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Reduced microbial diversity of the nasopharyngeal microbiome in household contacts with latent tuberculosis infection
2023
Ruiz-Tagle, C., Ugalde, J.A., Naves, R., Araos, R., Garcia, P., Balcells, M.E.
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Spatial co-occurrence patterns of benthic microbial assemblage in response to trace metals in the Atacama Desert Coastline
2023
Zarate, A., Molina, V., Valdés, J., Icaza, G., Vega, E.S., Castillo, A., Ugalde, J.A,. Dorador, C.
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Role of the multi-drug efflux systems on the baseline susceptibility to ceftazidime/avibactam and ceftolozane/tazobactam in clinical isolates of noncarbapenemase-producing carbapenem-resistant Pseudomonas aeruginosa
Contreras, M.J., Martinez, J.R., Rivas, L., Riquelme-Neira, R., Ugalde, J.A, Wozniak, A., Garcia, P., Munita, J.M., Olivares Pacheco, J.A., Alcalde-Rico, M.
2022
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Genetic characterization of clinically relevant class 1 integrons carried by multi-drug resistant bacteria (MDRB) isolated from the gut microbiota of highly antibiotic treated Salmo salar
Vasquez-Ponce, F., Higuera-Llanten, S., Paras-Silva, J., Gamboa-Acuña, N., Cortes, J., Opazo-Capurro, A., Ugalde, J.A, Alcalde-Rico, M., Olivares-Pacheco, J.
2022
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Digital Therapeutics Care Utilizing Genetic and Gut Microbiome Signals for the Management of Functional Gastrointestinal Disorders : Results from a Preliminary Retrospective Study
2022
Kumbhare, S.V., Lyon-Francis, P.A., Kachru, D., Uday, T., Irudayanathan, C., Muthukumar, K.M., Ricchetti R.R., Singh-Rambiritch, S., Ugalde, J., Dulai, P.S., Almonacid, D.E., Sinha, R.
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Annotating unknown species of urban microorganisms on a global scale unveils novel functional diversity and local environment association
2022
Wu, J., Danko, D., Afshinnekoo, E., Bezdan, D., Bhattacharya, M., Castro-Nallar, E., Chmielarczyk, A., Hazrin-Chong, N.H., Demg, Y., Dias-Neto, E., Frolova, A., Mason-Buck, G., Iraola, G., Jang, S., Łabaj, P., Lee, P.K.H., Nieto-Caballero, M., Osuolale, O., Ouzounis, C., Perlin, M.H., Prithiviraj, B., Rascovan, N., Rozanska, A., Schriml, L.M., Semmler, T., Suzuki, H., Ugalde, J.A., Young, B., Werner, J., Zambrano, M.M., Zhao, Y., Mason, C., Shi, T.
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Antimicrobial Resistance Dynamics in Chilean Shigella sonnei Strains Within Two Decades : Role of Shigella Resistance Locus Pathogenicity Island and Class 1 and Class 2 Integrons
2022
Toro, C.S., Salazar, J.C., Montero, D.A., Ugalde, J.A., Diaz, J., Cadiz, L.A., Henriquez, T., Garcia, C., Diaz, P., Camponovo R., Hermosilla, G., Ulloa, M.T.
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COVID-19 y ciudad : hacia un modelo integrado de vivienda, microbiología, ambiente y urbanismo Item
2021
Encinas, F., Soto-Liebe, K., Aguirre-Ñuñez, C.A., Gonzalez, B., Bustamente, W., Schueftan, A., Ugalde, J., Blondel, C., Trufello, R, Araya, P., Freed, C.
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Validation of the COVID-19 Indoor Test by Phylagen for Detection of SARS-CoV-2 Virus on Stainless Steel Surfaces AOAC Performance Tested Method 122004
2021
Fantin, N., Taft, B., Ugalde, J., Spring, K., Lam, H., Tran, A., Green, J.
