Missing microbes in infants and children in the COVID-19 pandemic: a study of 1,126 participants in Beijing, China

Sci China Life Sci. 2024 Aug;67(8):1739-1750. doi: 10.1007/s11427-023-2488-0. Epub 2024 May 9.

Abstract

The COVID-19 pandemic has caused many fatalities worldwide and continues to affect the health of the recovered patients in the form of long-COVID. In this study, we compared the gut microbiome of uninfected infants and children before the pandemic began (BEFORE cohort, n=906) to that of after the pandemic (AFTER cohort, n=220) to examine the potential impact of social distancing and life habit changes on infant/children gut microbiome. Based on 16S rRNA sequencing, we found a significant change in microbiome composition after the pandemic, with Bacteroides enterotype increasing to 35.45% from 30.46% before the pandemic. qPCR quantification indicated that the bacterial loads of seven keystone taxa decreased by 91.69%-19.58%. Quantitative microbiome profiling, used to enhance the resolution in detecting microbiome differences, revealed a greater explained variance of pandemic on microbiome compared to gender, as well as a significant decrease in bacterial loads in 15 of the 20 major genera. The random forest age-predictor indicated the gut microbiomes were less mature in the after-pandemic cohort than in the before-pandemic cohort in the children group (3-12 years old) and had features of a significantly younger age (average of 1.86 years). Lastly, body weight and height were significantly lower in the after-pandemic cohort than in the before-pandemic cohort in infants (<1 year of age), which was associated with a decrease in bacterial loads in the fecal microbiome.

Keywords: COVID-19 pandemic; children health; gut microbiome; quantitative microbiome profiling.

MeSH terms

  • Bacteria / classification
  • Bacteria / genetics
  • Bacteria / isolation & purification
  • Bacterial Load
  • Beijing / epidemiology
  • COVID-19* / epidemiology
  • COVID-19* / microbiology
  • COVID-19* / virology
  • Child
  • Child, Preschool
  • Cohort Studies
  • Feces* / microbiology
  • Feces* / virology
  • Female
  • Gastrointestinal Microbiome*
  • Humans
  • Infant
  • Male
  • Pandemics
  • RNA, Ribosomal, 16S* / genetics
  • SARS-CoV-2 / genetics
  • SARS-CoV-2 / isolation & purification

Substances

  • RNA, Ribosomal, 16S