This study, published in Science China Life Sciences, is reported by Jun Wang’s group from the Institute of Microbiology, Chinese Academy of Sciences, and Yutao Cui’s group from Dr. Cuiyutao Clinic, Beijing.


Since early 2020, the COVID-19 pandemic has had both direct and indirect impacts on health. A decrease in microbial diversity and an increase in opportunistic pathogens were reported in severe COVID-19 patients and were presumed to contribute to the deterioration of host immune functions.

The gut microbiomes of infants and children, which are required for the maturation of the human immune system and metabolic processes, have not been thoroughly investigated. The group of Jun Wang and Yutao Cui conducted a comparative analysis of the gut microbiome of 1,126 children and infants during the COVID-19 pandemic in the Beijing area, revealing the variation of their gut microbiome.

Significant changes

The team found significant changes in the gut microbiome after the pandemic by both 16s rRNA sequencing and qPCR quantification of seven key bacteria. They also used quantitative microbiome profiling (QMP), a method with higher resolution in detecting microbiome differences, and 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 that 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), with a significantly younger age (average of 1.86 years).

The authors further discovered significantly lower body weight and height 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. The authors speculated that the increased usage of antiseptics and social distancing since the beginning of the pandemic has contributed to the decrease in microbial loads and delay in microbiome succession, necessitating the long-term studies on the effects of these shifts in gut microbiomes.