A survey of computational approaches for characterizing microbial interactions in microbial mats

Autores
Perillo, Vanesa Liliana; Nute, Michael; Sapoval, Nicolae; Curry, Kristen D.; Golia, Logan; Yin, Yongze; Ogilvie, Huw A.; Nakhleh, Luay; Segarra, Santiago; Bhaya, Devaki; Cuadrado, Diana Graciela; Treangen, Todd J.
Año de publicación
2025
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
In this review, we use microbial mat communities as a general model system to highlight the strengths and limitations of current computational methods for analyzing interactions between members of microbial ecosystems. We describe the factors that make this environment have such a high degree of interaction, and we explore different categories of both laboratory and computational tools for studying these interactions. For each tool, we describe efforts to apply them to microbial mats in the past and, in the process, argue that genome-scale metabolic models have breakthrough potential for modeling microbial interactions in microbial mats.
Fil: Perillo, Vanesa Liliana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto Argentino de Oceanografía. Universidad Nacional del Sur. Instituto Argentino de Oceanografía; Argentina. Universidad Nacional del Sur. Departamento de Biología, Bioquímica y Farmacia; Argentina
Fil: Nute, Michael. Rice University; Estados Unidos
Fil: Sapoval, Nicolae. Rice University; Estados Unidos
Fil: Curry, Kristen D.. Rice University; Estados Unidos
Fil: Golia, Logan. Rice University; Estados Unidos
Fil: Yin, Yongze. Rice University; Estados Unidos
Fil: Ogilvie, Huw A.. Rice University; Estados Unidos
Fil: Nakhleh, Luay. Rice University; Estados Unidos
Fil: Segarra, Santiago. Rice University; Estados Unidos
Fil: Bhaya, Devaki. Carnegie Institution For Science;
Fil: Cuadrado, Diana Graciela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto Argentino de Oceanografía. Universidad Nacional del Sur. Instituto Argentino de Oceanografía; Argentina
Fil: Treangen, Todd J.. Rice University; Estados Unidos
Materia
TRANSDISCIPLINARY STUDIES
COMPUTATIONAL MODELS
MICROBIAL MATS
MICROBIAL EVOLUTION
ENVIRONMENTAL DATA
MICROBIAL ECOLOGY
META-OMICS
COMPARATIVE GENOMICS
METABOLIC MODELS
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/267617
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/267617
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling A survey of computational approaches for characterizing microbial interactions in microbial matsPerillo, Vanesa LilianaNute, MichaelSapoval, NicolaeCurry, Kristen D.Golia, LoganYin, YongzeOgilvie, Huw A.Nakhleh, LuaySegarra, SantiagoBhaya, DevakiCuadrado, Diana GracielaTreangen, Todd J.TRANSDISCIPLINARY STUDIESCOMPUTATIONAL MODELSMICROBIAL MATSMICROBIAL EVOLUTIONENVIRONMENTAL DATAMICROBIAL ECOLOGYMETA-OMICSCOMPARATIVE GENOMICSMETABOLIC MODELShttps://purl.org/becyt/ford/1.5https://purl.org/becyt/ford/1In this review, we use microbial mat communities as a general model system to highlight the strengths and limitations of current computational methods for analyzing interactions between members of microbial ecosystems. We describe the factors that make this environment have such a high degree of interaction, and we explore different categories of both laboratory and computational tools for studying these interactions. For each tool, we describe efforts to apply them to microbial mats in the past and, in the process, argue that genome-scale metabolic models have breakthrough potential for modeling microbial interactions in microbial mats.Fil: Perillo, Vanesa Liliana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto Argentino de Oceanografía. Universidad Nacional del Sur. Instituto Argentino de Oceanografía; Argentina. Universidad Nacional del Sur. Departamento de Biología, Bioquímica y Farmacia; ArgentinaFil: Nute, Michael. Rice University; Estados UnidosFil: Sapoval, Nicolae. Rice University; Estados UnidosFil: Curry, Kristen D.. Rice University; Estados UnidosFil: Golia, Logan. Rice University; Estados UnidosFil: Yin, Yongze. Rice University; Estados UnidosFil: Ogilvie, Huw A.. Rice University; Estados UnidosFil: Nakhleh, Luay. Rice University; Estados UnidosFil: Segarra, Santiago. Rice University; Estados UnidosFil: Bhaya, Devaki. Carnegie Institution For Science;Fil: Cuadrado, Diana Graciela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto Argentino de Oceanografía. Universidad Nacional del Sur. Instituto Argentino de Oceanografía; ArgentinaFil: Treangen, Todd J.. Rice University; Estados UnidosBioMed Central2025-05info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/267617Perillo, Vanesa Liliana; Nute, Michael; Sapoval, Nicolae; Curry, Kristen D.; Golia, Logan; et al.; A survey of computational approaches for characterizing microbial interactions in microbial mats; BioMed Central; Genome Biology; 26; 1; 5-2025; 1-201474-760XCONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://link.springer.com/article/10.1186/s13059-025-03634-2?utm_source=rct_congratemailt&utm_medium=email&utm_campaign=oa_20250616&utm_content=10.1186%2Fs13059-025-03634-2info:eu-repo/semantics/altIdentifier/doi/10.1186/s13059-025-03634-2info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T09:58:33Zoai:ri.conicet.gov.ar:11336/267617instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-03 09:58:33.954CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv A survey of computational approaches for characterizing microbial interactions in microbial mats
title A survey of computational approaches for characterizing microbial interactions in microbial mats
spellingShingle A survey of computational approaches for characterizing microbial interactions in microbial mats
Perillo, Vanesa Liliana
TRANSDISCIPLINARY STUDIES
COMPUTATIONAL MODELS
MICROBIAL MATS
MICROBIAL EVOLUTION
ENVIRONMENTAL DATA
MICROBIAL ECOLOGY
META-OMICS
COMPARATIVE GENOMICS
METABOLIC MODELS
title_short A survey of computational approaches for characterizing microbial interactions in microbial mats
title_full A survey of computational approaches for characterizing microbial interactions in microbial mats
title_fullStr A survey of computational approaches for characterizing microbial interactions in microbial mats
title_full_unstemmed A survey of computational approaches for characterizing microbial interactions in microbial mats
title_sort A survey of computational approaches for characterizing microbial interactions in microbial mats
dc.creator.none.fl_str_mv Perillo, Vanesa Liliana
Nute, Michael
Sapoval, Nicolae
Curry, Kristen D.
