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Deciphering the Microbial Fingerprint of COVID-19: A Multi-Layered Exploration of the Oral and Gut Microbiome Dysbiosis
The impact of SARS-CoV-2 infection on the human microbiome remains a dynamic and intricate puzzle. This study delves deeper into this mystery by revisiting the oral and gut microbial compositions of 53 COVID-19 patients before and after viral clearance, alongside comparisons to 76 healthy individual...
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AUC Knowledge Fountain
2024
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| _version_ | 1867613423981821952 |
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| access_status_str | Open Access |
| author | Sultan, Iman Mostafa |
| author_browse | Sultan, Iman Mostafa |
| author_facet | Sultan, Iman Mostafa |
| author_sort | Sultan, Iman Mostafa |
| collection | Thesis |
| description | The impact of SARS-CoV-2 infection on the human microbiome remains a dynamic and intricate puzzle. This study delves deeper into this mystery by revisiting the oral and gut microbial compositions of 53 COVID-19 patients before and after viral clearance, alongside comparisons to 76 healthy individuals. Through a comparative lens, we have emploed two distinct differential abundance methods – DeSeq2 and ANCOM – while drawing upon the thorough SILVA database encompassing the full-length 16S rRNA gene. The analysis underscores the crucial role of a diverse methodological choir in microbiome research. In certain instances, the congruence between DeSeq2 and ANCOM may exhibit variability or lack complete concordance. However, their contrasting perspectives reveal a richer tapestry of microbial dynamics in health and disease. By acknowledging and exploring these discrepancies, future research can unlock the true relationship between microbial recovery, resilience, and the post-COVID-19 landscape. Our findings paint a comprehensive picture of SARS-CoV-2 infection fingerprint on the microbial community, evident in shifts in both alpha and beta diversity. This multi-layered exploration not only contributes to our understanding of COVID-19's influence on the microbiome but also highlights the importance of methodological diversity in unraveling the complex language of microbial communities. Our analysis, comapring DeSeq2 and ANCOM, revealed DeSeq2’s enhanced suitability for microbiome compositional data compared to the alternative method. This was evidenced by the most detection of significantly differentiated taxa across various taxonomic levels, highlighting its robustness and effectiveness in identifying key microbial signatures. As we strive to decipher the secrets of our microbial counterparts, it is crucial to adopt a wide array of analytical methodologies to construct a thorough and cohesive account of the intricate relationship between health and disease. |
| format | Thesis |
| id | oai:fount.aucegypt.edu:etds-3350 |
| institution | American University in Cairo (Egypt) |
| last_indexed | 2026-06-10T12:35:55.364Z |
| license_str | Not specified — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from AUC Knowledge Fountain — bepress |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | AUC Knowledge Fountain |
| publisherStr | AUC Knowledge Fountain |
| record_format | dspace |
| source_str | AUC Knowledge Fountain — bepress |
| spelling | oai:fount.aucegypt.edu:etds-3350 Deciphering the Microbial Fingerprint of COVID-19: A Multi-Layered Exploration of the Oral and Gut Microbiome Dysbiosis Sultan, Iman Mostafa The impact of SARS-CoV-2 infection on the human microbiome remains a dynamic and intricate puzzle. This study delves deeper into this mystery by revisiting the oral and gut microbial compositions of 53 COVID-19 patients before and after viral clearance, alongside comparisons to 76 healthy individuals. Through a comparative lens, we have emploed two distinct differential abundance methods – DeSeq2 and ANCOM – while drawing upon the thorough SILVA database encompassing the full-length 16S rRNA gene. The analysis underscores the crucial role of a diverse methodological choir in microbiome research. In certain instances, the congruence between DeSeq2 and ANCOM may exhibit variability or lack complete concordance. However, their contrasting perspectives reveal a richer tapestry of microbial dynamics in health and disease. By acknowledging and exploring these discrepancies, future research can unlock the true relationship between microbial recovery, resilience, and the post-COVID-19 landscape. Our findings paint a comprehensive picture of SARS-CoV-2 infection fingerprint on the microbial community, evident in shifts in both alpha and beta diversity. This multi-layered exploration not only contributes to our understanding of COVID-19's influence on the microbiome but also highlights the importance of methodological diversity in unraveling the complex language of microbial communities. Our analysis, comapring DeSeq2 and ANCOM, revealed DeSeq2’s enhanced suitability for microbiome compositional data compared to the alternative method. This was evidenced by the most detection of significantly differentiated taxa across various taxonomic levels, highlighting its robustness and effectiveness in identifying key microbial signatures. As we strive to decipher the secrets of our microbial counterparts, it is crucial to adopt a wide array of analytical methodologies to construct a thorough and cohesive account of the intricate relationship between health and disease. 2024-06-15T07:00:00Z thesis application/pdf https://fount.aucegypt.edu/etds/2308 https://fount.aucegypt.edu/context/etds/article/3350/viewcontent/_MS_Thesis_IM.pdf Theses and Dissertations AUC Knowledge Fountain bioinformatics metagenomics covid-19 dysbiosis gut oral microbiome Bioinformatics Biotechnology Influenza Humans Medical Biotechnology Medical Microbiology Virus Diseases |
| spellingShingle | bioinformatics metagenomics covid-19 dysbiosis gut oral microbiome Bioinformatics Biotechnology Influenza Humans Medical Biotechnology Medical Microbiology Virus Diseases Sultan, Iman Mostafa Deciphering the Microbial Fingerprint of COVID-19: A Multi-Layered Exploration of the Oral and Gut Microbiome Dysbiosis |
| title | Deciphering the Microbial Fingerprint of COVID-19: A Multi-Layered Exploration of the Oral and Gut Microbiome Dysbiosis |
| title_full | Deciphering the Microbial Fingerprint of COVID-19: A Multi-Layered Exploration of the Oral and Gut Microbiome Dysbiosis |
| title_fullStr | Deciphering the Microbial Fingerprint of COVID-19: A Multi-Layered Exploration of the Oral and Gut Microbiome Dysbiosis |
| title_full_unstemmed | Deciphering the Microbial Fingerprint of COVID-19: A Multi-Layered Exploration of the Oral and Gut Microbiome Dysbiosis |
| title_short | Deciphering the Microbial Fingerprint of COVID-19: A Multi-Layered Exploration of the Oral and Gut Microbiome Dysbiosis |
| title_sort | deciphering the microbial fingerprint of covid 19 a multi layered exploration of the oral and gut microbiome dysbiosis |
| topic | bioinformatics metagenomics covid-19 dysbiosis gut oral microbiome Bioinformatics Biotechnology Influenza Humans Medical Biotechnology Medical Microbiology Virus Diseases |
| url | https://fount.aucegypt.edu/etds/2308 https://fount.aucegypt.edu/context/etds/article/3350/viewcontent/_MS_Thesis_IM.pdf |
| work_keys_str_mv | AT sultanimanmostafa decipheringthemicrobialfingerprintofcovid19amultilayeredexplorationoftheoralandgutmicrobiomedysbiosis |