Abstract
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.
School
School of Sciences and Engineering
Department
Biotechnology Program
Degree Name
MS in Biotechnology
Graduation Date
Summer 6-15-2024
Submission Date
2-18-2024
First Advisor
Ahmed Moustafa
Committee Member 1
Ahmed Moustafa
Committee Member 2
Ahmed Abdullatif
Committee Member 3
Ali Elbehary
Extent
65 p.
Document Type
Master's Thesis
Institutional Review Board (IRB) Approval
Not necessary for this item
Recommended Citation
APA Citation
Sultan, I. M.
(2024).Deciphering the Microbial Fingerprint of COVID-19: A Multi-Layered Exploration of the Oral and Gut Microbiome Dysbiosis [Master's Thesis, the American University in Cairo]. AUC Knowledge Fountain.
https://fount.aucegypt.edu/etds/2308
MLA Citation
Sultan, Iman Mostafa. Deciphering the Microbial Fingerprint of COVID-19: A Multi-Layered Exploration of the Oral and Gut Microbiome Dysbiosis. 2024. American University in Cairo, Master's Thesis. AUC Knowledge Fountain.
https://fount.aucegypt.edu/etds/2308
Included in
Bioinformatics Commons, Biotechnology Commons, Influenza Humans Commons, Medical Biotechnology Commons, Medical Microbiology Commons, Virus Diseases Commons