Gut microbiome analysis identifies potential aetiological factors in acute gastroenteritis

The morbidity and mortality resulting from acute gastroenteritis and associated chronic sequelae represent a substantial burden on health care systems worldwide. Few studies have investigated changes in the gut microbiome following an episode of acute gastroenteritis. Using non-directed 16S rRNA gene amplicon sequencing, the faecal microbiota of 475 patients with acute gastroenteritis was examined. Patient age was correlated to the overall microbial composition, with a decrease in Faecalibacterium observed in older patients. We observed the emergence of a potential Escherichia/Shigella dominated enterotype in a subset of patients, and this enterotype was predicted to be more pro-inflammatory than the other common enterotypes, with the latter dominated by Bacteroides or Faecalibacterium . Increased abundance of Escherichia/Shigella did not appear to be associated with infection with an agent of similar sequence similarity. Stool colour and consistency were associated with the diversity and composition of the microbiome, deviations from the norm (not brown and solid) showing increases in bacteria such as Escherichia/Shigella and Veillonella . Analysis of enriched outliers within the data identified a range of genera previously associated with gastrointestinal diseases including Treponema , Proteus , Capnocytophaga , Arcobacter , Campylobacter , Haemophilus , Aeromonas , and Pseudomonas . Our data represent the first in-depth analysis of gut microbiota in acute gastroenteritis. Phenotypic changes in the stool colour and consistency were associated with specific changes in the microbiota. Enriched bacterial taxa were detected in cases where no causative agent was identified using routine diagnostic tests, suggesting that in the future microbiome analyses may be utilised to improve diagnostics.