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



Phosphate-Arsenic Interactions in Halophilic Microorganisms of the Microbial Mat from Laguna Tebenquiche: from the Microenvironment to the GenomesL.A. Saona, M. Soria, V. Durán-Toro, J. Wörmer, L., Milucka, E. Castro-Nallar, C . Meneses, M. Contreras, M.E. FaríasMicrobial Ecology. 2021.
Radiation-induced toxicity in rectal epithelial stem cell contributes to acute radiation injury in rectumFelipe Rodriguez Tirado, Payel Bhanja, Eduardo Castro-Nallar , Ximena Diaz Olea, Catalina Salamanca & Subhrajit SahaStem Cell Research & Therapy. 2021.
COVID-19 drug practices risk antimicrobial resistance evolutionEbrahim Afshinnekoo, Chandrima Bhattacharya, Ana Burguete-García, Eduardo Castro-Nallar , et al. The Lancet Microbe. 2021.
Composition and structure of the skin microbiota of rorquals off the Eastern South PacificFrederick Toro, Jaime Alarcón, Sebastián Márquez, Juan Capella, Paulina Bahamonde, Fernando Esperón, Andrea Moreno-Switt, Eduardo Castro-NallarFEMS Microbiology Ecology. 2021.
Patterns in the Juan Fernandez fur seal faecal microbiomeConstanza Toro Valdivieso, Frederick Toro, Samuel Stubbs, Eduardo Castro-Nallar , Barbara BlacklawsAuthorea. 2021. DOI:10.22541/au.162030626.67490531/v1
Living to the high extreme: unraveling the composition, structure, and functional insights of bacterial communities thriving in the arsenic-rich Salar de Huasco – Altiplanic ecosystemJ Castro-Severyn, C Pardo-Esté, KN Mendez, J Fortt, S Marquez, F Molina, E Castro-Nallar , F Remonsellez, CP SaavedrabioRxiv. 2021.doi:
Rhodococcus comparative genomics reveals a phylogenomic-dependent non-ribosomal peptide synthetase distribution: insights into biosynthetic gene cluster connection to an orphan metaboliteAgustina Undabarrena, Ricardo Valencia, Andrés Cumsille, Leonardo Zamora-Leiva​, Eduardo Castro-Nallar , Francisco Barona-Gomez, Beatriz CámaraMicrobial Genomics. 2021. DOI10.1099/mgen.0.000621


Biotransformation of 2,4,6-Trinitrotoluene by Pseudomonas sp. TNT3 isolated from Deception Island, Antarctica Ma. Ángeles Cabrera, Sebastián L. Márquez, Carolina P. Quezada, Manuel I. Osorio, Eduardo Castro-Nallar, Fernando D. González-Nilo, José M. Pérez-Donoso Environmental Pollution. 2020.
In infants with severe bronchiolitis: dual-transcriptomic profiling of nasopharyngeal microbiome and host responseMichimasa Fujiogi, Carlos A. Camargo Jr., James P. Bernot, Robert J. Freishtat, Brennan Harmon, Jonathan M. Mansbach, Eduardo Castro-Nallar , Marcos Perez-Losada & Kohei Hasegawa Pediatric Research, 2020.
Copper-induced concomitant increases in photosynthesis, respiration, and C, N and S assimilation revealed by transcriptomic analyses in Ulva compressa (Chlorophyta)Daniel Laporte , Felipe Rodríguez , Alberto González , Antonio Zúñiga, Eduardo Castro-Nallar , Claudio A. Sáez and Alejandra Moenne.BMC Plant Biology. 2020.
Sequences of Endophytic Fungal and Bacterial Communities from Araucaria araucana [(Molina) K. Koch, 1869] in the Coastal and Andes Mountain Ranges, ChileJaime Alarcón, Sebastián Márquez, Guus Teunisse,a Carlos Mendoza,b Claudio Meneses, Aida Baldini, Patricio Parra,Pablo Zamora, Freddy Boehmwald, Eduardo Castro-NallaraMicrobioly Resource Announcements, 2020. 10.1128/MRA.00544-20.
Genomic Variation and Arsenic Tolerance Emerged as Niche Specific Adaptations by Different Exiguobacterium Strains Isolated From the Extreme Salar de Huasco Environment in Chilean – AltiplanoJuan Castro-Severyn, Coral Pardo-Esté, Katterinne N. Mendez, Naiyulin Morales, Sebastián L. Marquez, Franck Molina, Francisco Remonsellez, Eduardo Castro-Nallar and Claudia P. Saavedra.Frontier in Microbioly, 2020. doi: 10.3389/fmicb.2020.01632
Monitoring the occurrence of microplastic ingestion in Otariids along the Peruvian and Chilean coastsDiego J.Perez-Venegas, ConstanzaToro-Valdivieso, Félix Ayala, Beatriz Brito, Eduardo Castro-Nallar , et al.Marine Pollution Bulletin, 2020.
Origin, genomic diversity and microevolution of the Clostridium difficile B1/NAP1/RT027/ST01 strain in Costa Rica, Chile, Honduras and Mexico Enzo Guerrero-Araya, Claudio Meneses, Eduardo Castro-Nallar , et al., MICROBIAL GENOMICS, 2020.
Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environmentEduardo Castro-Nallar, et al.Nature. 2020.
Evaluation of computational methods for human microbiome analysis using simulated dataMatthieu J. Miossec , Sandro L. Valenzuela, Marcos Pérez-Losada, W. Evan Johnson, Keith A. Crandall, Eduardo Castro-Nallar.PeerJ, 2020. DOI.:10.7717/peerj.9688
Radiation induced toxicity in rectal epithelial stem cell contributes to acute radiation injury in rectumFelipe Rodriguez Tirado, Payel Bhanja, Eduardo Castro-Nallar, Ximena Diaz Olea, Catalina Salamanca, Subhrajit Sah.bioRxiv. 2020. doi:


