Bioinformatics and Genome Biology

Neira G, Vergara E, Cortez D, Holmes DS. A Large-Scale Multiple Genome Comparison of Acidophilic Archaea (pH≤ 5.0) Extends Our Understanding of Oxidative Stress Responses in Polyextreme Environments. Antioxidants. 2022 Jan;11(1):59. Doi: 10.3390/antiox11010059.

Cortez D, Neira G, González C, Vergara E, Holmes DS. A large-scale genome-based survey of acidophilic Bacteria suggests that genome streamlining is an adaption for life at low pH. Frontiers in Microbiology 13:803241. (March 2022). Doi: 10.3389/fmicb.2022.803241

González-Rosales CM, Vergara E, Dopson M, Valdés JH, Holmes DS. Integrative Genomics Sheds Light on Evolutionary Forces Shaping the Acidithiobacillia Class Acidophilic Lifestyle. Frontiers in Microbiology: 12:822229. (Feb. 2022) Doi: 10.3389/fmicb.2021.822229

Boase, K., González,C., Vergara, E., Neira, G., Holmes DS and Watkin E. Prediction and Inferred Evolution of Acid Tolerance Genes in the Biotechnologically Important Acidihalobacter Genus. Frontiers in Microbiology, 13:848410 (March 2022). Doi: 10.3389/fmicb.2022.848410

Bitencourt J, Scholte L, Oliveira R, Morais D, Nunes G, Nancucheo I, Valadares R, Holmes DS, Johnson DB, Alves R, Oliveira, G. (2022). Draft genome sequence of a novel moderately thermophilic, iron- and sulfur-oxidizing Firmicute strain Y002, isolated from an extremely acidic geothermal environment. Microbiol Resour Announc (May 2022). Doi: 10.1128/mra.00149-22

Vergara, E., Pakostova, E., Johnson DB., and Holmes, DS. Draft Genome Sequence of Firmicute Strain S 0 AB, a Heterotrophic Iron/Sulfur-Oxidizing Extreme Acidophile. Microbiology Resource Announcements e00271-22. (July 2022) Doi:10.1128/mra.00271

Carolina Gonzalez, María Yanquepe, Juan Pablo Cardenas, Jorge Valdes, Raquel Quatrini, David S. Holmes and Mark Dopson. Genetic variability of psychrotolerant Acidithiobacillus ferrivorans strains revealed by (meta)genomic analysis. (Research in Microbiology, Aug 27. pii: S0923-2508(14)00135-1. doi: 10.1016/j.resmic.2014.08.005, 2014.

Mark Dopson and David S. Holmes. Metal resistance in acidophilic microorganisms and its significance for biotechnologies. Appl Microbiol Biotechnol 98(19):8133-8144, 2014.

Ana Moya-Beltrán, Juan Pablo Cárdenas, Paulo Covarrubias, Francisco Issotta, Francisco Ossandon, David Holmes, Raquel Quatrini, and Barrie Johnson. Draft Genome Sequence of the Nominated Type Strain of “Ferrovum myxofaciens”: an Acidophilic, Iron-Oxidizing Betaproteobacterium, Genome Announcements, Aug 21;2(4). pii: e00834-14.

Harold Nuñez, David Loyola, Juan Pablo Cárdenas, David S Holmes, D. Barrie Johnson, and Raquel Quatrini.Multi Locus Sequence Typing scheme for Acidithiobacillus caldus strain evaluation and differentiation. Research in Microbiology, Aug 28. pii: S0923-2508(14)00116-8, 2014.

Francisco J. Ossandon, Juan Pablo Cárdenas, Melissa Corbett, Raquel Quatrini, David S. Holmes and Elizabeth Watkin. Draft genome sequence of the iron-oxidizing, acidophilic and halotolerant ‘Thiobacillus prosperus’ type strain DSM 5130. Genome Announcements, 2014 Nov 6;2(6). pii: e01153-14.

Juan Pablo Cárdenas, Marcelo Lazcano, Francisco J. Ossandon, Melissa Corbett, David S Holmes and Elizabeth Watkin. Draft genome sequence of the type strain of the iron oxidizing acidophile Leptospirillum ferriphilum DSM 14647T. Genome Announcements. 2014 Nov 6; 2(6).

Maria Liljeqvist, Francisco J. Ossandon, Carolina Gonzalez, Sukithar Rajan, Adam Stell, Jorge Valdes, David S. Holmes and Mark Dopson. Metagenomic Analysis Reveals Adaptations to a Cold Adapted Lifestyle in a Low Temperature Acid Mine Drainage Stream. FEMS Microbiol Ecol. 2015 Jan 27. pii: fiv011. [Epub ahead of print].

