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



3Cyclic AMP Regulates Bacterial Persistence through Repression of the Oxidative Stress Response and SOS-Dependent DNA Repair in Uropathogenic Escherichia coliRoberto C. Molina-Quiroz, Cecilia Silva-Valenzuela,a Jennifer Brewster, Eduardo Castro-Nallar , Stuart B. Levy, Andrew Camillia.Mbio. 2018. DOI: 10.1128/mBio.02144-17.
7Metagenomic exploration of soils microbial communities associated to Antarctic vascular plantsMarco A. Molina-Montenegro​, Gabriel I. Ballesteros,  Eduardo Castro-Nallar , Claudio Meneses, Cristian Torres-Díaz, Jorge Gallardo-Cerda.PeerJ. 2018. DOI 10.7287/peerj.preprints.26508v1
8The Tracheal Microbiota in Patients with a Tracheostomy Before, During, and After an Acute Respiratory Infection.Pérez-Losada M, Graham RJ, Coquillette M, Jafarey A,  Castro-Nallar E , Aira M, Hoptay C, Freishtat RJ, Mansbach JM.The Pediatric Infectious Disease Journal. 2018. doi: 10.1097/INF.0000000000001952
9Complete genome sequence of the marine Rhodococcus sp. H-CA8f isolated from Comau fjord in Northern Patagonia, ChileUndabarrena A., Salvà-Serra F., Jaén-Luchoro D., Castro-Nallar E ., Mendez K.N., Valencia R., Ugalde J.A., Moore E.R.B. , Seeger M. , Cámara B.Marine Genomics. 2018. DOI: 10.1016/j.margen.2018.01.004
10Comparative genomic analysis of a new tellurite-resistant Psychrobacter strain isolated from the Antarctic Peninsula.Muñoz-Villagrán CM, Mendez KN, Cornejo F, Figueroa M, Undabarrena A, Morales EH, Arenas-Salinas M, Arenas FA,  Castro-Nallar E , Vásquez CC.PeerJ. 2018. DOI: 10.7717/peerj.4402.
12Genome sequence of two members of the chloroaromatic-degrading MT community: Pseudomonas reinekei MT1 and Achromobacter xylosoxidans MT3.Gutierrez-Urrutia I,  Miossec MJ , Valenzuela SL, Meneses C, Dos Santos VAPM,  Castro-Nallar E, Poblete-Castro I.Journal of Biotechnology. 2018. DOI: 10.1016/j.jbiotec.2018.03.019.


111Computational Methods for Human Microbiome AnalysisMiossec MJ, Valenzuela SL, Mendez KN,  Castro-Nallar E.Current Protocol in Microbiology. 2017. DOI: 10.1002/cpmc.41
102Genome Sequence of Streptomyces sp. H-KF8, a Marine Actinobacterium Isolated from a Northern Chilean Patagonian FjordUndabarrena A, Ugalde JA,  Castro-Nallar E , Seeger M, Cámara B.GENOME ANNOUNCEMENTS. 2017. DOI: 10.1128/genomeA.01645-16.
100Mutation and recombination in pathogen evolution: Relevance, methods and controversiesMiguel Arenas, Natalia M.Araujo, Catarina Branco, Nadine Castelhano, Eduardo Castro-Nallar , MarcosPérez-Losada.Infection, Genetics and Evolution. 2017. DOI: 10.1016/j.meegid.2017.09.029
99Microbial sequence typing in the genomic era.Pérez-Losada Marco, Arenas Miguel,  Castro-Nallar Eduardo.Infection, Genetics and Evolution. 2017. DOI: 10.1016/j.meegid.2017.09.022
91The temporal dynamics of the tracheal microbiome in tracheostomised patients with and without lower respiratory infectionsPérez-Losada M, Graham RJ, Coquillette M, Jafarey A,  Castro-Nallar E , Aira M, Freishtat RJ, Mansbach JM.Plos One. 2017. DOI: 10.1371/journal.pone.0182520. eCollection 2017.
90Draft Genome Sequences of Five Enterococcus Species Isolated from the Gut of Patients with Suspected Clostridium difficile InfectionEduardo Castro-Nallar , Sandro L. Valenzuela, Sebastián Baquedano, Carolina Sánchez, Fabiola Fernández, and Annette N. TromberGenome Announcements. 2017. 10.1128/genomeA.00379-17.
77DNA Barcoding analysis of seafood accuracy in Washington, DC restaurants.Stern, D. B., Castro-Nallar, E ., Rathod, J., & Crandall, K. A. Peer J, 2017. DOI: 10.7717/peerj.3234
76Comparative genomics analysis of a new Exiguobacterium strain from Salar de Huasco reveals a repertoire of stress-related genes and arsenic resistance.Juan Castro-Severyn,  Francisco Remonsellez,  Sandro Luis Valenzuela,  Jonathan Fortt,  Pablo Aguilar, Coral Pardo-Esté,  Cristina Dorador,  Raquel Quatrini,  Franck Molina,  Eduardo Castro-Nallar , Claudia P Saavedra.Frontiers in Microbiology. 2017. DOI: 10.3389/fmicb.2017.00456
75Multilocus Sequence Typing of Pathogens.Pérez-Losada M., Arenas, M., and Castro-Nallar, E . Genetics and Evolution of Infectious Diseases. 2017. DOI: 10.1016/B978-0-12-799942-5.00016-0