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Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance
2021
Danko, D., Bezdan, D., Afshinnekoo, E., Ahsanuddin, S., Bhattacharya, C., Butler, D., Chng, K., Donnellan, D., Hecht, J., Jackson, K., Kuchin, K., Karasikov, M., Lyons, A., Mak, L., Meleshko, D., Mustafa, H., Mutai, B., Neches, R., Ng, A., Nikolayeva, O., Nikolayeva, T., Png, E., Ryon, K., Sanchez, J., Shaaban, H., Sierra, M., Thomas, D., Young, B., Abudayyeh, O., Alicea, J., Bhattacharyya, M., Blekhman, R., Castro-Nallar, E., Cañas, A., Chatziefthimiou, A., Crawford, R., De Filippis, F., Deng, Y., Desnues, C., Dias-Neto, E., Dybwad, M., Elhaik, E., Ercolini, D., Frolova, A., Gankin, D., Gootenberg, J., Graf, A., Green, D., Hajirasouliha, I., Hernandez, M., Iraola, G., Jang, S., Kahles, A., Kelly, F., Knights, K., Kyrpides, N., Labaj, P., Lee, P., Leung, M., Ljungdahl, P., Mason-Buck, G., McGrath, K., Meydan, C., Mongodin, E., Moraes, M., Nagarajan, N., Nieto-Caballero, M., Noushmehr, H., Oliveira, M., Ossowski, S., Osuolale, O., Özcan, O., Paez-Espino, D., Rascovan, N., Richard, H., Rätsch, G., Schriml, L., Semmler, T., Sezerman, O., Shi, L., Shi, T., Song, L., Suzuki, H., Court, D., Tighe, S., Tong, X., Udekwu, K., Ugalde, J.A, Valentine, B., Vassilev, D., Vayndorf, E., Velavan, T., Wu, J., Zambrano, M., Zhu, J., Zhu, S., Mason, C.
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An Integrative Bioinformatic Analysis for Keratinase Detection in Marine-Derived Streptomyces
2021
Valencia, R., Gonzalez, V., Undabarrena, A., Zamora-Leiva, L., Ugalde, J.A., Camara B.
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Bacteria isolated from the Antarctic sponge Iophon sp. reveals mechanisms of symbiosis in Sporosarcina, Cellulophaga, and Nesterenkonia
2021
Moreno-Pino, M., Ugalde, J.A., Vales, J.H., Rodriguez-Marconi, S., Parada-Pozo, G., Trefault, N.
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Distinctive Gene and Protein Characteristics of Extremely Piezophilic Colwellia
2020
Peoples, L.M., Kyaw, T., Ugalde, J.A., Mullane, K., Chastain, R., Yayanos, A., Kusube, M., Methe, B., Bartlett, D.H
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Bacterially produced metabolites protect C. elegans neurons from degeneration
2020
Urrutia, A., Garcia-Angulo, V.A., Fuentes, A., Caneo, M., Legue, M., Urquiza, S., Delgado, S.E., Ugalde J.A., Burdisso, P., Calixto, A.
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Draft Genome Sequence of Blautia luti DSM 14534T, Isolated from Human Stool
2020
Ortiz, R.L., Melis-Arcos, F., Covarrubias, P.C., Ugalde J.A, Apte, Z.S., Perez-Donoso, J., Cardenas, J.P., Almonacid, D.E.
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Evidence of a large and unique reservoir of antimicrobial resistance genes in the intestinal bacterial resistome of long-term care facility residents
2019
Araos, R., Battaglia, T., Ugalde, J.A., Blaser, M.J., D’Agata, E.M.C.
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A novel sequencing-based vaginal health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis
2019
Bik, E.M., Bird, S.W., Bustamante, J.P., Leon, L.E. Nieto, P.A., Addae, K., Alegria-Mera, V., Bravo, C., Bravo, D., Cardenas, J.P., Caughey, A., Covarrubias, P.C., Perez-Donoso, J., Gass, G., Gupta, S.L., Harman, K., Hongo, D.M.B., Jimenez, J.C., Kraal, L., Melis-Arcos, F., Morales, E.H., Morton, A., Navas, C.F., Nunez, H., Olivarez, E., Ordenes-Aenishanslins, N., Ossandon, F.J., Phan, R., Pino, R., Soto-Liebe, K., Varas, I., Walton, N.A., Vera-Wolf, P., Almonacid, D.E., Goddard, A.D., Ugalde, J.A., Richman, J., Apte, Z.S.