Golia, Logan
Yin, Yongze
Ogilvie, Huw A.
Nakhleh, Luay
Segarra, Santiago
Bhaya, Devaki
Cuadrado, Diana Graciela
Treangen, Todd J.
author Perillo, Vanesa Liliana
author_facet Perillo, Vanesa Liliana
Nute, Michael
Sapoval, Nicolae
Curry, Kristen D.
Golia, Logan
Yin, Yongze
Ogilvie, Huw A.
Nakhleh, Luay
Segarra, Santiago
Bhaya, Devaki
Cuadrado, Diana Graciela
Treangen, Todd J.
author_role author
author2 Nute, Michael
Sapoval, Nicolae
Curry, Kristen D.
Golia, Logan
Yin, Yongze
Ogilvie, Huw A.
Nakhleh, Luay
Segarra, Santiago
Bhaya, Devaki
Cuadrado, Diana Graciela
Treangen, Todd J.
author2_role author
author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv TRANSDISCIPLINARY STUDIES
COMPUTATIONAL MODELS
MICROBIAL MATS
MICROBIAL EVOLUTION
ENVIRONMENTAL DATA
MICROBIAL ECOLOGY
META-OMICS
COMPARATIVE GENOMICS
METABOLIC MODELS
topic TRANSDISCIPLINARY STUDIES
COMPUTATIONAL MODELS
MICROBIAL MATS
MICROBIAL EVOLUTION
ENVIRONMENTAL DATA
MICROBIAL ECOLOGY
META-OMICS
COMPARATIVE GENOMICS
METABOLIC MODELS
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.5
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv In this review, we use microbial mat communities as a general model system to highlight the strengths and limitations of current computational methods for analyzing interactions between members of microbial ecosystems. We describe the factors that make this environment have such a high degree of interaction, and we explore different categories of both laboratory and computational tools for studying these interactions. For each tool, we describe efforts to apply them to microbial mats in the past and, in the process, argue that genome-scale metabolic models have breakthrough potential for modeling microbial interactions in microbial mats.
Fil: Perillo, Vanesa Liliana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto Argentino de Oceanografía. Universidad Nacional del Sur. Instituto Argentino de Oceanografía; Argentina. Universidad Nacional del Sur. Departamento de Biología, Bioquímica y Farmacia; Argentina
Fil: Nute, Michael. Rice University; Estados Unidos
Fil: Sapoval, Nicolae. Rice University; Estados Unidos
Fil: Curry, Kristen D.. Rice University; Estados Unidos
Fil: Golia, Logan. Rice University; Estados Unidos
Fil: Yin, Yongze. Rice University; Estados Unidos
Fil: Ogilvie, Huw A.. Rice University; Estados Unidos
Fil: Nakhleh, Luay. Rice University; Estados Unidos
Fil: Segarra, Santiago. Rice University; Estados Unidos
Fil: Bhaya, Devaki. Carnegie Institution For Science;
Fil: Cuadrado, Diana Graciela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto Argentino de Oceanografía. Universidad Nacional del Sur. Instituto Argentino de Oceanografía; Argentina
Fil: Treangen, Todd J.. Rice University; Estados Unidos
description In this review, we use microbial mat communities as a general model system to highlight the strengths and limitations of current computational methods for analyzing interactions between members of microbial ecosystems. We describe the factors that make this environment have such a high degree of interaction, and we explore different categories of both laboratory and computational tools for studying these interactions. For each tool, we describe efforts to apply them to microbial mats in the past and, in the process, argue that genome-scale metabolic models have breakthrough potential for modeling microbial interactions in microbial mats.
publishDate 2025
dc.date.none.fl_str_mv 2025-05
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/267617
Perillo, Vanesa Liliana; Nute, Michael; Sapoval, Nicolae; Curry, Kristen D.; Golia, Logan; et al.; A survey of computational approaches for characterizing microbial interactions in microbial mats; BioMed Central; Genome Biology; 26; 1; 5-2025; 1-20
1474-760X
CONICET Digital
CONICET
url http://hdl.handle.net/11336/267617
identifier_str_mv Perillo, Vanesa Liliana; Nute, Michael; Sapoval, Nicolae; Curry, Kristen D.; Golia, Logan; et al.; A survey of computational approaches for characterizing microbial interactions in microbial mats; BioMed Central; Genome Biology; 26; 1; 5-2025; 1-20
1474-760X
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://link.springer.com/article/10.1186/s13059-025-03634-2?utm_source=rct_congratemailt&utm_medium=email&utm_campaign=oa_20250616&utm_content=10.1186%2Fs13059-025-03634-2
info:eu-repo/semantics/altIdentifier/doi/10.1186/s13059-025-03634-2
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
_version_ 1842269527807623168
score 13.13397

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