67Draft Genome Sequence of a Multi-Metal Resistant Bacterium Pseudomonas putida ATH-43 Isolated from Greenwich Island, Antarctica.
Rodríguez-Rojas F., Tapia P., Castro-Nallar E., Undabarrena A., Muñoz-Díaz P., Arenas-Salinas M., Díaz-Vásquez W., Valdés J., Vásquez C.Frontier in Microbiology. 2016. DOI: 10.3389/fmicb.2016.01777.
66Metataxonomic and Metagenomic Approaches vs. Culture-Based Techniques for Clinical PathologySarah K. Hilton, Eduardo Castro-Nallar, Marcos Pérez-Losada, Ian Toma, Timothy A. McCaffrey, Eric P. Hoffman, Marc O. Siegel, Gary L. Simon, W. Evan Johnson and Keith A. Crandall.Frontier in Microbiology. 2016. DOI: 10.3389/fmicb.2016.00484
48Genome Sequence of Clostridium paraputrificum 373-A1 Isolated in Chile from a Patient Infected with Clostridium difficileGuerrero-Araya E., Plaza-Garrido, Díaz-Yañez, Pizaro-Guajardo M., Valenzuela SL, Meneses C, Gil, Castro-Nallar E5, Paredes-Sabja D.Genome Announcement. 2016. DOI: 10.1128/genomeA.01178-16.
42Redefining Healthy Urine: A Cross-Sectional Exploratory Metagenomic Study of People With and Without Bladder DysfunctionGroah, SL; Perez-Losada, M.; Caldovic, L.; Ljungberg, IH.; Sprague, BM.; Castro-Nallar, E.; Chandel, Neel J.; Hsieh, Michael H.; Pohl, Hans G.Journal of Urology. 2016. DOI: 10.1016/j.juro.2016.01.088.


23Dual Transcriptomic Profiling of Host and Microbiota during Health and Disease in Pediatric Asthma.Pérez-Losada M, Castro-Nallar E, Bendall ML, Freishtat RJ, Crandall KA.Plos One. 2015. DOI: 10.1371/journal.pone.0131819
19Integrating microbial and host transcriptomics to characterize asthma-associated microbial communities.Castro-Nallar E, Shen Y, Freishtat RJ, Pérez-Losada M, Manimaran S, Liu G, Johnson WE, Crandall KA.BMC Medical Genomics. 2015. DOI: 10.1186/s12920-015-0121-1.
14Composition, taxonomy and functional diversity of the oropharynx microbiome in individuals with schizophrenia and controls Eduardo Castro-Nallar, Matthew L. Bendall, Marcos Pérez-Losada, Sarven Sabuncyan, Emily G. Severance, Faith B. Dickerson, Jennifer R. Schroeder, Robert H. Yolken and Keith A. CrandallPeerJ. 2015. DOI: 10.7717/peerj.1140.