Decoding the Gut Microbiome in Malnourished Pakistani Children: What We Are Learning

Childhood malnutrition remains one of the most significant public health challenges in Pakistan, with nearly 40% of children under five affected by stunting. While poor diet and infections are well-recognised drivers, emerging evidence suggests the gut microbiome — the trillions of bacteria inhabiting the intestinal tract — plays a far more central role than previously understood.

Our group has been characterising gut microbial communities in children from urban Peshawar and rural Khyber Pakhtunkhwa over the past five years. Using 16S rRNA amplicon sequencing on faecal samples, we have consistently found that stunted children harbour less diverse gut microbiomes compared to age-matched, adequately-nourished controls.

Specifically, we observe reduced abundance of short-chain fatty acid (SCFA)-producing bacteria such as Faecalibacterium prausnitzii, Roseburia intestinalis, and Bifidobacterium longum — all of which support intestinal barrier integrity, immune maturation, and nutrient absorption. In their place, we find enrichment of Proteobacteria and Enterobacteriaceae, which are associated with gut inflammation and increased intestinal permeability.

An intriguing finding from our Afghan refugee cohort is that gut microbial diversity is further reduced in children who experienced early displacement, independent of current dietary intake. This points to psychosocial stress and disrupted early-life colonisation as compounding factors that may require dedicated microbiome-targeted interventions beyond nutritional supplementation alone.

Our ongoing HEC-funded study aims to follow children from birth through two years of age, correlating microbiome trajectories with growth outcomes, dietary diversity scores, and biomarkers of intestinal inflammation. We hope these insights will eventually inform probiotic and prebiotic strategies tailored to the microbial deficits most predictive of growth faltering in Pakistani children.