
Interesting Facts About the Relationship Between Gut Microbes and Stunting in Children

Stunting is a condition of poor nutrition that causes a child’s height to be lower than the average. This condition results from inadequate nutrient intake over a prolonged period. Stunting can begin as early as in the womb and only become visible when the child reaches the age of two. It not only hampers physical growth but also weakens the immune system and impairs cognitive development. These problems can affect a child’s intelligence and productivity in adulthood.
- Factors Causing Stunting and the Role of the Environment
- How Gut Microbiota Develops in Children
- Differences in Gut Microbiota in Stunted and Non-Stunted Children
- Efforts to Modulate Gut Microbiota to Prevent Stunting
Factors Causing Stunting and the Role of the Environment
Stunting can be caused by chronic malnutrition linked to low socioeconomic status, inadequate maternal nutrition and health, a history of recurrent illnesses, and improper feeding practices in children. The condition often first appears as slow weight gain, known as weight faltering. According to the WHO, factors such as poor nutrition, environmental conditions, inadequate sanitation, low maternal education, and maternal health play significant roles in causing stunting.
Malnutrition can trigger Environmental Enteric Dysfunction (EED) in infants—a functional disorder of the small intestine. The development of EED can worsen with frequent exposure to microbial contamination from unclean food or water. Children with EED are at risk of stunting because their absorption of macro- and micronutrients is impaired.
How Gut Microbiota Develops in Children

The composition of a child’s gut microbiota changes with age and is influenced by maternal factors, type of delivery, diet, and environmental conditions. According to research by Mitchell et al. (2020), the mode of delivery (vaginal or cesarean) is the first factor determining the initial microbial colony composition in a newborn’s gut. Vaginally born babies have more Bifidobacterium spp. in their gut compared to babies delivered by cesarean section.
These bacteria are beneficial and play an important role in the infant’s gut, especially shortly after birth. Their benefits include training the baby’s immune system to distinguish between harmful and harmless substances, preventing excessive allergic reactions, aiding nutrient absorption, maintaining gut microbiota balance, supporting height growth and brain development, and more. Breastfeeding also affects gut microbiota composition compared to formula feeding, as breast milk is an excellent prebiotic and contains infant-type Bifidobacteria.
Differences in Gut Microbiota in Stunted and Non-Stunted Children
There are notable differences in gut microbiota composition between stunted and non-stunted children. In stunted children, levels of Bifidobacterium longum and Lactobacillus mucosae decrease, while Desulfovibrio spp. increase. The gut microbiota of stunted children is dominated by pro-inflammatory bacteria, whereas that of non-stunted children is dominated by probiotic bacteria.
One study in Africa found that stunted children had higher levels of E. coli, Enterobacteriaceae, and Campylobacter along with severe acute malnutrition. However, another study on Indonesian children aged 3–5 found that Enterobacteriaceae actually decreased and there was no significant difference in Campylobacter between stunted and normal children.
Read more:
Small but Mighty: Gut Microbes Fighting Toxins in the Body
Efforts to Modulate Gut Microbiota to Prevent Stunting
Preventing or reducing stunting and malnutrition can be done by modulating children’s gut microbiota. Three approaches are probiotics, prebiotics, and antibiotics. The suggested probiotic use involves consuming foods or beverages containing Lactobacillus.
Heuven et al. showed that Lactobacillus probiotics can increase body weight and height. Additionally, consuming probiotic-containing gummy candies for 50 days can boost beneficial colonies and reduce Enterobacteriaceae. If you're in the food, healthcare, or children's product industry, ensuring microbiological safety is a crucial step to prevent contamination risks that can impact children's health, including disruption of the gut microbiota.
IML Research provides comprehensive microbiology testing services, from bacterial identification and contaminant analysis to product quality evaluation. Discuss your testing needs with IML Research's team of experts to ensure your products are safe, reliable, and meet regulatory standards.
Author: Safira
Editor: Sabilla Reza
References:
Hardjo, J., & Selene, N. B. (2024). Stunting and gut microbiota: A literature review. Pediatric Gastroenterology, Hepatology & Nutrition, 27(3), 137–145. https://doi.org/10.5223/pghn.2024.27.3.137
Heuven LA, Pyle S, Greyling A, Melse-Boonstra A, Eilander A. Gut microbiota-targeted nutritional interventions improving child growth in low- and middle-income countries: a systematic review. Curr Dev Nutr 2021;5:nzab124
Mitchell CM, Mazzoni C, Hogstrom L, Bryant A, Bergerat A, Cher A, et al. Delivery mode affects stability of early infant gut microbiota. Cell Rep Med 2020;1:1-9



