Altered gut microbiota composition in children and their caregivers infected with the SARS-CoV-2 Omicron variant

Jan 10, 2023World journal of pediatrics : WJP

Changes in gut bacteria in children and their caregivers infected with the COVID-19 Omicron variant

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Abstract

Altered gut microbiota compositions were observed in COVID-19 children and their asymptomatic caregivers infected with the SARS-CoV-2 Omicron variant.

The fecal microbial community of COVID-19 children was found to be distantly related to healthy children.
Relative abundances of Actinobacteria and Firmicutes were decreased, while Bacteroidetes, Proteobacteria, and Verrucomicrobiota were increased in COVID-19 children.
Notable reductions in genera such as Blautia, Bifidobacterium, and Streptococcus were observed, alongside increases in Prevotella and Escherichia-Shigella.
Asymptomatic caregivers exhibited similar gut microbiota composition changes compared to COVID-19 children.
Metabolic activities related to KEGG and COG pathways were disrupted in feces from individuals infected with the Omicron variant.

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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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Altered gut microbiota composition in children and their caregivers infected with the SARS-CoV-2 Omicron variant

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