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Microbial biotransformations in the human distal gut
2018
Bik, E.M., Ugalde, J.A., Cousins, J., Goddard, A.D., Richman, J., Apte, Z.S.
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Distinctive archaeal composition of an artisanal crystallizer pond and functional insights into salt-saturated hypersaline environment adaptation
2018
Plominsky, A.M., Henriquez, C.A., Delherbe, N., Podell, S., Ramirez, S., Ugalde, J.A., Santibañez, J.F., Van Den Engh, G., Hanselmann, K., Ulloa, O., De La Iglesia, R., Allen, E.E., Trefault, N.
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Complete genome sequence of the marine Rhodococcus sp. H-CAF8f isolated from the Comau fjord in Northern Patagonia, Chile
2018
Undabarrena, A., Salva Serra, F., Jaen-Luchoro, D., Castro-Nallar, E., Mendez, K.N., Valencia, R., Ugalde, J.A., Moore, E., Seeger, M., Camara, B.
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The fecal microbiome among nursing home residents with advanced dementia and Clostridium difficile
2018
Araos, R., Andreatos, N., Ugalde, J.A., Mitchel, S., Mylonakis, E., D’Agata, E.M.C.
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Microbial disruption indices to detect colonization with multidrug-resistant organisms
2017
Araos, R., Montgomery, V., Ugalde, J.A., Snyder, G., D’Agata, E.M.C.
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The gut microbiota of healthy chilean subjects reveals a high abundance of the phylum Verrucomicrobia
2017
Fujio-Vejar, S., Vasquez, Y., Morales, P., Magne, F., Vera-Wolf, P., Ugalde, J.A., Navarrete, P., Gotteland, M.
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Phylogenomics insight into Salinispora (Bacteria, Actinobacteria) Species Designations
2017
Millán-Aguiñaga, Chavarria, K.L., Ugalde, J.A., Letzel, C.A., Rouse, G.W., Jensen, P.R
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Genomic data mining of the marine actinobacteria Streptomyces sp. H-KF8 unveils insights into multi-stress related genes and metabolic pathways involved in antimicrobial synthesis
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Genome sequence of Streptomyces sp. strain H-KF8, a marine actinomycete isolated from a northern Chilean Patagonian fjord
2017
Undabarrena, A., Ugalde, J.A., Castro-Nallar, E., Seeger, M., Cámara, B.
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A novel gene cluster allows preferntial utilization of fucosylated milk oligosaccharides in Bifidobactierium longum subsp. longum SC596
2016
Garrido, D., Ruiz-Moyano, S., Kirmiz, N., Davis, J.C., Totten, S.M., Lemay, D.G., Ugalde, J.A.., German, J.B., Lebrilla, C.B., Mills, D.A.
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Comparative transcriptome assembly and genome-guided profiling for Brettanomyces bruxellensis LAMAP2480 during p-coumaric acid stress.
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Genome Sequencing and Analysis of the First Complete Genome of Lactobacillus kunkeei strain MP2, an Apis mellifera gut isolate
2016
Asenjo, F., Olmos, A., Henriquez-Piskulich, P., Polanco, V., Aldea, P., Ugalde, J.A., Trombert, A.N
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Impact of Dietary Lipids on Colonic Function and Microbiota : An Experimental Approach Involving Orlistat-Induced Fat Malabsoprtion in Human Volunteers
2016
Morales, P., Fujio, S., Ugalde, J.A., Magne, F., Carrasco-Pozo, C., Tralma, K., Quezada, M.P., Hurtado, C., Covarrubias, N., Brignaerdello, J., Henriquez, D., Gotteland, M.
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Identification of Thiotetronic Acid Antibiotic Biosynthetic Pathways by Target-directed Genome Mining
2015
Tang, X., Li, J., Millán-Aguiñaga, N., Zhang, J.J., O’Neill, E., Ugalde, J.A., Jensen, P., Mantovani, S., Bradley, M.
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Evolution in the Indoor Biome
2015
Martin, L.J., Adams, R., Bateman, A., Bik, H.M., Haws, J., Hird, S.M., Hughes, D., Kembel, S.W., Kinney, K., Kolokotronis, S., Levy, G., McClain, C., Meadow, J.F., Medina, R.F., Mhuireach, G., Moreau, C.S., Munshi-South, J., Nichols, L., Palmer, C., Popova, L., Schal, C., Taeubel, M., Trautwein, M., Ugalde, J.A., Dunn, R.R.
