How does the gut microbiome differ in undernourished children living in low-income countries?

The gut microbiome in undernourished children living in low-income countries tends to be immature and less diverse compared to healthy children. This means it lacks the full range of beneficial bacteria needed for proper growth and immune function. Studies consistently find higher levels of certain bacteria, such as Proteobacteria, and lower levels of beneficial groups like Bifidobacterium. These differences may contribute to ongoing malnutrition and poor response to nutritional interventions.

What the research says

A meta-analysis of microbiome studies in undernourished children from sub-Saharan Africa and other low- and middle-income countries found that elevated levels of Pseudomonadota (a phylum that includes many pathogenic bacteria) were consistently linked to severe acute malnutrition ¹. This suggests that an overgrowth of potentially harmful bacteria is a common feature of malnutrition across different regions.

In a study of children aged 10 to 18 months living in urban slums of Mumbai, India, the gut microbiota was dominated by Bifidobacterium (over 80% relative abundance), with very low levels of Bacteroides, indicating an immature microbiome ⁹. Higher microbial diversity was associated with current breastfeeding and better growth measures, while lower diversity was linked to poorer nutritional status ⁹.

Research on the small intestine (duodenum) of Zambian children with stunting or severe acute malnutrition found that the microbiota was dominated by Streptococcus, Granulicatella, Gemella, and Klebsiella ¹⁰. Children with severe acute malnutrition had even lower bacterial diversity than those with stunting alone ¹⁰. A meta-analysis comparing duodenal samples from malnourished children across different countries showed similarities in bacterial composition by age, but the relative abundances and their links to nutritional status varied by geography ¹⁰.

A case report of a severely malnourished child with multidrug-resistant infections showed that after washed microbiota transplantation (transferring healthy donor stool), the child's gut microbiome improved and nutritional status gradually recovered ⁴. This highlights the potential role of microbiome repair in treating malnutrition.

A randomized trial in Bangladesh found that a microbiota-directed complementary food (MDCF-2) improved weight gain and repaired gut microbiota in children with moderate acute malnutrition, compared to a standard ready-to-use supplementary food ¹¹. This suggests that targeting the microbiome with specific nutrients can help restore a healthier gut community.

What to ask your doctor

• Could my child's gut microbiome be tested to see if it is immature or lacking beneficial bacteria?
• Are there specific foods or supplements that can help restore a healthy gut microbiome in undernourished children?
• What is the role of antibiotics or probiotics in managing malnutrition and gut health?
• Should I be concerned about high levels of certain bacteria like Klebsiella or Streptococcus in my child's gut?
• Are there any ongoing studies or programs in our area that focus on microbiome repair for malnourished children?