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Updated: Aug 14, 2025
Oral Biofilm Sampling for Microbiome Analysis in Healthy Children
Published on: December 31, 2017
Altered gut microbiota composition in children and their caregivers infected with the SARS-CoV-2 Omicron variant
Yi-Zhong Wang1,2, Jian-Guo Zhou3, Yan-Ming Lu4
1Department of Gastroenterology, Hepatology, and Nutrition, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, 355 Luding Road, Shanghai, 200062, China.
Insights
Gut microbiota changes were observed in children and caregivers infected with the Omicron variant of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2). These findings highlight the gut microbiome's role in COVID-19 pathogenesis.
Area of Science:
- Microbiology
- Virology
- Pediatrics
Background:
- Gut microbiota alterations are linked to COVID-19 pathogenesis.
- The severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) Omicron variant has raised concerns regarding its impact on public health.
- Understanding the gut microbiome's response to SARS-CoV-2 infection is crucial for developing effective treatments.
Purpose of the Study:
- To investigate gut microbiota alterations in children and asymptomatic caregivers infected with the SARS-CoV-2 Omicron variant.
- To compare the gut microbiota composition of infected individuals with healthy controls.
- To explore the functional implications of observed microbial changes.
Main Methods:
- Prospective cohort study involving 186 participants (COVID-19 children, asymptomatic caregivers, healthy children, healthy adults).
- Fecal samples analyzed using 16S rRNA gene sequencing for gut microbiota composition.
- Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) used for functional profiling.
Main Results:
- COVID-19 children showed distinct gut microbial communities compared to healthy children, with altered abundances of major phyla and genera.
- Specific genera like Prevotella and Bacteroides were increased, while Bifidobacterium and Blautia were decreased in infected children.
- Asymptomatic caregivers exhibited similar gut microbiota changes, and microbial metabolic pathways (KEGG, COG) were perturbed in infected individuals.
Conclusions:
- The SARS-CoV-2 Omicron variant significantly alters gut microbiota composition in both infected children and their asymptomatic caregivers.
- These findings underscore the critical role of the gut microbiome in the pathogenesis of COVID-19.
- Further research into gut microbiota modulation may offer therapeutic strategies for COVID-19.
Background:
Gut microbiota alterations have been implicated in the pathogenesis of coronavirus disease 2019 (COVID-19). This study aimed to explore gut microbiota changes in a prospective cohort of COVID-19 children and their asymptomatic caregivers infected with the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) Omicron variant.
Methods:
A total of 186 participants, including 59 COVID-19 children, 50 asymptomatic adult caregivers, 52 healthy children (HC), and 25 healthy adults (HA), were recruited between 15 April and 31 May 2022. The gut microbiota composition was determined by 16S rRNA gene sequencing in fecal samples collected from the participants. Gut microbiota functional profiling was performed by using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) software.
Results:
The gut microbiota analysis of beta diversity revealed that the fecal microbial community of COVID-19 children remained far distantly related to HC. The relative abundances of the phyla Actinobacteria and Firmicutes were decreased, whereas Bacteroidetes, Proteobacteria, and Verrucomicrobiota were increased in COVID-19 children. Feces from COVID-19 children exhibited notably lower abundances of the genera Blautia, Bifidobacterium, Fusicatenibacter, Streptococcus, and Romboutsia and higher abundances of the genera Prevotella, Lachnoclostridium, Escherichia-Shigella, and Bacteroides than those from HC. The enterotype distributions of COVID-19 children were characterized by a high prevalence of enterotype Bacteroides. Similar changes in gut microbiota compositions were observed in asymptomatic caregivers. Furthermore, the microbial metabolic activities of KEGG (Kyoto Encyclopedia of Genes and Genomes) and COG (cluster of orthologous groups of proteins) pathways were perturbed in feces from subjects infected with the SARS-CoV-2 Omicron variant.
Conclusion:
Our data reveal altered gut microbiota compositions in both COVID-19 children and their asymptomatic caregivers infected with the SARS-CoV-2 Omicron variant, which further implicates the critical role of gut microbiota in COVID-19 pathogenesis.
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