Our Digestive System

The digestive system is how your body takes apart food and absorbs the parts it can use. It's a single continuous tube running from your mouth to your anus, with a handful of supporting organs (the liver, gallbladder, and pancreas) feeding enzymes and fluids into it along the way. Food moves through in one direction, getting broken down mechanically and chemically at each stage, and the nutrients get absorbed into the bloodstream where the rest of the body can use them.

The digestive system is also home to roughly 70-80% of your immune system, it produces more serotonin than your brain does, and it houses trillions of bacteria that influence everything from mood to metabolism to inflammation.

Mouth and saliva

Digestion starts before food reaches your stomach. The mouth handles two jobs at once, mechanical breakdown through chewing and chemical breakdown through saliva.

Chewing physically reduces food into smaller pieces, increasing the surface area that enzymes and stomach acid can attack later. The harder you chew, the easier the rest of the digestive system has it. Eating too fast or barely chewing is one of the most common reasons people experience bloating and slow digestion, the stomach receives large pieces of food it then has to spend extra time and acid breaking down before they can move on.

Saliva contains amylase, an enzyme that starts breaking down starches into sugars while food is still in your mouth. If you chew bread or rice long enough, you'll notice it starts tasting sweet, that's amylase converting starch into glucose. Saliva also contains lipase (a small amount, the pancreas produces) and lysozyme, an antibacterial enzyme that kills some of the bacteria entering through food.

Saliva production is also one of the first signals the body uses to prepare for incoming food. Even the sight or smell of food triggers saliva release through the vagus nerve, the same nerve that signals the stomach to start producing acid and the pancreas to prepare enzymes.

Oesophagus

The oesophagus is the muscular tube that connects your mouth to your stomach, roughly 25cm long. It doesn't digest anything, its only job is to move food from one end to the other.

It does this through peristalsis, a coordinated wave of muscle contractions that pushes food downward whether you're sitting up, lying down, or upside down. This is why astronauts can swallow in zero gravity, peristalsis doesn't rely on gravity to work.

At the bottom of the oesophagus sits the lower oesophageal sphincter (LES), a ring of muscle that stays closed at rest and opens briefly to let food into the stomach. The LES is what stops stomach acid from flowing backwards into the oesophagus. When it weakens or relaxes inappropriately, acid splashes up and burns the oesophageal lining, this is acid reflux.

Stomach

The stomach is a muscular sac that sits just below the diaphragm. It's the main acid bath of digestion, where food gets chemically broken down into a thick paste called chyme before being released gradually into the small intestine.

The stomach lining produces three things that do the real work:

Hydrochloric acid (HCl) brings the inside of the stomach to a pH of around 1.5-2, roughly the same acidity as battery acid. This denatures proteins, unfolding them so digestive enzymes can attack their bonds. It also kills the vast majority of bacteria, viruses, and parasites that come in with food.

Pepsin is the enzyme that breaks down protein specifically. It's secreted as an inactive form called pepsinogen, which only becomes active in the presence of stomach acid.

Intrinsic factor is a protein that binds vitamin B12 and protects it through the rest of the digestive tract until it can be absorbed in the small intestine.

The stomach also produces a thick mucus layer that coats its own walls, protecting the tissue from being digested by its own acid and enzymes.

Gastric emptying

Food doesn't pass through the stomach all at once. It leaves gradually through a valve called the pyloric sphincter into the small intestine, a process called gastric emptying. How fast this happens depends on what you ate:

Liquids empty fastest (15-30 minutes for water)

Carbohydrates empty next (1-2 hours)

Proteins empty more slowly (2-3 hours)

Fats empty slowest (3-4 hours for a fatty meal)

This is why a high-fat meal keeps you full longer than a high-carb one, the food is physically still sitting in your stomach for longer.

Small intestine

The small intestine is where almost all nutrient absorption actually happens. It's divided into three sections: the duodenum (the first 25cm, where most chemical digestion finishes), the jejunum (the middle section, where most absorption happens), and the ileum (the final section, where the last specific nutrients like B12 and bile salts get absorbed).

The inside of the small intestine isn't smooth. The wall is covered in folds, the folds are covered in tiny finger-like projections called villi, and each villus is covered in even smaller hair-like projections called microvilli. Together they multiply the surface area of the intestinal wall by roughly 600 times. If you flattened the inner surface of your small intestine, it would cover an area the size of a tennis court.

Different nutrients cross the intestinal wall in different ways:

Glucose and amino acids are small enough to pass through the intestinal wall cells into capillaries on the other side. From there they flow directly to the liver via the portal vein.

Fat takes a separate route. Fatty acids get absorbed into intestinal wall cells, reassembled into triglycerides, packaged into particles called chylomicrons, and released into the lymphatic system rather than directly into the blood. The lymphatic system eventually drains into the bloodstream near the heart, which is why dietary fat bypasses the liver on its first pass

Water-soluble vitamins (B vitamins, vitamin C) get absorbed directly into the bloodstream.

