals rather than replacing them.

Why I wrote this

While working as a junior doctor at Mater Dei, Malta’s main public hospital, I watched patients lose limbs to diabetes who had never been told the most basic facts about food, the kind you are about to read here. They were not rare. I saw, again and again, that information this fundamental simply never reaches the people who need it most.

What troubles me is who hears this and who does not. The people I see now have usually arrived already informed, often because a problem no one had solved forced them to study their own health for years. In hospital wards I saw people who had suffered just as long, facing serious illness, who had never been given even the basics. The only difference was that no one ever told them. Everyone deserves this knowledge, and too few are ever given it. That is what I want to change.

I believe every bite you take is either building health or driving dysfunction. This is not new. Hippocrates said let food be thy medicine, and every traditional system of medicine built health on the same foundation. It is the kind of thing every patient should be told as an absolute basic, yet rarely is.

So this article is for everyone. It is the foundation I return to with my own patients before we personalise anything, and it is here, freely, for anyone who was never given it. It pairs with my practical guide to where to buy good quality food and water in Malta. How I build this into a personalised plan in clinic is set out under nutrition.

Food is information. It can drive inflammation, accelerate ageing and insulin resistance, or it can balance blood sugar, support repair, and feed the trillions of reactions happening in your body right now. It is one of the most powerful tools you have to change your health. Use it well.

Why the fundamentals get missed

To use food well, it helps to understand why it has become so easy to get wrong. Many of the chronic health conditions seen today reflect a mismatch between modern life and the body that lives it. Human physiology evolved over thousands of years in a world profoundly different from this one, and modern food systems, environmental exposures, and chronic stress now place a far greater load on the body and mind than it is well adapted to handle.1–3

At the same time, healthcare is rarely structured to teach any of this. Time pressures, financial incentives, and clinical training pathways mean diet is often reduced to brief advice or generic guidelines, while long-term management leans heavily on medications and procedures. It is therefore not only reasonable but necessary to take an active role in understanding what your body needs in order to function well. These fundamentals are the stable ground that everything else stands on. Individual responses to food genuinely vary, and the same meal can affect two people differently, which is why personalisation has real value, but it works best built on these basics rather than in place of them.4–6

Why Nutrition Advice Can Feel Confusing

Nutrition advice often appears contradictory. At different times, people are told to avoid fat, then carbohydrates; to eat plant-based, then ketogenic; to follow one dietary pattern, then abandon it. Individual studies may support one approach while others appear to refute it.

The confusion stems from the forces shaping how dietary information is generated and communicated. Research funding, commercial interests, study design, guideline politics, population-level simplification, and marketing all shape the messages that reach the public and healthcare providers alike.7, 8 Over time, this can obscure rather than clarify what genuinely supports human health, making it essential for all of us to remain curious, critically engaged, and willing to update our understanding.

Compounding this, highly processed foods are inexpensive to produce, easy to distribute, and extremely profitable. As a result, many traditional food practices that supported populations for generations have been displaced. When convenience and profit dominate food systems, clarity is lost, trust erodes, and people are left unsure of what to believe.1, 2, 9–16

The more useful path is to step back and return to first principles: what makes sense physiologically, historically, logically and intuitively. This framework begins there.

Nutrition As Nourishment

The human body evolved to process whole foods that retain their natural structure, nutrient density, and biological complexity. These foods provide the raw materials required to support normal physiological function and the body’s inherent capacity to adapt, repair, and heal.

Modern food processing alters this relationship. Refining and ultra-processing strip foods of fibre, minerals, and protective compounds, while often introducing substances the body is poorly adapted to handle in large amounts. Although such foods may still provide calories, they frequently fail to provide true nourishment.1, 2, 9–16

In addition to nutrient depletion, chronic exposure to environmental chemicals can increase physiological load, placing additional demand on detoxification and repair.3, 17, 18 Over time, this added load can impair the body’s ability to maintain balance and respond effectively to stress.

Nutrition is often reduced to macronutrients (protein, fats, and carbohydrates). Yet most people today are not suffering from a lack of calories. Calories from sugar have different metabolic effects than calories from vegetables.19, 20 What is far more common is a lack of balance, regulation, and overall nourishment. These needs remain consistent across cultures and time, yet they are often overlooked.

The body requires regular replenishment of nutrients, particularly during periods of illness or recovery. While high-quality food and clean water are essential, the nutritional value of food is shaped not only by what we eat, but also by how it is grown, processed, and prepared, all of which influence nutrient density and bioavailability. Personalisation matters because people can differ in digestive tolerance, immune reactivity, microbiome patterns, post-meal glycaemic responses, inherited biological traits, and responses to novel or alternative protein sources.4–6, 21–23 When these layers are ignored, dietary advice may appear precise on paper yet fail to produce meaningful or lasting improvements in health.

