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Updated: Jan 8, 2026
Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
Published on: October 15, 2019
Impacts of COVID-19 pandemic on early life gut microbiome
Lin Zhang1,2, Wenye Xu1,2, Henry Y H Meng3
1Microbiota I-Center (MagIC), The Chinese University of Hong Kong, Hong Kong SAR, China.
Insights
COVID-19 lockdowns altered infant gut microbiome development due to increased hygiene. This study observed changes in microbial diversity and antibiotic resistance genes in babies born during the pandemic.
Area of Science:
- Microbiome research
- Pediatric health
- Infectious disease epidemiology
Background:
- Increased hygiene and sanitation are linked to atopic diseases, potentially via the gut microbiome.
- The first year of life is critical for microbiome development influenced by environmental exposures.
Purpose of the Study:
- To investigate the impact of COVID-19 lockdown measures on early gut microbiome maturation in infants.
- To assess how heightened hygiene standards during the pandemic affected infant gut microbiome development.
Main Methods:
- Comparison of two large mother-baby cohorts (pre- and during-COVID-19) in China's Greater Bay Area.
- Analysis of gut microbiome diversity, composition, and functional gene content (resistance genes).
Main Results:
- Significant alterations in gut microbiome diversity, composition, and developmental trajectory were observed in infants during COVID-19.
- Decreased richness of antimicrobial peptide and antibiotic resistance genes was noted in the during-COVID cohort.
- Specific bacterial species showed altered antibiotic resistance gene profiles: *Staphylococcus epidermidis* had fewer resistance genes, while *Klebsiella pneumoniae* had more fluoroquinolone resistance genes.
Conclusions:
- COVID-19 hygiene measures significantly impacted early-life gut microbiome maturation.
- Findings highlight the need to consider microbiome alterations when evaluating hygiene interventions.
- Further research is required to understand the gut microbiome's role in disease development following pandemic-related hygiene changes.
Abstract:
Increased hygiene and sanitation are theorized to predispose to developing atopic diseases, a process potentially mediated by the gut microbiome. We hypothesized that the gut microbiome maturation has been altered by COVID-19 lockdown measures during the first year of life, a critical period when environmental exposure shapes human microbiome development. The two large pre- and during-COVID-19 mother-baby pairs cohorts in the Greater Bay Area of China provided the unique opportunity to assess the effect of increased hygiene standards on early gut microbiome maturation. Our results showed that the gut microbiome diversity, composition, and developmental trajectory were significantly altered between pre- and during-COVID-19 cohorts. Functionally, there was decreased richness in both antimicrobial peptide resistance genes and antibiotic resistance genes in the during-COVID cohort. Specially, Staphylococcus epidermidis carried a lower copy number of fluoroquinolone and beta-lactam antibiotics resistance genes while Klebsiella pneumoniae possessed a higher copy number of fluoroquinolone antibiotic resistance genes in gut microbiota of infants born during the COVID-19 pandemic. Our study underscores the importance of considering the microbiome when evaluating hygiene measures and the need for future research to ascertain the role of the gut microbiome in disease development.
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