How displacement reshapes refugees’ gut health
Refugee health is often discussed in terms of crises such as disease outbreaks, malnutrition and psychological distress. But some of the most serious effects of displacement are harder to see. One example is how forced migration can change the bacteria in the gut that support immunity and long-term health.
The human gut contains trillions of bacteria, viruses and fungi, together known as the gut microbiome. These microbes help digest food, support the immune system and protect against illness. A healthy gut microbiome is usually diverse and balanced, with plenty of beneficial bacteria that help protect against infection and inflammation.
Studies show that refugees often have gut microbiomes that look different from those of people who have not experienced displacement. Researchers describe distinct gut microbiome profiles, typically with fewer types of microbes and changes in which bacteria are most common. These differences are not genetic. Instead, they reflect the extreme conditions many refugees face before, during and after displacement.
Understanding these differences can help improve healthcare for refugees, but it also shows how social inequality can become physically embedded in the body over time.
One common finding is higher levels of harmful bacteria and antibiotic-resistant organisms in refugee gut microbiomes. Antibiotic-resistant bacteria can survive medicines designed to kill them, making infections harder to treat and easier to pass on.
Poor sanitation and contaminated environments play a major role. Many refugees come from, or travel through, areas affected by conflict or disaster, where access to clean water and toilets is limited. Drinking unsafe water or eating contaminated food increases the chance that disease-causing bacteria will settle in the gut and multiply, a process known as colonisation.
Common examples include E coli, Salmonella and Shigella. These bacteria can cause diarrhoea, vomiting and fever, and in severe cases may lead to dehydration, blood infection, poor growth in children or long-term digestive problems.
Repeated stomach and bowel infections, especially in crowded places with poor sanitation, disturb the normal balance of gut microbes. Over time, harmful species can take over, while the overall range of microbes shrinks. Having fewer different types of gut bacteria is widely recognised as a sign of poor gut health.
Chronic stress makes these problems worse. Refugees are often exposed to prolonged stress linked to war, violence, forced movement, separation from family and ongoing uncertainty. Rates of mental health challenges are high, and stress affects physical health through the gut–brain axis, the communication system between the brain and the digestive system.
Long-term stress alters immune responses, hormone levels and the gut lining. These changes increase inflammation and make it easier for harmful microbes to grow, while reducing beneficial bacteria such as Lactobacillus and Bifidobacterium.
Antibiotic use is another major factor driving poor gut health and antibiotic resistance. In low-resource or conflict settings, antibiotics are often used frequently because infections are common and access to testing is limited. Refugees may receive multiple courses without a clear diagnosis or follow-up. While these medicines can save lives, repeated or unnecessary use allows resistant bacteria to survive and spread.
Antibiotics also destroy helpful microbes that keep the gut healthy. Repeated courses reduce the number and variety of beneficial bacteria, weakening the gut’s ability to protect itself.
As a result, antibiotic-resistant strains such as E coli that can neutralise antibiotics can become established in the gut, making infections much harder to treat.
Poor conditions and malnutrition
Living conditions during displacement further increase the risk of gut infection and the spread of antibiotic-resistant bacteria. Refugees camps and temporary shelters are often overcrowded and lack basic hygiene facilities, allowing infectious diseases to spread easily.
Dietary disruption also affects gut health. Sudden shifts from traditional diets rich in fibre to emergency food aid high in refined carbohydrates deprive beneficial gut bacteria of fuel. Low-fibre diets weaken gut defences and allow harmful bacteria to thrive.
Malnutrition further increases vulnerability, especially in children, whose gut microbiomes are still developing.
After resettlement, refugees may still carry antibiotic-resistant bacteria picked up earlier. Barriers to healthcare can slow recovery. Language barriers, limited access to culturally appropriate healthcare and delayed treatment can lead to antibiotics being prescribed as a precaution rather than based on confirmed diagnosis. This sustains cycles of microbiome disruption rather than recovery.
The spread of harmful and antibiotic-resistant bacteria in refugee populations is a public health issue, not a personal one. Addressing them requires coordinated public health interventions, including improved sanitation, careful antibiotic use, stress-aware care and nutritional support that helps restore a healthy gut.
Understanding how all these factors interact is essential for developing humane, effective healthcare strategies that protect both refugee communities and wider public health.
Manal Mohammed does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.