November 16, 2015

Microbial Genomics Lab

Eduardo Castro-Nallar

Research Professor
+56-2-2770 3520

Microorganisms are the most abundant life form in and on the planet. They are able to colonize and thrive in most environments ranging from the human body to under water thermal vents. In the Castro Lab, we are interested in understanding the causes and consequences of microbial genetic diversity, and how we can apply this knowledge to gain insights into pathogen diagnostics and discovery, microbial distribution and epidemiology, and novel adaptations. For this, we use molecular and computational biology tools such as high-throughput sequencing, recombinant DNA technology, Bayesian statistics and phylogenetics, transcriptomics and metagenomics.

In the Castro Lab, we study patterns of genetic diversity in space and time in an evolutionary context. Specifically, we are interested in understanding how microorganisms spread (phylogeography; molecular clocks; population dynamics), what makes some microorganisms pathogenic (gene function; molecular adaptations; comparative genomics), and what role they play in microbial ecosystems (metagenomics; metatranscriptomics), relative to the environment and to host-microbe interactions. The lab particularly focuses on understanding the structure and function of the microbiome, specifically that of the human oral and gut microbiome. We have worked on asthma, COPD, and respiratory diseases, as well as microbiota shifts associated with inflammatory diseases of the intestines. We are now expanding the biological systems where we study the microbiome to include endangered animals such as mane wolves and black rhinos.

The lab also focuses on molecular epidemiology of bacteria and viruses using population dynamics and genome-scale phylogenetic tools. Specifically, we use computational and statistical methods to sequence data to gain insights into viral dynamics, and geographic circulation of bacteria and viruses. Lastly, we combine all of the above into an integrated  approach to contribute to the understanding of microbial genetic diversity, which is applicable to infectious disease surveillance, pathogen discovery and diagnostics, and host-microbe interactions. Our research is supported by collaborations worldwide in order  to complement our expertise with others. We have collaborated with researchers on disparate issues such as finding determinants of pathogenicity in RNA viruses, estimating  HIV past population dynamics, and studying the microbiota of schizophrenia subjects. Collaborative research is part of the lab, as modern science problems require multidisciplinary approaches to obtain novel and meaningful solutions. Find more at