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Updated: Aug 3, 2025
Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
Published on: October 15, 2019
Evaluation of the gut microbiome associated with COVID-19
Reza Maddah1, Vahid Goodarzi2, Seyedeh-Leili Asadi-Yousefabad3
1Department of Bioprocess Engineering, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran.
Introduction:
In 2019, a new virus from the coronavirus family called SARS-CoV-2, infected populations throughout the world. Coronavirus disease 2019 (COVID-19), an illness induced by this virus, attacks vital organs in the body, such as the respiratory system and the gastrointestinal tract. Recent studies have confirmed changes in the gut microbiome caused by the COVID-19 disease. We examined the alteration of the gut microbiome in COVID-19 patients compared to healthy individuals.
Materials And Methods:
in this study, the 16s metagenomics dataset, publicly available in the Sequence Read Archive (SRA) database, was used for analysis (accession number PRJNA636824). The analysis processes were performed using the CLC Microbial Genomics Module 20.1.1 (Qiagen). At first, the sequence reads of samples were trimmed and classified into operational taxonomic units (OTUs) with 97% similarity and then assigned to the Greengenes reference database (v138). Differential abundance analysis was used to determine statistically significant differences in OTUs between COVID-19 and healthy groups. Next, biodiversity analyses including the alpha diversity (intragroup diversity) and beta diversity (intergroup diversity) using defined indexes were estimated. Then, the co-occurrence network at the species level was constructed using the Pearson correlation coefficient calculation between pairs of OTUs in R software and visualized using Cytoscape software. Ultimately, the hub OTUs at the species level were identified using the cytoHubba plugin of Cytoscape based on Maximal Clique Centrality (MCC) algorithm.
Results:
The results of the metagenomic analysis revealed that the intestinal microbiome in healthy individuals has a higher biodiversity compared to COVID-19 patients. Indeed, healthy people also have a higher percentage of beneficial bacteria such as bifidobacteria adolescentis compared to COVID-19 patients; in contrast, COVID-19 patients have higher levels of opportunistic and pathogenic bacteria such as Streptococcus anginosus than healthy people. Also, by constructing a co-occurrence network at the species level, Bifidobacterium longum in the healthy group and Veillonella parvulain the COVID-19 group were found as hub species.
Conclusion:
The results of this study shed light on the relationship between the gut microbiome and COVID-19. These results could be helpful for understanding the pathogenesis, clinical features, and treatment of COVID-9.
Insights
COVID-19 patients exhibit reduced gut microbiome diversity and beneficial bacteria compared to healthy individuals. This study highlights significant alterations in the gut microbiome composition due to SARS-CoV-2 infection.
Area of Science:
- Microbiology
- Virology
- Genomics
Background:
- Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) causes COVID-19, impacting multiple organs including the gastrointestinal tract.
- Emerging evidence indicates significant alterations in the gut microbiome composition following COVID-19 infection.
Purpose of the Study:
- To investigate and compare the gut microbiome alterations in COVID-19 patients versus healthy individuals.
- To identify specific bacterial taxa and community structures affected by SARS-CoV-2 infection.
Main Methods:
- Utilized 16S metagenomic sequencing data from the SRA database (PRJNA636824).
- Performed sequence trimming, operational taxonomic unit (OTU) classification, and assignment to the Greengenes database.
- Conducted differential abundance, alpha, and beta diversity analyses.
- Constructed and analyzed co-occurrence networks to identify hub species using R and Cytoscape.
Main Results:
- COVID-19 patients displayed lower gut microbiome biodiversity compared to healthy controls.
- Reduced abundance of beneficial bacteria (e.g., Bifidobacterium adolescentis) and increased opportunistic pathogens (e.g., Streptococcus anginosus) were observed in COVID-19 patients.
- Hub species identified were Bifidobacterium longum in healthy individuals and Veillonella parvula in COVID-19 patients.
Conclusions:
- The gut microbiome is significantly altered in individuals with COVID-19.
- Findings provide insights into the gut microbiome's role in COVID-19 pathogenesis and clinical presentation.
- Results may inform future therapeutic strategies targeting the gut microbiome for COVID-19 management.
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