Food Quality and Modern Food Systems

Alongside processing, modern farming practices also influence the biological quality of food. In some agricultural systems, staple crops including wheat, oats, corn, legumes, and canola may be treated with glyphosate-based herbicides, sometimes close to harvest. These crops also form the basis of many processed foods and animal feeds, contributing to cumulative dietary exposure. Glyphosate has been shown to influence gut microbial balance and microbial metabolic pathways in experimental models and has also been classified as “probably carcinogenic to humans” by the International Agency for Research on Cancer. While EFSA’s 2023 risk assessment did not identify critical areas of concern under assessed uses, court-released Roundup litigation documents have raised concerns about industry efforts to influence the scientific record and regulatory debate.24–29

From a practical perspective, while prioritising organic foods in general is preferable where affordable and accessible, giving particular priority to organic versions of wheat, oats, corn, legumes, and canola, especially if these foods are consumed regularly or appear frequently in animal feed and processed foods, is a reasonable way to reduce unnecessary exposure.30–36

One of the most practical ways to protect your health is to understand where your food comes from. Clean drinking water and wholesome, properly prepared food play a central role in supporting health.

The sections that follow translate these principles into clear, practical guidance, beginning with water and then moving through vegetables, fruits, grains, legumes, and animal foods. Each section focuses on what matters most, allowing informed choices to be made without unnecessary complexity.

Water - The Primary Foundation

Water is one of the body’s most fundamental nutrients, making up approximately two-thirds of total body mass. Every cell, tissue, and biochemical process depends on adequate hydration to support circulation, nutrient and oxygen transport, electrolyte balance, detoxification, nerve transmission, muscle function, and tissue repair.37–39

However, in the modern world, the challenge is drinking water that is both clean and mineralised, not simply enough of it. Drinking water can contain agricultural runoff, industrial residues, sewage by-products, pharmaceuticals, heavy metals, fluoride, chlorine-based disinfectants, and disinfection by-products. Chronic exposure to these substances can place an additional burden on elimination pathways and cellular function.40–44

At the same time, many modern filtration methods strip water of its naturally occurring minerals. Adequate mineral content helps support cellular communication, electrical balance, and waste elimination. In simple terms, what we remove from water matters, but what we leave in or restore matters just as much.37, 45–47

This is particularly relevant during illness, recovery, heat exposure, exercise, or increased stress, when the body has to work harder and fluid and mineral needs can increase.

Finally, although some bottled waters are genuinely mineral-rich and clearly labelled, marketing claims can be misleading. In addition, bottled water stored in plastic containers can leach hormone-disrupting compounds over time, particularly when exposed to heat or prolonged storage.44, 48, 49

In general, prioritise:

  • Filtered water that removes chemicals, heavy metals, and microbes
  • Water that contains minerals, either naturally (e.g. high-quality spring water) or through remineralisation after filtration
  • Using a reusable container and filling it with filtered, mineralised water at home
  • Drinking water consistently throughout the day, rather than in large volumes at once
  • Adjusting intake to body size, activity level, climate, heat exposure, illness, caffeine use and sweating
  • Using natural mineral salt in cooking to support electrolyte balance alongside hydration

In general, limit:

  • Reliance on sugary drinks, sodas, flavoured waters, or commercial beverages for hydration
  • Unfiltered tap water
  • Water stored in plastic containers
  • Long-term exclusive use of distilled or reverse-osmosis water without remineralisation

Vegetables and Fruits - The Core of Dietary Regulation

Vegetables and fruits form the foundation of a nourishing diet because they provide far more than calories. Whole plant foods supply fibre, minerals, antioxidants, phytochemicals, natural prebiotics, plant pigments, nitrates, and naturally occurring compounds that support metabolic regulation, gut health, vascular function, immune balance, and efficient cellular energy production.50–54

One of the key reasons these foods are so protective is their role in regulating inflammation and oxidative stress, processes that underlie much of modern chronic disease and ageing. Diets rich in vegetables and fruits are consistently associated with improved metabolic health, better blood flow, and longer healthspan across diverse populations.50–54

The benefits arise from the overall structure of the diet, specifically how much it prioritises whole, minimally processed plant foods.51–57

Colour is a practical guide to quality. The pigments that give plants their colour are themselves biologically active compounds: chlorophyll in leafy greens, anthocyanins in berries and purple vegetables, carotenoids in orange and yellow produce, and lycopene in red fruits and vegetables. As a general rule, the deeper and more varied the colour, the greater the density of protective phytonutrients.52–54, 57 Herbs and spices are particularly concentrated sources, while mushrooms contribute unique micronutrients not found elsewhere in the plant kingdom.

