Advances in experimental and computational methodologies for the study of microbial-surface interactions at different omics levels

Artículo de revisión

Detalles Bibliográficos
Autores: González Plaza, Juan José, Furlan, Cristina, Rijavec, Tomaž, Lapanje, Aleš, Barros García, Rocío, Tamayo Ramos, Juan Antonio, Suarez Diez, Maria
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2022
País:España
Institución:Universidad de Burgos (UBU)
Repositorio:Repositorio Institucional de la Universidad de Burgos (RIUBU)
OAI Identifier:oai:riubu.ubu.es:10259/9490
Acceso en línea:http://hdl.handle.net/10259/9490
Access Level:acceso abierto
Palabra clave:Biofilms
Genomics
Transcriptomics
Metabolomics
Proteomics
Omics data integration
Systems biology
Química física
Chemistry, Physical and theoretical
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spelling Advances in experimental and computational methodologies for the study of microbial-surface interactions at different omics levelsGonzález Plaza, Juan JoséFurlan, CristinaRijavec, TomažLapanje, AlešBarros García, RocíoTamayo Ramos, Juan AntonioSuarez Diez, MariaBiofilmsGenomicsTranscriptomicsMetabolomicsProteomicsOmics data integrationSystems biologyQuímica físicaChemistry, Physical and theoreticalArtículo de revisiónThe 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).Frontiers Media202420242022info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfhttp://hdl.handle.net/10259/9490reponame:Repositorio Institucional de la Universidad de Burgos (RIUBU)instname:Universidad de Burgos (UBU)InglésFrontiers in Microbiology. 2022, V. 13https://doi.org/10.3389/fmicb.2022.1006946Atribución 4.0 Internacionalhttp://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:riubu.ubu.es:10259/94902026-05-28T07:56:11Z
dc.title.none.fl_str_mv Advances in experimental and computational methodologies for the study of microbial-surface interactions at different omics levels
title Advances in experimental and computational methodologies for the study of microbial-surface interactions at different omics levels
spellingShingle Advances in experimental and computational methodologies for the study of microbial-surface interactions at different omics levels
González Plaza, Juan José
Biofilms
Genomics
Transcriptomics
Metabolomics
Proteomics
Omics data integration
Systems biology
Química física
Chemistry, Physical and theoretical
title_short Advances in experimental and computational methodologies for the study of microbial-surface interactions at different omics levels
title_full Advances in experimental and computational methodologies for the study of microbial-surface interactions at different omics levels
title_fullStr Advances in experimental and computational methodologies for the study of microbial-surface interactions at different omics levels
title_full_unstemmed Advances in experimental and computational methodologies for the study of microbial-surface interactions at different omics levels
title_sort Advances in experimental and computational methodologies for the study of microbial-surface interactions at different omics levels
dc.creator.none.fl_str_mv González Plaza, Juan José
Furlan, Cristina
Rijavec, Tomaž
Lapanje, Aleš
Barros García, Rocío
Tamayo Ramos, Juan Antonio
Suarez Diez, Maria
author González Plaza, Juan José
author_facet González Plaza, Juan José
Furlan, Cristina
Rijavec, Tomaž
Lapanje, Aleš
Barros García, Rocío
Tamayo Ramos, Juan Antonio
Suarez Diez, Maria
author_role author
author2 Furlan, Cristina
Rijavec, Tomaž
Lapanje, Aleš
Barros García, Rocío
Tamayo Ramos, Juan Antonio
Suarez Diez, Maria
author2_role author
author
author
author
author
author
dc.subject.none.fl_str_mv Biofilms
Genomics
Transcriptomics
Metabolomics
Proteomics
Omics data integration
Systems biology
Química física
Chemistry, Physical and theoretical
topic Biofilms
Genomics
Transcriptomics
Metabolomics
Proteomics
Omics data integration
Systems biology
Química física
Chemistry, Physical and theoretical
description Artículo de revisión
publishDate 2022
dc.date.none.fl_str_mv 2022
2024
2024
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10259/9490
url http://hdl.handle.net/10259/9490
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Frontiers in Microbiology. 2022, V. 13
https://doi.org/10.3389/fmicb.2022.1006946
dc.rights.none.fl_str_mv Atribución 4.0 Internacional
http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv Atribución 4.0 Internacional
http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Frontiers Media
publisher.none.fl_str_mv Frontiers Media
dc.source.none.fl_str_mv reponame:Repositorio Institucional de la Universidad de Burgos (RIUBU)
instname:Universidad de Burgos (UBU)
instname_str Universidad de Burgos (UBU)
reponame_str Repositorio Institucional de la Universidad de Burgos (RIUBU)
collection Repositorio Institucional de la Universidad de Burgos (RIUBU)
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15.812429

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