Juan Pablo Cárdenas, Rodrigo Ortiz, Paul R. Norris, Elizabeth Watkin and David S. Holmes.Reclassification of “Thiobacillus prosperus” (Huber and Stetter 1989) as Acidihalobacter prosperus sp. nov., gen. nov., a member of the Ectothiorhodospiraceae. Int J Syst Evol Microbiol. Oct;65(10):3641-3644 (2015)

Mario Esparza, Eugenia Jedlicki, Mark Dopson, and David S. Holmes. Expression and activity of the Calvin-Benson-Bassham cycle transcriptional regulator CbbR from Acidithiobacillus ferrooxidans in Ralstonia eutropha. FEMS Microbiol Lett. Aug;362(15) (2015)

Sophie R. Ullrich, Anja Poehlein, Carolina González, Judith S. Tischler, Francisco Ossandon, Rolf Daniel, David S. Holmes, Michael Schlömann, Martin Mühling. Genome Analysis of the Biotechnologically Relevant Acidophilic Iron Oxidising Strain JA12 Indicates Phylogenetic and Metabolic Diversity within the Novel Genus “Ferrovum”. PLoS One. Jan 25;11(1): e0146832. doi: 10.1371 (2016)

Francisco Issotta, Pedro Galleguillos, Ana Moya-Beltrán, Carol S. Davis-Belmar, George Rautenbach, Paulo C. Covarrubias, Mauricio Acosta G., Francisco J. Ossandon, Yasna Contador, David S. Holmes, Sabrina Marín-Eliantonio, Raquel Quatrini, Cecilia Demergasso. Draft genome sequence of chloride-tolerant Leptospirillum ferriphilum Sp-Cl from industrial bioleaching operations in northern Chile. Stand Genomic Sci. 2016 Feb 27;11:19. eCollection (2016)

Alberto J.M. Martin, Calixto Dominguez, J. Sebastian Contreras-Riquelme, David S. Holmes, Tomas Perez-Acle.A graphlet-based metric for the comparison of dynamic Gene Regulatory Networks. Plos One. Oct 3;11(10):e0163497 (2016).

J-P Cardenas, R. Quatrini and D. S. Holmes. The Genomics of Acidophiles. Chapter 11, pp 179-197 in Acidophiles, eds R. Quatrini and D. B. Johnson, Caister Academic Press, UK (2016)

Juan Pablo Cardenas, Raquel Quatrini and David S. Holmes. Aerobic lineages of the oxidative stress response protein rubrerythrin emerged in an ancient microaerobic, (hyper)thermophilic environment. Front Microbiol. Nov 18;7:1822 (2016).

Sophie R. Ullrich, Anja Poehlein, Carolina González, Judith S. Tischler, Francisco Ossandon, Rolf Daniel, David S. Holmes, Michael Schlömann, Martin Mühling. Gene loss and horizontal gene transfer contributed to the genome evolution of the extreme acidophile “Ferrovum”. Front. Microbiol. 7:797. doi: 10.3389/fmicb.2016.00797 (2016)

Jorquera R., Ortiz R., Ossandon F., Cárdenas J.P., Sepúlveda R and Holmes D. S. SinEx DB: A Database for Single Exon Coding Sequences in Mammalian Genomes. DataBase, baw095 doi:10.1093/database/baw095 (2016)

Carolina González, Marcelo Lazcano, Jorge Valdés and David S. Holmes. Bioinformatic Analyses of Unique (Orphan) Core Genes of the Genus Acidithiobacillus: Functional Inferences and Use as Molecular Probes for Genomic and Metagenomic/Transcriptomic Interrogation. Front. Microbiol. 7:2035. doi: 10.3389/fmicb.2016.02035 (2016).

J-P Cárdenas, R. Quatrini and D. S. Holmes. Genomic and Metagenomic Challenges and Opportunities for Bioleaching: a mini-review. Res Microbiol. Sep;167(7):529-38 (2016).

Mark Dopson, David S Holmes, Marcelo Lazcano, Timothy J McCredden, Kieran T Mulroney, Elizabeth LJ Watkin. Multiple osmotic stress responses in Acidihalobacter prosperous results in a greater tolerance to chloride ions than in Acidithiobacillus ferrooxidans. Front. Microbiol. 05 January, doi.org/10.3389/fmicb.2016.02132 (2017).

Braulio Valdevenito-Maturana, Jose Antonio Reyes-Suarez, Jaime Henriquez, David S. Holmes, Raquel Quatrini, Ehmke Pohl, Mauricio Arenas-Salinas. MUTANTELEC: an In Silico Mutation Simulation Platform for Comparative Electrostatic Potential Profiling of Proteins. J. of Computational Chemistry 38, 467–474 (2017).