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Genome sequence of Vibrio VPAP30, isolated from an episode of massive mortality of reared larvae of the scallop Argopecten purpuratus
2015
Rojas, M., Miranda, C.D., Romer, J., Asenjo, F., Valderrama, K., Segovia, C., Ugalde, J.A., Santander, J.
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Metagenome Sequencing of the Microbial Community of a Solar Saltern Crystallizer Pond
2014
Plominsky, A.M., Delherbe, N., Ugalde, J.A., Allen, E.E., Blanchet, M., Ikeda, P., Santibañez, Hanselmann, K., Ulloa, O., De La Iglesia, R., von Dassow, P., Astorga, M., Gálvez, M.J., González., M.L., Henríquez-Castillo, C., Vaulot, D., Lopes do Santos, A., van den Engh, G., Gimpel, C., Bertoglio, F., Delgado, Y., Docman, F., Elizondo-Patrone, C., Narváez, S., Sorroche, F., Rojas-Herrera, M., Trefault, N.
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Draft genome sequence of Salmonella enterica serovar Typhi strain STH2370
2014
Valenzuela, C., Ugalde, J.A., Mora, G.C., Alvarez, S., Contreras, I., Santiviago, C.A.
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Microbial mechanisms coupling carbon and phosphorous cycles in phosphorous-limited northern Adriatic Sea, and response to phosphorous enrichment
2014
Malfatti, F., Turk, V., Tinta, T., Mozetič, P., Manganelli, M., Samo, T., Ugalde J.A., Kovač, N., Stefanelli, M., Antonioli, M., Fonda-Umani, S., Del Negro, P., Cataletto, B., Hozić, A., Ivošević Denardi, N., Žutić, V., Svetličić, V., Mišić Radić,T., Radić, T., Fuchs D., Azam, F.
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Seasonal Fluctuations in Ionic Concentrations Drive Microbial Succession in a Hypersaline Lake Community
2014
Podell, S., Emerson, J., Jones, C.M., Ugalde, J.A., Welch, S., Heidelberg, K.B., Banfield, J.F., Allen, E.E.
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Draft Genome Sequence of “Candidatus Halobonum tyrrellensis” Strain G22, Isolated from the Hypersaline Waters of Lake Tyrrell, Australia
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Diversity of composite bacterial hopanoids and their microbial producers across oxygen gradients in the water column of the California Current
2013
Kharbush, J., Ugalde J.A., Hogle, S., Allen, E.E., Aluwihare, L.
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Microbial Life in a Fjord : Metagenomic Analysis of a Microbial Mat in Chilean Patagonia
2013
Ugalde, J.A., Gallardo, M.J, Belmar, C., Muñoz, P., Ruiz-Tagle, N., Ferrada-Fuentes, S., Espinoza, C., Allen, E.E., Gallardo, V.A.
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Assembly-Driven Community Genomics of a Hypersaline Microbial Ecosystem
2013
Podell, S., Ugalde, J.A., Narasingarao, P., Banfield, J.F., Heidelberg, K.B., Allen, E.E.
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De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities
2012
Narasingarao, P., Podell, S., Ugalde, J.A., Brochier-Armanet, C., Emerson, J.B., Brocks, J.J., Heidelberg, K.B., Banfield, J.F., Allen, E.E.
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Xenorhodopsins, an enigmatic new class of microbial rhodopsins horizontally transferred between archaea and bacteria
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Comparative genomic analysis of carbon and nitrogen assimilation mechanisms in three indigenous bioleaching bacteria : predictions and validations
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Applications of ancestral protein reconstruction in understanding protein function : GFP-like proteins
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GFP-like proteins as ubiquitous Metazoan superfamily : evolution of functional features and structural complexity
2004
Shagin, D.A., Barsova, E.V., Yanushevich, Y.G., Fradkov, A.F., Lukyanov, K.A., Labas, Y.A., Semenova, T.N., Ugalde, J.A., Meyer, A., Nunes, J.M., Widder, E.A., Lukyanov, S.A., Matz, M.V.
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Evolution of coral colors recreated