When the gut does not settle after an infection

Healthy state

A gut infection is heavy work for the gut. Pathogens or their toxins irritate the lining. Its cells release water and salt into the gut, the muscles speed up, and the diarrhoea flushes out part of the pathogens. At the same time, defence cells run hot: T cells, mast cells Mast cells Immune cells beneath the skin and mucous membranes, filled with histamine and other messengers. They raise the alarm in allergies, infections and stress. More in the chapter “Mast cells: alarm cells in the gut, histamine and the disputed MCAS” (immune cells that store messengers such as histamine Histamine A messenger substance of the body that is also found in aged and fermented foods. Too much can cause headache, flushing or diarrhoea. More in the chapter “Histamine intolerance: much searched, little proven”) and enteroendocrine cells (hormone cells of the lining) that release serotonin, among other things. In the gut, serotonin is not a mood substance but a pacemaker: it triggers waves of movement and reports stimuli to the nerves.

After the infection, the system normally powers down again. The lining renews itself completely within a few days because its top cell layer is constantly replaced. The connections between the cells (tight junctions Tight junctions Protein connections that hold the cells of the gut wall tightly together. They determine what can pass between the cells. More in the chapter “The gut barrier”) seal again, the inflammatory cells retreat, and the gut microbiota Microbiome, gut microbiota The community of all microbes in the gut, mainly bacteria, plus viruses, fungi and archaea. Most live in the colon. More in the chapter “Building microbial diversity”, thrown off by the diarrhoea and possibly antibiotics, rebuilds over weeks.

A few weeks of aftershocks are therefore normal: soft stool, more bloating, a more sensitive abdomen, sometimes a temporary intolerance to milk sugar because the digestive enzymes on the cell border of the damaged lining are missing at first. What matters is the direction: it should get better from week to week.

How long and how strongly an infection echoes depends on the pathogen. Viruses such as norovirus or rotavirus usually leave only short traces. Bacteria such as Campylobacter, Salmonella or Shigella, toxin-producing E. coli and protozoa such as Giardia penetrate deeper or last longer and leave something behind more often. By the usual criteria, IBS Irritable bowel syndrome Recurring abdominal pain linked to bowel movements, without tests finding another cause. Today it is understood as a disorder of gut–brain interaction. More in the chapter “The gut-brain axis” is only diagnosed when symptoms last at least three months.

Disrupted state: causes and effects

Depending on the pathogen, some people develop lasting new symptoms: diarrhoea, abdominal pain, bloating. In studies the range is about 3 to 36 percent; after Campylobacter infections it is up to about a quarter. Overall, the risk in the first year after a gut infection is about four times higher, afterwards still a good two times higher. Viruses usually have only a short aftermath, bacteria and protozoa a longer one. Experts call this post-infectious IBS.

Who gets it is not random. A long and severe initial illness, a toxin-producing pathogen, fever and blood in the stool raise the risk most. Added to this are an age under 60, in several studies female sex, smoking, and anxiety, low mood or strong body awareness before the infection. So it is an interplay of pathogen and person, not a sign of weakness and not imagination.

Part of what stays behind in the gut can be measured. After Campylobacter infections, researchers found more serotonin-producing cells and more T cells in the rectal lining months later, plus higher permeability. More serotonin means faster movement and stronger pain signalling, so diarrhoea and cramps. Mast cells often sit right next to nerve endings and can sensitise them, so that normal stretching arrives as pain (visceral hypersensitivity). This explains why the gut reports “too loudly” although under the microscope it hardly looks inflamed any more.

Other players come in, with different weight from person to person. Bile acids Bile acids Substances made by the liver that make fat digestible. About 95 percent are reabsorbed in the last part of the small intestine; gut bacteria transform the rest. More in the chapter “Bile acids: when bile causes diarrhoea”: some people with diarrhoea have more primary and fewer converted bile acids in the stool; too many of them in the colon act like a laxative. Microbiota: diarrhoea and antibiotics change it, and it sometimes needs longer to recover. After a Giardia infection, a cohort still showed more IBS and fatigue six years later. IBS is also more common after Covid-19, which suggests that infections in general, not only bacteria, can reset the gut.

When should you look more closely? Behind “IBS after an infection” other treatable things can hide: a pathogen that stayed (Giardia, rarely C. difficile Clostridioides difficile A bacterium that can spread after antibiotics and cause severe diarrhoea with its toxins. More in the chapter “After antibiotics: C. difficile and faecal transplants”), bile acid loss, microscopic colitis, triggered coeliac disease Coeliac disease An autoimmune disease in which gluten damages the lining of the small intestine. It is diagnosed with a blood test and usually a biopsy while you are still eating gluten. More in the chapter “Lactose, fructose, gluten: making sense of intolerances” or a first flare of inflammatory bowel disease Inflammatory bowel disease Umbrella term for Crohn’s disease and ulcerative colitis: long-term, relapsing inflammation of the gut that needs medical treatment. More in the chapter “Immune system and inflammation”. Blood in the stool, weight loss, night-time diarrhoea, fever, or symptoms that get worse rather than better after the first weeks should be checked by a doctor. The good news remains: in many people symptoms fade over months to a few years, even without knowing exactly what helped.