Q&A (Coffee Part 1): What coffee is and what’s inside?

Take-Home Messages 🔑  

 Introduction☕

Coffee is one of the most widely consumed beverages globally, yet its complexity is often underestimated (1, 2). Far from being a simple drink, it encompasses a diverse spectrum of products shaped by species, processing and preparation methods, and a rich chemical composition that together influence its flavour, functionality and potential health effects.

In Part 1 of this two-part series, I provide a comprehensive overview of coffee—from its botanical origins and major species (Arabica and Robusta) to the wide range of coffee types and preparation methods used worldwide. I then examine its chemical composition, focusing on key bioactive compounds such as caffeine, chlorogenic acids, diterpenes and prebiotic components, as well as how factors such as roasting, grinding and brewing influence these constituents. In addition, I consider variations in commercial products (e.g. instant, decaf and coffee bags), additives and formulations, and emerging alternatives to coffee.

This foundational understanding is essential for interpreting the complex and often context-dependent health effects of coffee consumption, which are explored in Part 2.

What is coffee? Types, forms and preparation 🫘

Coffee is a brewed beverage made from roasted seeds of berries of the Coffea genus, part of the Rubiaceae family (3). The two most widely cultivated and consumed species are Coffea arabica (Arabica or Ethiopian coffee), valued for its smooth flavour and lower caffeine content, accounting for around 60–70% of global production; and Coffea canephora (Robusta), which has a stronger, more bitter taste, higher caffeine content and greater resistance to disease. Less common species, such as Coffea liberica and Coffea excelsa, are grown in smaller quantities and appreciated for their unique flavour profiles (3).

Coffee comes in many forms and names depending on how it is brewed, the ratio of ingredients and regional preferences. From espresso-based drinks such as cappuccinos and flat whites to regional specialties such as Turkish coffee and café Cubano, each variation offers a unique flavour and cultural experience. Coffee’s taste is influenced by the coffee species, origin, roast level, grind size and preparation method. Roast level alters the chemical composition of the beans, affecting flavour notes, acidity and bitterness, while grind size impacts the extraction rate, shaping the balance between sourness, sweetness and bitterness.

Table: Summary of coffee types

*Steamed milk with very fine, uniform bubbles that create a smooth, velvety texture

Kopi Luwak or civet coffee, is a rare and expensive coffee made from coffee beans (mostly Arabica) excreted by Asian palm civets after consuming ripe coffee cherries. While it is prized for its smooth, low-acid flavour, its production raises ethical concerns, especially when civets are kept in captivity. Consumers are advised to choose products sourced from wild civets and verified by reputable sources.

Black Ivory Coffee is a rare and expensive coffee made from Thai Arabica beans that are eaten, digested and excreted by elephants. The fermentation process in the elephant’s gut reduces bitterness and results in a smooth, earthy flavour. Produced in small quantities, it supports elephant conservation and local communities, making it a more ethically conscious option than civet coffee.

Instant coffee is widely consumed for its convenience, though some purists argue it lacks the flavour complexity and freshness of traditionally brewed coffee, raising debates about whether it qualifies as "real" coffee. Both types originate from roasted beans, and studies suggest instant coffee retains many bioactive compounds (caffeine and antioxidants) linked to potential health benefits (4). Several brands offer 3-in-1 or 2-in-1 instant coffee sachets that combine instant coffee, sugar and non-dairy creamer. Marketed for convenience and a sweet, café-style flavour, these products require no milk or extra ingredients. The non-dairy creamers often contain hydrogenated or partially hydrogenated vegetable oils—typically from coconut or palm kernel oil—which are high in saturated fatty acids. Their high saturated fat content raises concerns about heart health, especially with regular intake (5). Additionally, palm oil production contributes to deforestation, biodiversity loss and greenhouse gas emissions. Beyond palm oil, conventional coffee farming also impacts the environment through deforestation, heavy water use and pesticide application, leading to the growth of sustainable certification schemes such as Fairtrade, Rainforest Alliance and organic labels.