Fat-soluble vitamins (A, D, E, K) hitch a ride with dietary fat through the lymphatic system, which is why these vitamins can't be absorbed without fat in the meal

The intestinal wall is a single layer of cells held together by tight junctions, which act like the seals between floor tiles. They're selective: they let absorbed nutrients pass through into the bloodstream but block larger molecules, bacteria, and partially digested food from getting through.

When tight junctions loosen, larger molecules can slip through the wall into the bloodstream, and the immune system has to deal with them. This is increased intestinal permeability, commonly called leaky gut.

Intestinal permeability is a real, measurable thing. It clearly increases in coeliac disease, Crohn's, ulcerative colitis, heavy alcohol use, chronic NSAID use, and certain infections. It's also been observed in association with autoimmune conditions and food sensitivities.

The cells lining the small intestine turn over every 3-5 days, faster than almost any other tissue in the body. This is why the gut responds quickly to dietary changes, both positive and negative, and why nutrient deficiencies (zinc, vitamin A, protein) show up first as digestive symptoms.

Pancreas

In the digestive system the pancreas produces the enzymes that finish breaking down food in the small intestine.

The pancreas produces three main types of digestive enzyme:

Lipase breaks fat down into fatty acids your body can absorb. The pancreas produces the majority of the body's lipase, the stomach produces a smaller amount called gastric lipase that starts the job earlier

Amylase breaks carbohydrates and starches down into simple sugars. Saliva contains some amylase too, but pancreatic amylase does most of the work

Proteases (mainly trypsin and chymotrypsin) break proteins down into individual amino acids

The pancreatic enzymes get released as inactive forms and only switch on once they reach the intestine. This is a safety mechanism. Active digestive enzymes inside the pancreas itself would start digesting the organ. When that safety mechanism fails, usually from a blocked duct, heavy alcohol use, or gallstones, the enzymes activate prematurely and the pancreas begins digesting itself. This is pancreatitis, and it's one of the more dangerous abdominal emergencies because the pancreas has no good way to repair the damage once it starts.

Liver

The liver is the most metabolically active organ in your body.

Every nutrient absorbed from the intestine flows directly to the liver first through a dedicated vessel called the portal vein, before anything reaches the rest of the body. This gives the liver first access to everything that enters the bloodstream from digestion, food, drugs, alcohol, toxins, supplements, and it gets to process all of it before letting it through.

What the liver actually does:

Processes incoming nutrients. Stores excess glucose as glycogen, converts excess glucose to fat when glycogen is full, manufactures new glucose during fasting (gluconeogenesis), and distributes amino acids and other nutrients to where they're needed.

Detoxifies. Breaks down alcohol, drugs, medications, hormones, ammonia (a toxic byproduct of protein metabolism), and environmental toxins.

Produces proteins. The liver makes most of the proteins circulating in your blood, including albumin (the most abundant), clotting factors, SHBG (which binds sex hormones), and CRP (the inflammation marker)

Manages cholesterol. Produces about 80% of the cholesterol in your body, packages it into LDL and HDL particles for distribution, and clears it from circulation.

Clears hormones. Oestrogen, testosterone, cortisol, and thyroid hormones all eventually pass through the liver for metabolism and clearance. Poor liver function means hormones build up in circulation longer than they should

Produces bile. The fluid that emulsifies fat during digestion, covered below

The liver is one of the few organs that can regenerate, you can remove up to 70% of it and it will grow back.

Fatty liver disease is the most common modern liver problem, fat accumulating inside liver cells when the rate of fat conversion outpaces the rate of export. It comes in two main forms based on cause. AFLD (alcoholic fatty liver disease) is the alcohol-driven version, the result of chronic heavy drinking. NAFLD (non-alcoholic fatty liver disease, the metabolic version, driven by excess calories, fructose, insulin resistance, and obesity.

These are present in roughly 25% of adults globally and is the most common chronic liver condition. Continued damage progresses to fibrosis (scarring), then cirrhosis (extensive scarring that impairs function), then liver failure.

Bile

Bile is a digestive fluid the liver produces continuously, stored in the gallbladder between meals. When you eat fat, the gallbladder squirts bile into the small intestine.

Bile's job isn't to break fat down chemically. It emulsifies fat, the same thing dish soap does to grease in a pan. Fat naturally clumps together in the watery environment of the digestive system, forming large globules. The enzyme that actually breaks fat down (lipase) is water-based and can only attack the surface of those globules. Bile breaks the globules into millions of tiny droplets, multiplying the surface area lipase can work on by thousands of times.

Bile emulsifies fat into tiny droplets → lipase breaks those droplets into fatty acids → the fatty acids get absorbed through the intestinal wall into the lymphatic system.

Bile itself is mostly water, bile salts, and cholesterol. When bile becomes oversaturated with cholesterol, it can crystallise inside the gallbladder. These crystals are gallstones. They can sit silently for years or block the bile duct and cause severe pain, often after a fatty meal. A blocked duct can also trigger pancreatitis if the blockage extends to the pancreatic duct.

Rapid weight loss significantly increases gallstone risk. When you lose weight fast, the liver dumps more cholesterol into bile as it processes mobilised fat, oversaturating it faster than the gallbladder can clear it.

