Research | Zuniga Lab | Computational Biotechnology Research ...

Our Lab Research focuses on

Experimental and computational Biology

Focus Area 1

Development of computational tools to characterize microbial communities and microbiome for health and bioenergy applications.

Microbial communities are pervasive throughout Earth. However, experimental limitations to quantitatively characterize the members and role of these communities often hinders the study of community composition and interspecies interactions at a deeper level. This provides a challenge for an in-depth and mechanistic understanding of the role of microbial communities. Through the integration of multi-omics analysis and genome-scale metabolic modeling, we have been able to obtain quantitative information about interspecies interactions between individual species. Deploying this advanced quantitative biology toolbox in conjunction with systems biology approaches allows for a mechanistic understanding of interactions and the capability to predict phenotypes under diverse environmental and genetic stages. Over the last few years, we have developed these community systems biology methods to understand interactions between phototrophs and heterotrophs as well as pathogens and nonpathogens under different earth ecosystems and host-specific microenvironments.

Focus Area 2

Characterization of microorganisms with novel metabolic pathways for sustainable food production.

Isolation is one of the main challenges in developing a new bioprocess for bioremediation of water, soil, and air. I developed high-throughput methods that allow for the cultivation of novel microbes using minimal media with selective carbon sources. Accessing microorganisms lays the foundation for in-depth studies in biology, biotechnology, and environmental technology. Currently, I develop model-driven strategies to make progress toward the cultivation of so far uncultured human and plant pathogenic microorganisms. Model-driven strategies result in rational experimental design.

“To date, my techniques and methods are still being used for isolation and characterization”

Focus Area 3

Systems biology and development of computational methods for the reconstruction of metabolic models of prokaryotic and eukaryotic organisms.

Innovative genome-scale computational tools are necessary to effectively predict and control phenotypes. I have been at the forefront of developing and deploying Next Generation computational models for bacteria and eukaryotic microorganisms. Metabolic models of eukaryotic microorganisms account for a large fraction of organelle-specific annotated genes, significantly broadening the scope and predictability of microbial systems biology.

“My team is currently applying computational methods developed for microalgae to improve the organelle-specific annotation of other eukaryotic microorganisms for improved net-zero bioproduction.”