2026-04-21T06:34:34Zhttps://riubu.ubu.es/oai/request

oai:riubu.ubu.es:10259/94902024-07-27T00:05:25Zcom_10259_9491com_10259_5086com_10259_2604com_10259_6168col_10259_9492col_10259_6169

González Plaza, Juan José Furlan, Cristina Rijavec, Tomaž Lapanje, Aleš Barros García, Rocío Tamayo Ramos, Juan Antonio Suarez Diez, Maria 2024-07-26T07:48:27Z 2024-07-26T07:48:27Z 2022-11-28 1664-302X http://hdl.handle.net/10259/9490 10.3389/fmicb.2022.1006946 1664-302X Artículo de revisión The study of the biological response of microbial cells interacting with natural and synthetic interfaces has acquired a new dimension with the development and constant progress of advanced omics technologies. New methods allow the isolation and analysis of nucleic acids, proteins and metabolites from complex samples, of interest in diverse research areas, such as materials sciences, biomedical sciences, forensic sciences, biotechnology and archeology, among others. The study of the bacterial recognition and response to surface contact or the diagnosis and evolution of ancient pathogens contained in archeological tissues require, in many cases, the availability of specialized methods and tools. The current review describes advances in in vitro and in silico approaches to tackle existing challenges (e.g., low-quality sample, low amount, presence of inhibitors, chelators, etc.) in the isolation of high-quality samples and in the analysis of microbial cells at genomic, transcriptomic, proteomic and metabolomic levels, when present in complex interfaces. From the experimental point of view, tailored manual and automatized methodologies, commercial and in-house developed protocols, are described. The computational level focuses on the discussion of novel tools and approaches designed to solve associated issues, such as sample contamination, low quality reads, low coverage, etc. Finally, approaches to obtain a systems level understanding of these complex interactions by integrating multi omics datasets are presented. This project has received funding under the European Union’s Horizon 2020 research & Innovation programme under grant agreement no. 952379, SURFBIO project. JG-P is currently supported by Junta de Castilla y León-FEDER under grant N° BU058P20 (NANOCOMP). application/pdf eng Frontiers Media Frontiers in Microbiology. 2022, V. 13 https://doi.org/10.3389/fmicb.2022.1006946 Atribución 4.0 Internacional http://creativecommons.org/licenses/by/4.0/ info:eu-repo/semantics/openAccess Biofilms Genomics Transcriptomics Metabolomics Proteomics Omics data integration Systems biology Química física Chemistry, Physical and theoretical Advances in experimental and computational methodologies for the study of microbial-surface interactions at different omics levels info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion Frontiers in Microbiology 13