In-Depth Genomic and Phenotypic Characterization of the Antarctic Psychrotolerant Strain Pseudomonas sp. MPC6 Reveals Unique Metabolic Features, Plasticity, and Biotechnological PotentialMatias Orellana-Saez, Nicolas Pacheco, José I. Costa, Katterinne N. Mendez, Matthieu J. Miossec , Claudio Meneses, Eduardo Castro-Nallar , Andrés E. Marcoleta, Ignacio Poblete-Castro.Frontier in Micronbiology. 2019.
Genomic and Physiological Traits of the Marine Bacterium Alcaligenes aquatilis QD168 Isolated From Quintero Bay, Central Chile, Reveal a Robust Adaptive Response to Environmental StressorsRoberto E. Durán, Valentina Méndez, Laura Rodríguez-Castro, Bárbara Barra-Sanhueza, Francisco Salvà-Serra, Edward R. B. Moore, Eduardo Castro-Nallar and Michael Seeger.Frontier in Micronbiology. 2019.
Variability in Genomic and Virulent Properties of Porphyromonas gingivalis Strains Isolated From Healthy and Severe Chronic Periodontitis IndividualsKatterinne N. Mendez, Anilei Hoare, Cristopher Soto, Isaac Bugueño, Marcela Olivera, Claudio Meneses, Jose Manuel Pérez-Donoso, Eduardo Castro-Nallar and Denisse Bravo.Fontier in Cellular and Infection Microbiology. 2019.
Arsenic response of three altiplanic Exiguobacterium strains with different tolerance levels against the metalloid species: a proteomics studyJuan Castro-Severy, Coral Pardo-Esté, Yoelvis N. Sulbaran Bracho, Carolina E. Cabezas, Valentina Gariazzo, Alan C. Briones, Naiyulin Morales, Mathilde Decourcelle, Martial Séveno, Nicolas Salvetat, FRANCISCO REMONSELLEZ, Eduardo Castro-Nallar, Franck Molina, Laurence Molina and Claudia P. Saavedra.Frontier in Microbiology. 2019. doi: 10.3389/fmicb.2019.02161
Altered middle ear microbiome in children with chronic otitis media with effusion and respiratory illnessesAllison R. Kolbe, Eduardo Castro-Nallar, Diego Preciado and Marcos Perez-Losada.Frontiers in Cellular and Infection Microbiology. 2019. doi: 10.3389/fcimb.2019.00339
A first insight into the structure and function of rhizosphere microbiota in Antarctic plants using shotgun metagenomicMarco A. Molina-Montenegro, Gabriel I. Ballesteros, Eduardo Castro-Nallar, Claudio Meneses, Jorge Gallardo-Cerda, Cristian Torres-Díaz.Polar Biology. 2019.
Global Genetic Cartography of Urban Metagenomes and Anti-Microbial ResistanceDavid C. Danko, Daniela Bezdan, Ebrahim Afshinnekoo, Sofia Ahsanuddin, Josue Alicea, Chandrima Bhattacharya, Malay Bhattacharyya, Ran Blekhman, Daniel J Butler, Eduardo Castro-Nallar, Ana M Cañas, Aspassia D Chatziefthimiou, Kern Rei Chng, David A Coil, Denise Syndercombe Court,...BioRxiv the preprint server for biology. 2019.


114Cyclic 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.
118Metagenomic 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
119The 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
120Complete 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
121Comparative 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.
122Genome 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.
133Genomic Analysis of 48 Paenibacillus larvaeBacteriophagesCasey Stamereilers, Christopher P. Fajardo, Jamison K. Walker, Katterinne N. Mendez, Eduardo Castro-Nallar, Julianne H. Grose, Sandra Hope and Philippos K. Tsourkas.Viruses. 2018. DOI:10.3390/v10070377
139Copper-induced increased expression of genes involved in photosynthesis, carotenoid synthesis and C assimilation in the marine alga Ulva compressaFelipe E. Rodríguez, Daniel LaporteEmail author, Alberto González, Katterinne N. Mendez, Eduardo Castro-Nallar, Claudio Meneses, Juan Pablo Huidobro-Toro and Alejandra MoenneBMC Genomics. 2018.
140The transcription factor SlyA from Salmonella Typhimurium regulates genes in response to hydrogen peroxide and sodium hypochloriteCarolina E.Cabezasa Alan C.Brionesa Camila Aguirre Coral Pardo-Esté Juan Castro-Severyna César R.Salinasa María S.Baquedano Alejandro A.Hidalgo Juan A.Fuentes Eduardo H.Morales Claudio A.Meneses EduardoCastro-Nallar Claudia Paz Saavedra.Research in Microbiology. 2018.


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.