Dietary diversity is highly useful. Different parts of plants, including leaves, roots, stems, fruits, and seeds, provide distinct nutrients and protective compounds. Regularly rotating plant foods, colours, and textures is one of the simplest and most reliable ways to support resilience and long-term health.52–54, 58 Traditional systems also used visual patterns in nature as teaching tools, where the shape of foods served as a simple mnemonic to reinforce dietary variety and respect for the body’s inherent intelligence. This is why eating a wide variety of plant foods, colours, and shapes is such a useful principle, one that appears consistently in both modern nutrition science and traditional medical systems.

Ripeness matters, particularly for fruit. Ripeness can influence the concentration of certain natural defence compounds in fruits, which may affect digestibility and tolerance, especially in individuals with sensitive digestion. Whole fruits consumed fully ripe, in season, and with intact structure provide a balanced combination of fibre, sugars, and protective compounds compared with fruits bred primarily for sweetness, uniformity, transport, or shelf life.59–61

In general, prioritise:

  • 4 or more servings of vegetables daily, especially leafy greens
  • Whole fruit daily, adjusted to tolerance, consumed fully ripe with intact structure and natural pigmentation
  • A wide variety of plant foods, colours, and textures
  • Mushrooms as a regular addition
  • Regular use of herbs and spices
  • Fresh, seasonal, organic and locally grown produce where possible
  • Gentle cooking methods that preserve structure and nutrients

In general, limit:

  • Refined plant products (e.g. white flours, sugars, syrups, sweets)
  • Highly processed or structurally altered plant foods

Whole Grains, Legumes, Nuts and Seeds - Structure and Preparation Matter

Whole grains differ fundamentally from refined grains because they retain their natural structure. A whole grain contains three parts: the bran, germ, and endosperm. The bran and germ provide fibre, minerals, essential fats, and protective phytochemicals, while the endosperm is primarily starch. Modern refining removes the bran and germ, leaving mostly starch with a higher glycaemic load and far fewer regulatory nutrients. For this reason, refined grains are consistently associated with poorer metabolic and digestive outcomes.62–64

Legumes provide a complementary role as a source of plant-based protein, fibre, and micronutrients. They are rich in folate, iron, and B vitamins and supply both soluble fibre, which supports cholesterol regulation, and insoluble fibre, which nourishes the gut microbiome. When combined with whole grains, legumes provide a complete amino acid profile, supporting protein needs while also adding fibre and micronutrients.64–66

Both whole grains and legumes naturally contain phytic acid and lectins, concentrated in seeds and outer layers. When foods are poorly prepared, these compounds can reduce mineral absorption and irritate the gut. Soaking followed by thorough cooking is one of the most useful preparation steps, helping reduce phytic acid and lectin activity while improving digestibility and mineral availability. Cooking after soaking completes this process. Beans and legumes are less forgiving than grains and should preferably be soaked and introduced gradually, particularly in individuals with sensitive digestion.61, 67–73

Nuts and seeds provide concentrated sources of healthy fats, minerals, antioxidants, and fibre. They contribute nutrients important for nerve function, bone health, and cellular protection, including magnesium, zinc, manganese, vitamin E, and folate.74, 75 Soaking nuts may improve digestibility by reducing compounds such as phytates that can interfere with digestive enzymes, although the evidence for soaking nuts specifically is weaker than for grains and legumes.69–71, 75–77 Most seeds are easier to tolerate and may not require soaking. Because these foods are energy-dense, they are best used as additions to meals rather than dietary staples.

Phytates, found in whole grains, legumes, nuts, and seeds, are not inherently harmful. When foods are properly prepared, phytates may support metabolic health by binding excess metals and have been associated with reduced risk of cardiovascular disease, diabetes, and kidney stones.69, 76

The underlying principle is simple: structure, preparation, and context determine whether foods support regulation or create metabolic stress. This applies equally to plant and animal foods, which is explored in the following section.