Coffee bags are single-serve sachets of ground coffee in a porous filter, designed to be steeped in hot water using an immersion method similar to tea bags. They offer a convenient, low-equipment option with a smooth, mild flavour, though extraction is less efficient than drip or espresso methods. While many coffee bags are made primarily from paper-based filter materials similar to traditional coffee filters, some may incorporate plastic fibres for strength or sealing, raising concerns about potential microplastic release during brewing (6), although the extent and health implications remain uncertain. Widely available in the UK and Japan but still niche elsewhere, coffee bags occupy a middle ground between instant coffee and traditional brewing in terms of both quality and convenience.

Decaffeinated (decaf) coffee is produced from regular coffee beans by removing most of the caffeine before roasting, using water-based, solvent-based (e.g., dichloromethane or ethyl acetate) or high-pressure CO₂ extraction methods (7). The Swiss Water Process, for example, uses carbon filtration to selectively remove caffeine via diffusion while preserving flavour compounds. Although not completely caffeine-free, a typical cup of decaf contains around 2 mg of caffeine compared to ~95 mg in regular coffee and it retains much of the original flavour as well as most of its antioxidant content (7).

Coffee-flavoured products are not coffee; they are items infused with artificial or natural flavouring compounds that mimic the taste of coffee but do not contain brewed coffee itself.

Key compounds in coffee 🧪 🔬

Coffee contains a complex mixture of over 800 volatile compounds—substances that easily evaporate and contribute to the aroma and flavour of coffee (4). Among these, caffeine and chlorogenic acids are the most prominent bioactive components. Coffee is a major source of antioxidants, such as chlorogenic acid and quinines, which help combat oxidative stress and inflammation. Coffee contains prebiotic compounds, including soluble dietary fibres and polyphenols, that promote the growth of beneficial gut bacteria, supporting digestive health and enhancing nutrient absorption. Additionally, coffee contains small amounts of essential micronutrients including potassium, magnesium, phosphorus and several B vitamins (4). I do not explore additions to coffee such as milk, cream, sugar or sugar alternatives here; however, these components have their own chemical composition and nutritional effects, and should be considered when evaluating the overall impact of coffee consumption.

Table: Coffee components

LDL, low density lipoprotein

Caffeine🧬

Caffeine is a naturally occurring white, crystalline alkaloid synthesised by various plants as a chemical defence mechanism against insect predation. Caffeine is a natural stimulant from the methylxanthine class and is the most widely consumed psychoactive substance. Caffeine enhances alertness and concentration by acting on the central nervous system. Caffeine blocks adenosine, a chemical that normally promotes relaxation and sleep (8). By preventing adenosine from binding to its receptors, caffeine reduces feelings of drowsiness (8). In response, the brain releases more adrenaline—a hormone involved in the body's fight-or-flight response—and dopamine, a neurotransmitter that plays a key role in motivation, mood and feelings of pleasure (8, 9). With regular use, the brain adjusts by increasing adenosine receptors, making caffeine less effective over time and leading to a need for higher doses.

A standard cup (approximately 240 mL) of instant coffee typically contains 60–80 mg of caffeine, whereas freshly brewed coffee contains a broader range, approximately 60–120 mg, depending on preparation methods. Decaffeinated coffee offers an alternative for those sensitive to caffeine, with only about 2–5 mg per cup. A cup of tea contains roughly 40 mg of caffeine, although this amount can vary based on factors such as brewing time and tea type. Notably, some teas—such as herbal or rooibos—contain no caffeine at all.

For healthy adults (excluding pregnant women), up to 400 mg per day—roughly 4 cups of coffee or 2.5 energy drinks—is considered safe, with a single dose not exceeding 200 mg (10-12). Children should not consume caffeine (13, 14). Caffeine-related deaths, though rare, have been documented—primarily among infants, psychiatric patients and athletes—and are typically linked to high-dose exposures, highlighting the need for greater awareness of its potential toxicity and the risks associated with easy access to pure caffeine (15).