Valdebenito‐Maturana, B., Reyes‐Suarez, J. A., Henriquez, J., Holmes, D. S., Quatrini, R., Pohl, E., & Arenas‐Salinas, M. Mutantelec: An In Silico mutation simulation platform for comparative electrostatic potential profiling of proteins. Journal of Computational Chemistry, 38(7), 467-474. DOI: 10.1002/jcc.24712 (2017) | PDF

Quatrini, R., Escudero, L. V., Moya-Beltrán, A., Galleguillos, P. A., Issotta, F., Acosta, M., Cárdenas, J. P., Nuñez, H., Holmes, D. S., Demergasso, C. Draft genome sequence of Acidithiobacillus thiooxidans CLST isolated from the acidic hypersaline Gorbea salt flat in northern Chile. Standards in Genomic Sciences, 12(1), 84. DOI: 10.1186/s40793-017-0305-8 (2017). | PDF

Castro, M., Moya-Beltrán, A., Covarrubias, P. C., Gonzalez, M., Cardenas, J. P., Issotta, F., Salgado, O. A., Acuña, L. G., Encina, G., Holmes, D. S., Johnson, D. B. Draft genome sequence of the type strain of the sulfur-oxidizing acidophile, Acidithiobacillus albertensis (DSM 14366). Standards in genomic sciences, 12(1), 77. DOI: 10.1186/s40793-017-0282-y (2017). | PDF

Issotta, F., Covarrubias, P. C., Moya-Beltrán, A., Bellenberg, S., Thyssen, C., Sand, W., Nuñez, H., Mena, C., Holmes, D.S., Quatrini, R., Vera Véliz, M. 16S rRNA and multilocus phylogenetic analysis of the iron oxidizing acidophiles of the acidiferrobacteraceae family. In Solid State Phenomena (Vol. 262, pp. 339-343). Trans Tech Publications Ltd. DOI:10.4028/www.scientific.net/SSP.262.339 (2017). | PDF

Jorquera, R., González, C., Clausen, P., Petersen, B., Holmes, D. S. Improved ontology for eukaryotic single-exon coding sequences in biological databases. Database, 2018. DOI: 10.1093/database/bay089 (2018). | PDF

Khaleque, H. N., González, C., Kaksonen, A. H., Boxall, N. J., Holmes, D. S., Watkin, E. L. Genome-based classification of two halotolerant extreme acidophiles, Acidihalobacter prosperus V6 (= DSM 14174= JCM 32253) and ‘Acidihalobacter ferrooxidans’ V8 (= DSM 14175= JCM 32254) as two new species, Acidihalobacter aeolianus sp. nov. and Acidihalobacter ferrooxydans sp. nov., respectively. International journal of systematic and evolutionary microbiology, 69(6), 1557-1565. DOI: 10.1099/ijsem.0.003313 (2019). | PDF

Khaleque, H. N., González, C., Shafique, R., Kaksonen, A. H., Holmes, D. S., Watkin, E. L.Uncovering the mechanisms of halotolerance in the extremely acidophilic members of the Acidihalobacter genus through comparative genome analysis. Frontiers in microbiology, 10, 155. DOI: 10.3389/fmicb.2019.00155 (2019) | PDF

Esparza, M., Jedlicki, E., González, C., Dopson, M., Holmes, D. S. Effect of CO2 Concentration on Uptake and Assimilation of Inorganic Carbon in the Extreme Acidophile Acidithiobacillus ferrooxidans. Frontiers in microbiology, 10, 603. DOI: 10.3389/fmicb.2019.00603 (2019) | PDF

Osorio, H., Mettert, E. L., Kiley, P., Dopson, M., Jedlicki, E., Holmes, D. S.Identification and Unusual Properties of the Master Regulator FNR in the Extreme Acidophile Acidithiobacillus ferrooxidans. Frontiers in microbiology, 10, 1642. DOI: 10.3389/fmicb.2019.01642 (2019) | PDF

Vergara, E., Neira, G., González, C., Cortez, D., Dopson, M., Holmes, D. S.Evolution of Predicted Acid Resistance Mechanisms in the Extremely Acidophilic Leptospirillum Genus. Genes, 11(4), 389. DOI: 10.3390/genes11040389 (2020) | PDF

Neira, G., Cortez, D., Jil, J., Holmes, D. S. AciDB 1.0: A database of acidophilic organisms, their genomic information and associated metadata. Bioinformatics (Oxford, England) DOI: 10.1093/bioinformatics/btaa638 (2020). | PDF

Himel N. Khaleque, Carolina González, Barry Johnson, Anna H. Kaksonen, David S. Holmes and Elizabeth L.J. Watkin. “Genome-based classification of “Acidihalobacter prosperus F5” (=DSM 14174 =JCM 32253) as Acidihalobacter yilgarnensisT sp. nov. International Journal of Systematic and Evolutionary Microbiology 70.12 (2020): 6226-6234

Khaleque, Himel Nahreen, et al. “Unlocking Survival Mechanisms for Metal and Oxidative Stress in the Extremely Acidophilic, Halotolerant Acidihalobacter Genus”. Genes 11.12 (2020): 1392.

Jorquera R, González C, Clausen P.T.L.C., Petersen B and Holmes D.S. “SinEx DB 2.0 update 2020: Database for Eukaryotic Single-Exon Coding Sequences”. Database, Volume 2021, 2021, baab002, https://doi.org/10.1093/database/baab002