Impact of WaSH and dietary practices on age-driven gut microbiome in stunted young children

Background Stunting, defined as height-for-age below −2 standard deviations of the WHO child growth standards median, is influenced by nutritional and environmental factors. It remains a public health challenge in Tanzania, particularly in Iringa (prevalence 57%, exceeding the national average of 30%), despite abundant food production. This study explored the gut bacteriome as a potential biomarker for child growth and its association with water, sanitation, and hygiene (WaSH) practices in food-secure settings.

A community-based cross-sectional study (September-October 2024) enrolled children aged 5–23 months in Iringa, collecting fecal samples and household data on growth metrics, WaSH, feeding practices, and illness. The V3–V4 region of the 16S rRNA gene was sequenced using Illumina MiSeq and analysed with QIIME2 and R for alpha and beta diversity, differential abundance (ANCOM-BC), and random forest (RF) modelling.

Overall, 60.5% of 297 children were stunted. Stunting was associated with older age, male gender, discontinued breastfeeding, poor feeding diversity, toilet sharing, and residence location (p < 0.001, p = 0.049, p = 0.001, p = 0.001, p = 0.001, and p = 0.005, respectively). Significant differences in bacterial community composition were observed between stunted and normally growing children (Shannon p = 0.0053; Bray-Curtis p = 0.001). A shared core bacteriome was identified in both groups, influenced by environmental and dietary factors. Normally growing children were enriched with Bifidobacterium, Rothia, Olsenella, Slackia, Lactobacillus, Gemella, and Oscillibacter, while stunted children showed enrichment of Prevotella, Akkermansia, Fusobacterium, Acinetobacter, Alistipes, Odoribacter, Fournierella, and the Ruminococcus torques group.

Age was the most consistent predictor of gut microbial diversity. Stunting does not appear to be caused by a completely different gut microbiome; instead, shared environmental and dietary factors shape both gut bacteria and child growth. Promoting diverse complementary feeding, continued breastfeeding, and improved hygiene could mitigate risks and inform targeted interventions in food-secure regions. Competing Interest Statement The authors have declared no competing interest.