Recovering microbial genomes from metagenomes in hypersaline environments: The Good, the Bad and the Ugly

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Título: Recovering microbial genomes from metagenomes in hypersaline environments: The Good, the Bad and the Ugly
Autor/es: Ramos-Barbero, María Dolores | Martín Cuadrado, Ana Belén | Viver, Tomeu | Santos, Fernando | Martinez-Garcia, Manuel | Anton, Josefa
Grupo/s de investigación o GITE: Ecología Microbiana Molecular
Centro, Departamento o Servicio: Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología
Palabras clave: Microdiversity | Binning | Hypersaline | Haloquadratum | Salinibacter | Halorubrum
Área/s de conocimiento: Microbiología
Fecha de publicación: ene-2019
Editor: Elsevier
Cita bibliográfica: Systematic and Applied Microbiology. 2019, 42(1): 30-40. doi:10.1016/j.syapm.2018.11.001
Resumen: Current metagenomic tools allow the recovery of microbial genomes directly from the environment. This can be accomplished by binning metagenomic contigs according to their coverage and tetranucleotide frequency, followed by an estimation of the bin quality. The public availability of bioinformatics tools, together with the decreasing cost of next generation sequencing, are democratizing this powerful approach that is spreading from specialized research groups to the general public. Using metagenomes from hypersaline environments, as well as mock metagenomes composed of Archaea and Bacteria frequently found in these systems, we have analyzed the advantages and difficulties of the binning process in these extreme environments to tackle microbial population diversity. These extreme systems harbor relatively low species diversity but high intraspecific diversity, which can compromise metagenome assembly and therefore the whole binning process. The main goal is to compare the output of the binning process with what is previously known from the analyzed samples, based on years of study using different approaches. Several scenarios have been analyzed in detail: (i) a good quality bin from a species highly abundant in the environment; (ii) an intermediate quality bin with incongruences that can be solved by further analyses and manual curation, and (iii) a low-quality bin to investigate the failure to recover a very abundant microbial genome as well as some possible solutions. The latter can be considered the “great metagenomics anomaly” and is mainly due to assembly problems derived from the microdiversity of naturally co-existing populations in nature.
Patrocinador/es: This research was supported by the Spanish Ministry of Economy project CLG2015 66686-C3-3 (to JA), which also included European Regional Development Fund (FEDER) funds.
URI: http://hdl.handle.net/10045/88593
ISSN: 0723-2020 (Print) | 1618-0984 (Online)
DOI: 10.1016/j.syapm.2018.11.001
Idioma: eng
Tipo: info:eu-repo/semantics/article
Derechos: © 2018 Elsevier GmbH.
Revisión científica: si
Versión del editor: https://doi.org/10.1016/j.syapm.2018.11.001
Aparece en las colecciones:INV - EMM - Artículos de Revistas

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