The half-life of caffeine—defined as the time required for the body to eliminate 50% of the ingested dose—ranges from approximately 2 to 12 hours, with considerable interindividual variability. This variability is primarily influenced by genetic polymorphisms. Genes affecting caffeine metabolism e.g., the CYP1A2 gene, which encodes the cytochrome P450 1A2 enzyme, the main hepatic enzyme responsible for caffeine metabolism. Individuals with the fast-metabolising CYP1A2 variant may clear caffeine more rapidly, whereas those with slow-metabolising variants experience prolonged caffeine exposure (16).

The ADORA2A gene encodes the adenosine A2A receptor, which is involved in promoting sleep and regulating anxiety. Caffeine exerts many of its stimulant effects by blocking adenosine receptors, particularly A2A. Genetic variations (e.g., the rs5751876 polymorphism) in ADORA2A influence caffeine sensitivity. Individuals with certain variants (e.g. the TT genotype at rs5751876) tend to experience greater anxiety, disrupted sleep or increased alertness after caffeine intake (17).

Antioxidants🥛

Coffee is a rich source of antioxidants such as chlorogenic acids. Chlorogenic acids may reduce atherosclerosis by inhibiting artery-hardening mechanisms (18). Adding milk can influence coffee’s antioxidant capacity. Casein, the primary protein in milk, has been shown to bind to polyphenols such as chlorogenic acids, potentially reducing their bioavailability and antioxidant activity (19). The extent of this reduction depends on the amount and type of milk added, as higher protein content may lead to greater binding (20). However, the impact may vary between individuals and is still under investigation.

Cafestol 🟢 🔴 🧬

Cafestol exhibits both beneficial and adverse health effects. On the positive side, supplementation in individuals with increased waist circumference has been shown to reduce body weight, visceral fat volume and gamma-glutamyl transferase (GGT) levels—a marker of liver function—though it did not improve insulin sensitivity or glucose tolerance (21). However, cafestol is also known to raise serum LDL cholesterol levels, particularly when consumed through unfiltered or machine-brewed coffee, which contains higher concentrations of cholesterol-raising diterpenes i.e. cafestol and kahweol than paper-filtered brews (22). This poses a potential cardiovascular health concern with regular intake of insufficiently filtered coffee.

Cafestol and kahweol may also exert protective effects in other areas. Both compounds exhibit anticancer properties across various in vitro and in vivo models (23). Their actions include inducing apoptosis, inhibiting cell proliferation and growth and—specifically for kahweol—suppressing cell migration. Notably, these effects appear to selectively target cancer cells while sparing normal cells, highlighting their potential as natural antitumor agents.

Prebiotics and chicory 🦠🌿

Chicory root is often blended with coffee—particularly in products such as South Africa’s Ricoffy or traditional French-style coffee—to reduce caffeine content, add a roasted, slightly nutty flavour and enhance its nutritional profile (24). One of chicory’s key components is inulin, a type of soluble dietary fibre that functions as a prebiotic. Prebiotics are non-digestible food components that selectively stimulate the growth and activity of beneficial gut bacteria, particularly Bifidobacteria and Lactobacilli, thereby supporting a healthy microbiome (24).

Regular consumption of inulin-rich chicory has been associated with improved digestive health, enhanced mineral absorption and potential immune-modulating effects (25, 26). Additionally, by contributing to feelings of satiety, chicory may play a role in appetite regulation (27). Including chicory in coffee formulations not only broadens flavour complexity but also transforms coffee into a functional drink with potential gut-health and metabolic benefits (28).

Exploring coffee alternatives: Caffeine-free and functional options 🌿☕🚫🍵🥛

Not everyone tolerates or chooses to consume coffee, whether due to caffeine sensitivity, personal preference, religious reasons or health perceptions. Fortunately, a variety of plant-based, herbal and grain-derived beverages offer similar warmth, comfort and ritual—without the caffeine. While these drinks are not made from coffee beans and differ in chemical composition, they often mimic coffee's roasted flavour or provide additional functional benefits. From chicory and dandelion roots to functional mushrooms and grain-based blends, these alternatives are gaining popularity for their unique taste profiles and perceived health-promoting properties. The table below highlights key coffee substitutes, their main ingredients and what to expect in terms of flavour and function.

