How does the digestive system work?

Your digestive system is one long tube that runs right through you, from your mouth to your anus. In a living adult it is about 5 to 7 metres long. Food inside it is not yet really inside your body: it only gets in once it crosses the tube's lining. We are facing the person, so their right side is on your left.

In order, food passes the mouth, the pharynx (throat), the oesophagus (food pipe, about 25 cm), the J-shaped stomach, the small intestine (3 to 5 m, starting with the C-shaped duodenum), and the wider large intestine or colon (about 1.5 m), which frames the coils. It ends at the rectum and anus. Rings of muscle called sphincters, like the one at the bottom of the oesophagus and the pylorus at the stomach's exit, work as one-way gates.

Food never passes through the accessory organs, but they are vital. Three pairs of salivary glands make about a litre of saliva a day. The liver makes bile, stored in the gallbladder. The pancreas makes a juice with enzymes for every kind of food. Bile and pancreatic juice enter the duodenum through one small opening.

Each organ has its own box: StomachClear, IntestineClear, LiverClear, PancreasClear and TongueClear. This box is about how they work together. Click an organ on the model to find its box.

Follow a thali: rice, dal, sabzi and curd. The clock on this chapter runs in log steps, so seconds, hours and days all fit on one slider.

In the mouth, teeth grind each bite for about 20 seconds while saliva wets it. Your tongue pushes the soft ball, the bolus, to the back, and the swallow reflex takes over: the airway closes for a moment and the bite enters the oesophagus. A ring of muscle squeezes behind it and travels down, a wave called peristalsis. It works even upside down, and takes about 8 seconds.

The stomach stores the meal, churns it with acid into a thick soup, chyme, and lets it through the pylorus a spoonful at a time. Most of a meal leaves in about 2 to 4 hours. Fatty food leaves more slowly.

The small intestine takes about 3 to 5 hours. Here most of the digesting and nearly all the absorbing happen, so the leftovers shrink as they go.

The colon is the slow part: usually 10 to 59 hours, typically a day and a half. It soaks up water, its bacteria ferment the fibre from your sabzi and dal, and a few strong mass movements a day push the stool towards the rectum, often after a meal.

Your body can only absorb small molecules. Digestion is the work of making them.

Mechanical digestion makes pieces smaller: your teeth chew, the stomach churns, and the small intestine squeezes back and forth. Chemical digestion cuts the molecules themselves. It is done by enzymes, proteins that work like molecular scissors, each cutting one kind of bond.

Carbohydrates like the starch in rice are long chains of sugar. Amylase in saliva starts cutting them in your mouth, pancreatic amylase carries on in the duodenum, and enzymes on the gut wall split the last pairs into single glucose units.

Proteins, as in dal, are chains of amino acids. Pepsin in the stomach starts on them, trypsin and chymotrypsin from the pancreas cut them shorter, and peptidases on the gut wall finish the job.

Fats, as in ghee and curd, don't mix with water. Bile from the liver breaks big blobs into tiny droplets, like washing-up liquid, and lipase from the pancreas cuts them into fatty acids.

Each enzyme has a favourite pH. The stomach is very acidic, about pH 1.5 to 3.5, perfect for pepsin. Then the pancreas pours in bicarbonate and the duodenum rises to about pH 6 to 7, where trypsin and lipase work and pepsin stops. More in StomachClear, PancreasClear and IntestineClear.

Once food is cut into small molecules, it has to cross the lining of the small intestine. The more lining, the faster that goes, so the gut folds it three times.

Big circular folds give about 1.6 times the area of a plain tube. They are covered in millions of tiny fingers called villi, each 0.5 to 1 mm tall, which give about 6.5 times more. Each lining cell carries a fuzz of microvilli, about 13 times more again. In all, about 30 m², the size of a small flat. Old books said "a tennis court", about 260 m², but careful measurements in 2014 by Helander and Fändriks showed that was far too big.

Inside each villus are capillaries and a lymph vessel called a lacteal. Sugars and amino acids go into the blood and travel by the portal vein straight to the liver, which checks and stores them (see LiverClear). Fats are packed into tiny parcels that go into the lacteals, travel in the lymph, and join the blood near your neck.

The gut also recycles water. About 9 litres go in each day, but only about 2 come from food and drink: the rest is your own juices. The small intestine takes back most of it, the colon nearly all the rest, and only about 0.1 to 0.2 litres leave in the stool. When that fails, as in diarrhoea, you can lose water very fast.

Digestion runs itself. The gut wall holds its own enteric nervous system, about 200 to 600 million nerve cells in two thin nets. It can run peristalsis even when cut off from the brain, which is why it is nicknamed the second brain.

The brain still listens and talks through the vagus nerve, the gut–brain axis. Most of its fibres, about 80%, carry news up from the gut. And messages go down too: just smelling food starts your stomach making acid, as Pavlov showed with dogs.

Gut cells also send hormones through the blood. Gastrin from the stomach turns up the acid. Secretin, the first hormone ever found, tells the pancreas to neutralise acid arriving in the duodenum. CCK squeezes the gallbladder and calls for enzymes when fat arrives. GLP-1 from lower down boosts insulin and makes you feel full; drugs that copy it are now used for diabetes and weight loss (see PancreasClear).

Your colon is home to about 38 trillion bacteria, the gut microbiome, about as many as your own cells. They eat the fibre you cannot digest, from dal, vegetables, whole grains and fruit, and turn it into short-chain fatty acids that feed your colon lining. WHO suggests at least 25 g of fibre a day for adults.

Almost everyone has tummy trouble sometimes. This chapter explains common problems; it cannot tell what is going on in your own body. For that, see a doctor, especially if you notice blood in stool or vomit, black stools, weight loss you can't explain, trouble swallowing, or pain that won't go away.

Acidity or reflux happens when stomach acid leaks up past the valve at the bottom of the oesophagus, causing heartburn. Frequent reflux is called GERD. Constipation means hard or infrequent stools; fibre, water and moving about usually help.

Diarrhoea can drain water and salts fast, and kills about 440,000 young children a year worldwide. The cure that saved millions is simple: oral rehydration salts (ORS), salt and sugar in clean water, which the gut can still absorb. Food poisoning comes from germs in food or water; handwashing, cooking well and safe water prevent most of it.

About two in three adults worldwide absorb lactose, milk sugar, poorly, because they make little lactase. Curd is often easier, because its bacteria have already eaten much of the lactose. IBS is pain with changed bowel habits, linked to the gut's nerves and the gut–brain axis. Ulcers are sores in the stomach or duodenum, mostly caused by the germ H. pylori or by painkillers.

Colon cancer is the third most common cancer in the world. It usually grows from small polyps over years, so screening can find and remove them early.