Studying the Gut Microbiome in Afghan Refugee Children: Challenges, Insights, and Implications

Pakistan hosts one of the largest refugee populations in the world, with over 1.3 million registered Afghan refugees — a significant proportion of whom are children under five. While the health challenges of displacement are well-documented at the epidemiological level, the microbiological effects of forced migration on children's gut health remain poorly characterised. Our lab set out to address this gap.

Working in partnership with UNHCR health partners and community health workers in the Peshawar refugee settlements, we recruited 120 Afghan refugee children aged 6–36 months for gut microbiome profiling using shotgun metagenomics. Their profiles were compared to age- and sex-matched Pakistani urban and rural children from our existing CHAMP cohort.

The refugee children showed the lowest gut microbial diversity of any group in our study — even lower than Pakistani urban children living in high-density, sanitation-compromised areas. This was characterised by extreme enrichment of Escherichia-Shigella species (accounting for over 25% of relative abundance in some samples), near-absence of Akkermansia muciniphila (a key mucus-layer protector), and severely depleted Bacteroidetes populations.

Strikingly, even refugee children who were not acutely malnourished showed these microbial patterns, suggesting that displacement per se — through mechanisms including psychosocial stress, disrupted sleep, monotonous diet, and frequent infections — drives microbiome dysbiosis independent of nutritional status.

These findings have important implications for how we design nutritional interventions for displaced children. Standard therapeutic food protocols address caloric and micronutrient deficits but do not specifically target the gut microbiome. Our data suggest that adjunctive microbiome-targeted strategies — such as fermented food provision or targeted prebiotic supplements — may be important components of care for refugee children, particularly in the early post-displacement period.