Table: Coffee alternatives (not coffee)

Conclusion☕

Understanding what coffee is—and what it contains—is essential for interpreting its effects on health and nutrition. As this overview shows, coffee is far more than a source of caffeine; it is a chemically complex, culturally diverse and functionally nuanced beverage, laying the foundation for evaluating its role in health, which is explored in Part 2.

Reflections on coffee intake ☕🔄💭

🔍 Am I consuming coffee habitually or purposefully?
Is my intake driven by routine or am I using coffee to compensate for fatigue, stress or inadequate sleep?

📊 Am I aware of my total caffeine exposure?
Have I considered cumulative intake from all sources—including coffee, tea, chocolate and energy drinks—and how this aligns with recommended limits?

🧠 How does coffee affect me personally?
Do I experience changes in sleep, anxiety, concentration or physical symptoms that may reflect individual sensitivity or genetic variability?

⏱️ Are my consumption patterns optimised?
Would adjusting timing (e.g. avoiding late-day intake), portion size or frequency improve sleep quality, energy regulation or overall wellbeing?

🌿 What alternatives or adjustments could I consider?
Could incorporating decaffeinated options or caffeine-free alternatives, such as chicory or herbal infusions, provide similar enjoyment with fewer physiological effects?

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References 📚

1.         Reyes CM, Cornelis MC. Caffeine in the Diet: Country-Level Consumption and Guidelines. Nutrients. 2018;10(11).

2.         Landais E, Moskal A, Mullee A, Nicolas G, Gunter MJ, Huybrechts I, et al. Coffee and Tea Consumption and the Contribution of Their Added Ingredients to Total Energy and Nutrient Intakes in 10 European Countries: Benchmark Data from the Late 1990s. Nutrients. 2018;10(6).

3.         Patay ÉB, Bencsik T, Papp N. Phytochemical overview and medicinal importance of Coffea species from the past until now. Asian Pacific journal of tropical medicine. 2016;9(12):1127-35.

4.         Nieber K. The impact of coffee on health. Planta medica. 2017;83(16):1256-63.

5.         Perna M, Hewlings S. Saturated Fatty Acid Chain Length and Risk of Cardiovascular Disease: A Systematic Review. Nutrients. 2023;15(1):30.

6.         Hernandez LM, Xu EG, Larsson HCE, Tahara R, Maisuria VB, Tufenkji N. Plastic Teabags Release Billions of Microparticles and Nanoparticles into Tea. Environmental Science & Technology. 2019;53(21):12300-10.

7.         Ramalakshmi K, Raghavan B. Caffeine in Coffee: Its Removal. Why and How? Critical Reviews in Food Science and Nutrition. 1999;39(5):441-56.

8.         Daly JW, Shi D, Nikodijević O, Jacobson KA. The role of adenosine receptors in the central action of caffeine.  Caffeine and behavior: Current views & research trends: CRC Press; 2020. p. 1-16.

9.         Xie X, Ramkumar V, Toth LA. Adenosine and dopamine receptor interactions in striatum and caffeine-induced behavioral activation. Comparative medicine. 2007;57(6):538-45.

10.       EFSA Panel on Dietetic Products N, Allergies. Scientific Opinion on the safety of caffeine. EFSA Journal. 2015;13(5):4102.

11.       Wikoff D, Welsh BT, Henderson R, Brorby GP, Britt J, Myers E, et al. Systematic review of the potential adverse effects of caffeine consumption in healthy adults, pregnant women, adolescents, and children. Food and chemical toxicology. 2017;109:585-648.

12.       Doepker C, Franke K, Myers E, Goldberger JJ, Lieberman HR, O'Brien C, et al. Key Findings and Implications of a Recent Systematic Review of the Potential Adverse Effects of Caffeine Consumption in Healthy Adults, Pregnant Women, Adolescents, and Children. Nutrients. 2018;10(10).

