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 of Sciences and Engineering


Biotechnology Program

Degree Name

MS in Biotechnology

Graduation Date

Summer 6-15-2024

Submission Date


First Advisor

Ahmed Moustafa

Committee Member 1

Ahmed Moustafa

Committee Member 2

Ahmed Abdullatif

Committee Member 3

Ali Elbehary


65 p.

Document Type

Master's Thesis

Institutional Review Board (IRB) Approval

Not necessary for this item

Available for download on Monday, February 17, 2025