In general, prioritise:

  • 1 or more servings a day of whole grains clearly labelled “whole grain”
  • 1 or more servings a week of legumes, introduced gradually and prepared properly
  • 1 or more servings a week of nuts and seeds as additions rather than staples, soaked if preferred or if digestion is sensitive
  • Whole grains and legumes soaked before cooking where appropriate, especially beans and lentils
  • Traditionally prepared breads made from whole grains (e.g. true whole-grain sourdough)
  • Organic beans and lentils where possible, due to pesticide and imported GMO crop exposure
  • Less processed grain products (e.g. steel-cut oats, al dente pasta, stone-ground breads)

In general, limit:

  • Refined grains, white flour, and refined baked goods
  • Added sugars and refined carbohydrates
  • Fast-rise commercial breads without soaking or fermentation
  • Beans cooked without prior soaking, especially for people with sensitive digestion

Animal Foods in the Modern World - Sourcing & Context Matter

Modern food systems have fundamentally altered how animal foods interact with human health. The nutritional impact of animal foods depends not only on the species consumed but on how animals are raised, fed, sourced, processed, and prepared. While some species are inherently more suitable than others, modern industrial practices, including corn- and soy-based feeding, overcrowded confinement, routine use of antibiotics and hormones, environmental contamination, and heavy processing, can significantly reduce nutritional quality and increase physiological burden.36, 78–85

These effects extend beyond the animals themselves. Antibiotics administered to livestock are excreted in manure, which is commonly used as fertiliser. Residual drug compounds can persist in soil and be taken up by crops, highlighting the complexity of modern food systems and the importance of informed sourcing.82, 83

When animals and fish are raised in conditions closer to their natural environment, with appropriate movement, clean surroundings, and species-appropriate diets, their nutrient profiles may be more balanced and they may contain fewer contaminants. Under these conditions, animal foods can support strength, repair, and resilience rather than placing additional strain on the body.81, 84, 85

Traditional medical systems, including Ayurveda and Traditional Chinese Medicine, approached animal foods with nuance rather than as blanket recommendations. Different meats, fish, eggs, and animal products were selected according to constitution, season, health status, and therapeutic purpose. Animal foods were recognised for their nourishing and strengthening properties, but were used selectively and prepared carefully. Traditional methods such as slow cooking, stewing, fermenting, and using the whole animal helped reduce digestive burden and improve nutrient availability.

Fish occupy a unique position. They are a valuable source of high-quality protein and omega-3 fats (EPA and DHA), yet may also accumulate environmental contaminants. In general, smaller, wild-caught fish tend to contain fewer pollutants and offer a more favourable nutritional profile than large predatory species or heavily farmed options. When chosen carefully and consumed in moderation, the health benefits of fish appear to outweigh potential risks.79, 80

The central principle is discernment. As with plant foods, quality, sourcing, preparation, and context determine whether animal foods support health or contribute to physiological burden.

In general, prioritise:

  • Organic, grass-fed or pasture-raised meats
  • Local, pasture-raised poultry and eggs
  • Wild-caught, smaller cold-water fish
  • Minimally processed cuts and whole-food forms
  • Traditional, simple preparation methods (slow cooking, stewing, gentle heat)

In general, limit:

  • Highly processed, cured, smoked, or refined animal products
  • Large predatory or heavily farmed fish

Frequently Asked Questions

Do I need to eat organic? Where you can afford it, organic is preferable, it lowers your cumulative exposure to pesticides and other residues. But it does not need to be all or nothing. If cost is a constraint, prioritise organic for the staple crops that are most heavily treated and most frequently eaten, such as wheat, oats, corn, legumes and canola, and worry less about the rest. For most other produce, eating a wide variety of fresh, well-washed plants matters more than whether every item is certified organic.

Is tap water safe to drink? In most regulated supplies it meets safety standards. Many people still choose to filter at home to reduce chlorine, by-products and trace contaminants. If you use reverse osmosis, which removes minerals as well as contaminants, it is worth remineralising the water or making sure minerals come from elsewhere in the diet.

Do I need to soak nuts, grains and beans? Soaking grains where appropriate, and especially beans before cooking, can help reduce phytic acid and lectin activity, improve mineral availability, and make beans easier to digest. The case for soaking nuts specifically is weaker, so treat that as optional rather than essential.

Is red meat bad for me? It depends on which category and how it is produced. Processed meat carries the clearest cancer-risk signal and is best limited. Unprocessed meat from animals raised closer to their natural environment, eaten in sensible amounts and simply prepared, is a different question from heavily processed products.

What is the single most important change? For most people, shifting away from ultra-processed foods toward whole, minimally processed foods, and drinking clean water, does more than any individual supplement or trend. The fundamentals carry most of the benefit.

Medical Disclaimer

This framework is general educational information and is not individual medical or dietary advice. It does not replace assessment by a qualified clinician. Do not make significant changes to your diet, or to any prescribed treatment, based on this page alone, particularly if you have an existing medical condition, are pregnant, or take regular medication. If you have specific concerns, speak with your doctor or a registered dietitian.

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