13.       Pediatrics AAo. Clinical Report—Sports drinks and energy drinks for children and adolescents: Are they appropriate. Pediatrics. 2011;127(6):1182-9.

14.       Organization WH. Guideline: sugars intake for adults and children: World Health Organization; 2015.

15.       Cappelletti S, Piacentino D, Fineschi V, Frati P, Cipolloni L, Aromatario M. Caffeine-Related Deaths: Manner of Deaths and Categories at Risk. Nutrients. 2018;10(5).

16.       Fulton JL, Dinas PC, Carrillo AE, Edsall JR, Ryan EJ, Ryan EJ. Impact of Genetic Variability on Physiological Responses to Caffeine in Humans: A Systematic Review. Nutrients. 2018;10(10).

17.       Alsene K, Deckert J, Sand P, de Wit H. Association between A2a receptor gene polymorphisms and caffeine-induced anxiety. Neuropsychopharmacology. 2003;28(9):1694-702.

18.       Li L, Su C, Chen X, Wang Q, Jiao W, Luo H, et al. Chlorogenic acids in cardiovascular disease: A review of dietary consumption, pharmacology, and pharmacokinetics. Journal of agricultural and food chemistry. 2020;68(24):6464-84.

19.       Tagliazucchi D, Helal A, Verzelloni E, Conte A. The type and concentration of milk increase the in vitro bioaccessibility of coffee chlorogenic acids. Journal of Agricultural and Food Chemistry. 2012;60(44):11056-64.

20.       Al-Ghafari AB, Alharbi RH, Al-Jehani MM, Bujeir SA, Al Doghaither HA, Omar UM. The effect of adding different concentrations of cows’ milk on the antioxidant properties of coffee. Biosciences Biotechnology Research Asia. 2017;14(1):177-84.

21.       Mellbye FD, Nguyen MD, Hermansen K, Jeppesen PB, Al-Mashhadi ZK, Ringgaard S, et al. Effects of 12-Week Supplementation with Coffee Diterpene Cafestol in Healthy Subjects with Increased Waist Circumference: A Randomized, Placebo-Controlled Trial. Nutrients. 2024;16(19).

22.       Orrje E, Fristedt R, Rosqvist F, Landberg R, Iggman D. Cafestol and kahweol concentrations in workplace machine coffee compared with conventional brewing methods. Nutrition, Metabolism and Cardiovascular Diseases. 2025:103933.

23.       Eldesouki S, Qadri R, Abu Helwa R, Barqawi H, Bustanji Y, Abu-Gharbieh E, et al. Recent updates on the functional impact of kahweol and cafestol on cancer. Molecules. 2022;27(21):7332.

24.       Harshitha MN, Sirisha KL, Shafia S, Murthy PS. Coffee and chicory blend: properties, nutrition, and health implications. Journal of Food Science and Technology. 2025;62(7):1213-27.

25.       Malik B, Rehman RU. Chicory Inulin: A Versatile Biopolymer with Nutritional and Therapeutic Properties. In: Aftab T, Hakeem KR, editors. Medicinal and Aromatic Plants: Healthcare and Industrial Applications. Cham: Springer International Publishing; 2021. p. 373-90.

26.       Ahmadirad H, Omrani M, Azmi N, Saeidian AH, Jahromi MK, Mirtavoos-Mahyari H, et al. Dietary phytochemical index and the risk of cancer: A systematic review and meta-analysis. PloS one. 2025;20(4):e0319591.

27.       Wijlens AGM, Mars M, Dull DB, De Graaf K. Short term effect of chicory root fibre on appetite ratings and energy intake. Appetite. 2013;71:490.

28.       Akram H, Zafar H, Abbasi BH. The chicory root (Cichorium intybus var. sativum) frontier: pioneering biotechnological advancements. Phytochemistry Reviews. 2025:1-25.

In developing this work, the author utilised ChatGPT-4 to assist with language editing.