My expertise is molecular phylogeny and evolution of eukaryotic cells. During my PhD at the University of Ulsan, I worked on ciliated protozoa. Protozoa are the very first eukaryotes, and all the multicellular lineages (e.g., plants, animals, fungi) arise from the protozoan lineages. Ciliates are considered as a model eukaryotic organism and are used widely for genome evolution and medical research work. Like humans, ciliates have distinct germline and somatic genomes within every cell, and the somatic macronuclear genomes develop from zygotic nuclei through a complex series of epigenetically regulated processes. Ciliates are also important for cell biology, genomics, ecotoxicology, ecology and environment biology research, but their genome evolution and species delimitation remain questionable due to high morphological and genome plasticity. In my PhD research, I uncovered the systematics and phylogeny of poorly known ciliates and developed a molecular methodology for species delimitation, which could be tested on a single or multicellular organism, as species identification at the molecular level is essential to know who (organism) is doing what (function).
Highlighted Articles:
Shazib, S. U. A., Vd’ačný, P., Kim, J. H., Jang, S. W., & Shin, M. K. (2014). Phylogenetic relationships of the ciliate class Heterotrichea (Protista, Ciliophora, Postciliodesmatophora) inferred from multiple molecular markers and multifaceted analysis strategy. Molecular phylogenetics and evolution, 78, 118-135. (weblink).
Shazib, S.U.A., Vďačný, P., Kim, J.H., Jang, S.W., Shin, M.K. (2016). Molecular phylogeny and species delimitation within the ciliate genus Spirostomum (Ciliophora, Postciliodesmatophora, Heterotrichea), using the internal transcribed spacer region. Molecular phylogenetics and evolution, 102, 128-144. (weblink).
Chen, X., Shazib, S. U. A*., Kim, J. H., Kim, M. S., & Shin, M. K. (2018). New contributions to Gruberia lanceolata (Gruber, 1884) Kahl, 1932 based on analyses of multiple populations and genes (Ciliophora, Heterotrichea, Gruberiidae). European Journal of Protistology. 68, 16-30. (weblink).
As a Research Professor at the University of Ulsan, South Korea, I carried out phylogenomic studies using transcriptome data analyses to understand the evolutionary patterns of Heterotrich ciliates, specifically of the genus Spirostomum, which are model organisms for studies on human pathogenic bacteria, while others are sensitive to toxic substances and are thus useful as bioindicators. Genus Spirostomum comprises several complex, cryptic species. I used integrated approaches (including microscopic data, sequencing data, and phylogenetic approach) for species delimitation of Spirostomum congeners and species differentiation patterns. My research analysis shows that this kind of work opens new horizons for understanding the phylogenetics of biological species. I received a competitive, three-year grant from the Korean Research Foundation (NRF) to conduct this work.
Highlighted Articles:
Shazib, S. U. A., Cote-L'Heureux, A., Ahsan, R., Muñoz-Gómez, S. A., Lee, J., Katz, L. A., & Shin, M. K. (2025). Phylogeny and species delimitation of ciliates in the genus Spirostomum (class Heterotrichea) using single-cell transcriptomes. BMC Ecology and Evolution, 25(1), 17. (weblink).
Shazib, S.U.A., Vďačný, P., Slovák, M., Gentekaki, E., & Shin, M. K. (2019). Deciphering phylogenetic relationships and delimiting species boundaries using a Bayesian coalescent approach in protists: A case study of the ciliate genus Spirostomum (Ciliophora, Heterotrichea). Scientific Reports. 9, 16360 . (weblink).
Akter, S., Shazib, S.U.A., & Shin, M. K. (2019). Segnochrobactrum spirostomi gen. nov., sp. nov., isolated from the ciliate Spirostomum yagiui and description of a novel family, Segnochrobactraceae fam. nov. within the order Rhizobiales of the class Alphaproteobacteria. International Journal of Systematic and Evolutionary Microbiology. (weblink).
For my postdoctoral research at Smith College, I was invited to conduct research work funded by the U.S. National Science Foundation (NSF). For this project, I assessed the distributions of reproductively isolated species and used a novel method to characterize regions of the ciliate genome. I applied a single cell ‘omics approach to understanding the function of planktonic ciliates in marine ecology and genome evolution in protists. Single-cell ‘omics technologies refer to sequencing a single-cell whole genome and transcriptome to obtain genomic, transcriptome, and other multi-omics information to understand cell population differences and cellular evolutionary relationships. This kind of work requires skills and knowledge both in computational and molecular biology.
Highlighted Articles:
Shazib, S. U. A., Ahsan, R., Leleu, M., McManus, G. B., Katz, L. A., & Santoferrara, L. F. (2025). Phylogenomic workflow for uncultivable microbial eukaryotes using single-cell RNA sequencing− A case study with planktonic ciliates (Ciliophora, Oligotrichea). Molecular Phylogenetics and Evolution, 108239. (weblink).
Timmons, C., Shazib, S. U. A., & Katz, L. (2022). Epigenetic influences of mobile genetic elements on ciliate genome architecture and evolution. Journal of Eukaryotic Microbiology. (weblink)
At Ohio State University, I work with the single-cell fungi Candida albican, the most prevalent human fungal pathogen. My research focused on the evolution and gene family extension of the relatively unexplored telomere-associated (TLO) genes, which are the most expanded gene family within the opportunistic pathogen C. albicans. However, the functional fates of individual paralogs (duplicated genes) in expanded gene families, and the degree of overlapping and unique molecular and biological roles, remain largely unexplored. The TLO genes regulate a distinct set of target genes involved in fungal virulence. Recent research suggests that expansion of the TLO gene family in C. albicans could have contributed to its ability to adapt rapidly to different environmental conditions and colonise diverse niches. Therefore, single cell fungi C. albicans is an ideal system to understand how each gene holds individual or overlapping functions with other genes in the gene family.
Highlighted Articles:
Dunn, M. J., Shazib, S. U. A., Simonton, E., Slot, J., & Anderson, M. Z. (2022). Architectural groups of a subtelomeric gene family evolve along distinct paths in Candida albicans. G3: Genes|Genomes|Genetics, 12(12), jkac28. (weblink)
Highlighted Work:
Shazib SUA, Schwartz KC, Kim D, Muñoz-Gómez SA, 2024. Evaluating Resource Investment into Mitochondria Across Nutrient Environments. Joint meeting of the American Society for Cell Biology (ASCB) and European Molecular Biology Organization (EMBO) 2024, San Diego, USA (December 14-18, 2024). (Poster Presentation)
Shazib SUA, Bauer T, Kreutz M, Hess S, Muñoz-Gómez SA, 2023. The evolution of a purple-and-green photosymbiosis and further insights into the phylogeny of the ciliate genus Pseudobleparisma. 40 Years of Endocytobiology, hosted by the International Society of Endocytobiology, Field Museum, Chicago, USA. (September 10-14, 2023). (Oral Presentation) (Program Abstract)
I will continue my single-cell ‘omics work to understand the genome evolution of single-cell eukaryotes. This research will focus on the origin and evolution of eukaryotes and organelles, bringing a strongly mechanistic approach to understanding how life on earth has developed, as well as the evolution of eukaryotic microbial pathogens, how genome evolution correlates with pathogenicity, and dating major evolutionary events that are associated with environmental changes. Additionally, I am interested in studying the coevolution of species, as it is important to understand the origins of most human diseases, which often originate from other species.