Evaluation of the gut microbiome associated with COVID-19
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...
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| Format: | Article |
| Language: | English |
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Elsevier
2023-01-01
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| Series: | Informatics in Medicine Unlocked |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2352914823000813 |
| _version_ | 1797845026436284416 |
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| author | Reza Maddah Vahid Goodarzi Seyedeh-Leili Asadi-Yousefabad Mahbobe Abbasluo Parvin Shariati Amir Shafiei Kafraj |
| author_facet | Reza Maddah Vahid Goodarzi Seyedeh-Leili Asadi-Yousefabad Mahbobe Abbasluo Parvin Shariati Amir Shafiei Kafraj |
| author_sort | Reza Maddah |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-09T17:33:00Z |
| format | Article |
| id | doaj.art-db115da471d34311a67eec63d370ba84 |
| institution | Directory Open Access Journal |
| issn | 2352-9148 |
| language | English |
| last_indexed | 2024-04-09T17:33:00Z |
| publishDate | 2023-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Informatics in Medicine Unlocked |
| spelling | doaj.art-db115da471d34311a67eec63d370ba842023-04-18T04:09:02ZengElsevierInformatics in Medicine Unlocked2352-91482023-01-0138101239Evaluation of the gut microbiome associated with COVID-19Reza Maddah0Vahid Goodarzi1Seyedeh-Leili Asadi-Yousefabad2Mahbobe Abbasluo3Parvin Shariati4Amir Shafiei Kafraj5Department of Bioprocess Engineering, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran; Corresponding author. Shahrak-e Pajoohesh, km 15, Tehran - Karaj Highway, Tehran, Iran.Department of Anesthesiology, Rasoul-Akram Medical Center, Iran University of Medical Sciences (IUMS), Tehran, IranDepartment of Molecular Medicine, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, IranIslamic Azad University, Ashkezar Branch, Department of Biology, Yazd, IranDepartment of Bioprocess Engineering, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran; Corresponding author. Shahrak-e Pajoohesh, km 15, Tehran - Karaj Highway, Tehran, Iran.Department of Bioprocess Engineering, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, IranIntroduction: 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.http://www.sciencedirect.com/science/article/pii/S2352914823000813MicrobiomeGutCOVID-19Healthy individualsBiodiversityCo-occurrence network |
| spellingShingle | Reza Maddah Vahid Goodarzi Seyedeh-Leili Asadi-Yousefabad Mahbobe Abbasluo Parvin Shariati Amir Shafiei Kafraj Evaluation of the gut microbiome associated with COVID-19 Informatics in Medicine Unlocked Microbiome Gut COVID-19 Healthy individuals Biodiversity Co-occurrence network |
| title | Evaluation of the gut microbiome associated with COVID-19 |
| title_full | Evaluation of the gut microbiome associated with COVID-19 |
| title_fullStr | Evaluation of the gut microbiome associated with COVID-19 |
| title_full_unstemmed | Evaluation of the gut microbiome associated with COVID-19 |
| title_short | Evaluation of the gut microbiome associated with COVID-19 |
| title_sort | evaluation of the gut microbiome associated with covid 19 |
| topic | Microbiome Gut COVID-19 Healthy individuals Biodiversity Co-occurrence network |
| url | http://www.sciencedirect.com/science/article/pii/S2352914823000813 |
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