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.
Supplementary Information
The online version contains supplementary material available at 10.1007/s12519-022-00659-6.