Gut Microbiota Dynamics in Infectious Diarrhea

The gut harbours a complex microbial ecosystem that maintains nutrient absorption, immune modulation and colonisation resistance. Infectious diarrhoea precipitates acute dysbiosis, characterised by loss of obligate anaerobes, bloom of Proteobacteria and shifts in the virome. These perturbations impair mucosal integrity, alter short‐chain fatty acid production and prolong symptom duration. Recovery involves staged recolonisation by commensal Bacteroides and Firmicutes, yet factors such as antibiotic use, age and nutritional status modulate restoration trajectories. In low-resource settings, repeated diarrhoeal episodes exacerbate malnutrition and compound dysbiosis, with long-term consequences for growth and immunity. Integrative metagenomic and metabolomic studies reveal interkingdom interactions between bacteria, viruses and host metabolites, pointing to microbial succession patterns that could inform interventions. Therapeutic approaches under investigation include targeted probiotics, faecal microbiota transplantation and precision antimicrobials designed to restore resilience and prevent recurrence.

Research from Nature Portfolio

Recent studies have shown a marked reduction in microbial diversity in severe viral gastroenteritis among hospitalised children, with enrichment of Campylobacteraceae, Neisseriaceae and Enterobacteriaceae in complicated cases. Rotavirus infection yields a greater loss of Bacteroidetes and Firmicutes compared with norovirus, correlating with more severe clinical scores. Another investigation into mixed viral–bacterial aetiologies demonstrated that co-infections with enteroaggregative Escherichia coli amplify dysbiosis, marked by increased Bifidobacteriaceae alongside substantial depletion of Bacteroides, and associate with heightened illness severity. These findings underscore the bidirectional interplay between the virome and bacterial community structure, suggesting specific microbial shifts as potential biomarkers of disease complexity.

Gut Microbiota Dynamics in Infectious Diarrhea publication trend

The graph below shows the total number of articles in gut microbiota dynamics in infectious diarrhea across all publications each year (not limited to Nature Index journals).

Technical terms

Gut microbiota: The community of microorganisms inhabiting the gastrointestinal tract.
Dysbiosis: An imbalance in microbial composition associated with disease.
Alpha diversity: A measure of species richness and evenness within a single sample.
Beta diversity: A measure of compositional differences between microbial communities.
16S rRNA sequencing: A molecular method for profiling bacterial taxa based on ribosomal RNA gene sequences.
Metagenomics: The study of genetic material recovered directly from environmental samples, allowing analysis of community composition and function.

References

1. Viral metagenomics of the gut virome of diarrheal children with Rotavirus A infection. Gut Microbes (2023).
2. The impact of antibiotics on the gut microbiota of children recovering from watery diarrhoea. npj Antimicrobials and Resistance (2024).
3. Intestinal microbiome in children with severe and complicated acute viral gastroenteritis. Scientific Reports (2017).
4. Mixed Viral-Bacterial Infections and Their Effects on Gut Microbiota and Clinical Illnesses in Children. Scientific Reports (2019).