Large intestine

The large intestine is the final stretch of the digestive tract, roughly 1.5 metres long but much wider than the small intestine. By the time food reaches here, most nutrients have already been absorbed. What's left is water, electrolytes, fibre, and the trillions of bacteria that live in your gut.

The large intestine has three main jobs:

Absorb water. Roughly 9 litres of fluid enter the digestive tract each day, only about 2 litres come from what you drink, the rest is digestive juices the body itself produces (saliva, stomach acid, bile, pancreatic enzymes, intestinal secretions). Almost all of that fluid gets reabsorbed before it reaches the end. The small intestine handles most of it, the large intestine reclaims the last litre or so. When this absorption fails (from infection, inflammation, or certain medications), the result is diarrhoea. When it overworks (from low fibre, low fluid intake, or slow transit), the result is constipation.

Reabsorb electrolytes. Sodium, potassium, and chloride get pulled back out of what's passing through, alongside the water. This is one reason severe diarrhoea is dangerous, you lose not just fluid but the electrolytes that keep your nerves, muscles, and heart functioning.

House the microbiome. The vast majority of your gut bacteria live in the large intestine. They ferment the fibre and resistant starches your own enzymes couldn't break down, producing short-chain fatty acids (acetate, propionate, butyrate) that the cells lining your colon use as their primary fuel. Butyrate in particular is what keeps the colon lining healthy. Without enough fibre reaching the large intestine, the bacteria run low on substrate and the colon lining suffers.

By the time the remaining material reaches the end of the large intestine, it's been compacted into stool, roughly 75% water and 25% solids (mostly dead bacteria, undigested fibre, and shed intestinal cells). Transit time through the entire digestive tract typically runs 24-72 hours, with most of that time spent in the large intestine.

The microbiome

Your large intestine houses roughly 40 trillion bacteria spanning hundreds of different species. Collectively this community is called the gut microbiome. They actively run jobs your own cells can't do, and the composition of your microbiome influences almost every system. Roughly 99% live in the large intestine.

What the microbiome does

Breaks down what you can't. Your own digestive enzymes can't process fibre. Gut bacteria ferment it in the large intestine and produce butyrate as a byproduct, the main fuel that keeps the cells lining your colon alive and healthy. Without enough fibre reaching the colon, the bacteria run low on substrate, butyrate production drops, and the colon lining suffers.

Produces vitamins. Gut bacteria synthesise vitamin K, biotin, and several B vitamins (B12, folate, riboflavin), which then get absorbed through the colon wall. People with disrupted microbiomes (from heavy antibiotic use, certain diseases, or chronic dysbiosis) often have deficiencies in these.

Trains and regulates the immune system. Roughly 70-80% of your immune system lives in or around the gut. The microbiome is in constant dialogue with these immune cells, teaching them which bacteria are friendly, which are threats, and how strongly to respond.

Produces neurotransmitters. The microbiome influences mood, anxiety, and cognition through several routes. Gut bacteria produce neurotransmitters (serotonin, dopamine, GABA), shape how much tryptophan is available to the brain for its own serotonin production, send constant signals to the brain through the vagus nerve, and modulate brain inflammation. Roughly 90% of the body's serotonin is produced in the gut, though most of it stays local and regulates intestinal function rather than crossing into the brain. The effect on mood is modest.

Influences weight and metabolism. The composition of the microbiome affects how many calories you extract from food, how readily you store fat, and how your body responds to insulin. People with obesity and metabolic syndrome consistently show different microbiome compositions than lean people.

Competes with pathogens. A healthy microbiome takes up physical space and resources that pathogens would otherwise occupy. When the microbiome gets wiped out (by antibiotics, for example), opportunistic pathogens can take over (gut infection)

The microbiome is modifiable:

Fibre intake is the biggest. Different bacteria feed on different types of fibre, so dietary diversity (varied plants, not just one fibre source) builds a more diverse microbiome.

Fermented foods (kefir, sauerkraut, kimchi, yogurt, kombucha) introduce live bacteria and the compounds bacteria produce. Most "probiotic" benefits come from a regular fermented food.

Antibiotics wipe out large portions of the microbiome, including beneficial species. The microbiome typically recovers within weeks to months, but some species may not return.

Stress measurably alters microbiome composition through the gut-brain axis, partly through cortisol and partly through altered gut motility and immune signalling.

Sleep deprivation disrupts microbiome composition.

Birth method and early-life feeding set the initial microbiome. Vaginally born and breastfed infants develop a different starting microbiome than those delivered by C-section and formula-fed.

Alcohol in excess shifts the microbiome toward pro-inflammatory species.

Artificial sweeteners (sucralose, aspartame, saccharin) have been shown to alter microbiome composition in ways that may impair glucose tolerance.

The interventions with the strongest evidence remain the boring ones: eat a wide variety of plants, eat fermented foods regularly, don't take antibiotics unnecessarily, sleep well, manage stress, and limit alcohol and artificial sweeteners. Most “microbiome” supplements are way ahead of science.