Phage-hunting: mapping viromes against 8000 bacterial genomes

Several prophage-finding tools have been developed since the 2000's, but these tools rely mostly on available databases and phage-related predicted proteins. Recently, more and more virome sequencing projects are becoming available, most of them with only partial analyses, thus increasing the a...

Full description

Autores:
Pardo Madrid Malo, Esteban
Tipo de recurso:
Trabajo de grado de pregrado
Fecha de publicación:
2017
Institución:
Universidad de los Andes
Repositorio:
Séneca: repositorio Uniandes
Idioma:
eng
OAI Identifier:
oai:repositorio.uniandes.edu.co:1992/39990
Acceso en línea:
http://hdl.handle.net/1992/39990
Palabra clave:
Genomas bacterianos
Bacteriófagos
Microbiología
Rights
openAccess
License
http://creativecommons.org/licenses/by-nc-sa/4.0/
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dc.title.es_CO.fl_str_mv Phage-hunting: mapping viromes against 8000 bacterial genomes
title Phage-hunting: mapping viromes against 8000 bacterial genomes
spellingShingle Phage-hunting: mapping viromes against 8000 bacterial genomes
Genomas bacterianos
Bacteriófagos
Microbiología
title_short Phage-hunting: mapping viromes against 8000 bacterial genomes
title_full Phage-hunting: mapping viromes against 8000 bacterial genomes
title_fullStr Phage-hunting: mapping viromes against 8000 bacterial genomes
title_full_unstemmed Phage-hunting: mapping viromes against 8000 bacterial genomes
title_sort Phage-hunting: mapping viromes against 8000 bacterial genomes
dc.creator.fl_str_mv Pardo Madrid Malo, Esteban
dc.contributor.advisor.none.fl_str_mv Reyes Muñoz, Alejandro
dc.contributor.author.none.fl_str_mv Pardo Madrid Malo, Esteban
dc.subject.keyword.es_CO.fl_str_mv Genomas bacterianos
Bacteriófagos
topic Genomas bacterianos
Bacteriófagos
Microbiología
dc.subject.themes.none.fl_str_mv Microbiología
description Several prophage-finding tools have been developed since the 2000's, but these tools rely mostly on available databases and phage-related predicted proteins. Recently, more and more virome sequencing projects are becoming available, most of them with only partial analyses, thus increasing the available data in public databases. In this study, 60 Gb of purified virome reads, from three different projects (one from oceanic samples and two from human gut) were mapped using Bowtie2 against 8164 bacterial genomes. Genomes were first filtered according to read coverage, then several statistical parameters were computed for the 3000 remaining candidates, in order to determine possible discriminative criteria. By manual curation using IGV, forty final candidates were selected and compared with other phage-prediction tools. Ten additional genomes were evaluated for concordance between bacterial environments and viral-reads sources. Twelve new prophages were detected. Here, a potential new method for phage detection and discovery is proposed, which will expand the current knowledge and reveal a more realistic estimation of both bacteriophages and host diversity
publishDate 2017
dc.date.issued.none.fl_str_mv 2017
dc.date.accessioned.none.fl_str_mv 2020-06-10T16:43:33Z
dc.date.available.none.fl_str_mv 2020-06-10T16:43:33Z
dc.type.spa.fl_str_mv Trabajo de grado - Pregrado
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dc.format.extent.es_CO.fl_str_mv 17 hojas
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dc.publisher.es_CO.fl_str_mv Universidad de los Andes
dc.publisher.program.es_CO.fl_str_mv Microbiología
dc.publisher.faculty.es_CO.fl_str_mv Facultad de Ciencias
dc.publisher.department.es_CO.fl_str_mv Departamento de Ciencias Biológicas
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spelling Al consultar y hacer uso de este recurso, está aceptando las condiciones de uso establecidas por los autores.http://creativecommons.org/licenses/by-nc-sa/4.0/info:eu-repo/semantics/openAccesshttp://purl.org/coar/access_right/c_abf2Reyes Muñoz, Alejandrovirtual::714-1Pardo Madrid Malo, Esteban97d6b1c9-43c5-4651-bf3e-78a9b99e35fa5002020-06-10T16:43:33Z2020-06-10T16:43:33Z2017http://hdl.handle.net/1992/39990u807569.pdfinstname:Universidad de los Andesreponame:Repositorio Institucional Sénecarepourl:https://repositorio.uniandes.edu.co/Several prophage-finding tools have been developed since the 2000's, but these tools rely mostly on available databases and phage-related predicted proteins. Recently, more and more virome sequencing projects are becoming available, most of them with only partial analyses, thus increasing the available data in public databases. In this study, 60 Gb of purified virome reads, from three different projects (one from oceanic samples and two from human gut) were mapped using Bowtie2 against 8164 bacterial genomes. Genomes were first filtered according to read coverage, then several statistical parameters were computed for the 3000 remaining candidates, in order to determine possible discriminative criteria. By manual curation using IGV, forty final candidates were selected and compared with other phage-prediction tools. Ten additional genomes were evaluated for concordance between bacterial environments and viral-reads sources. Twelve new prophages were detected. Here, a potential new method for phage detection and discovery is proposed, which will expand the current knowledge and reveal a more realistic estimation of both bacteriophages and host diversity"Múltiples herramientas de detección de profagos han sido desarrolladas desde los años 2000, pero estas se basan principalmente en bases de datos disponibles y proteínas predichas relacionadas a profagos. Recientemente, han surgido cada vez más proyectos de secuenciación de viromas, muchos con análisis parciales, pero aumentando drásticamente la disponibilidad de datos públicos. En este estudio, 60 Gb de lecturas purificadas de viromas, de tres proyectos diferentes (uno de muestras oceánicas y dos de intestino humano) fueron "mapeadas" usando Bowtie2 contra 8164 genomas bacterianos. Estos genomas fueron inicialmente filtrados según la cobertura de las lecturas, luego, múltiples parámetros estadísticos fueron calculados para los 3000 candidatos restantes, con el fin de identificar posibles criterios discriminatorios. Por verificación manual usando IGV, cuarenta candidatos finales fueron seleccionados y comparados con otras herramientas de predicción de profagos. Diez genomas adicionales fueron evaluados para analizar la concordancia entre el ambiente de la bacteria y el origen de las lecturas virales. Doce nuevos profagos fueron detectados. En este estudio, se propone un potencial nuevo método para la detección de profagos, lo que contribuirá a ampliar el conocimiento actual y revelar estimados más realísticos sobre la diversidad de tanto bacteriófagos como de sus hospederos."--Tomado del Formato de Documento de GradoMicrobiólogoPregrado17 hojasapplication/pdfengUniversidad de los AndesMicrobiologíaFacultad de CienciasDepartamento de Ciencias Biológicasinstname:Universidad de los Andesreponame:Repositorio Institucional SénecaPhage-hunting: mapping viromes against 8000 bacterial genomesTrabajo de grado - Pregradoinfo:eu-repo/semantics/bachelorThesishttp://purl.org/coar/resource_type/c_7a1fhttp://purl.org/coar/version/c_970fb48d4fbd8a85Texthttp://purl.org/redcol/resource_type/TPGenomas bacterianosBacteriófagosMicrobiologíaPublicationhttps://scholar.google.es/citations?user=hbXF8UEAAAAJvirtual::714-10000-0003-2907-3265virtual::714-1https://scienti.minciencias.gov.co/cvlac/visualizador/generarCurriculoCv.do?cod_rh=0000395927virtual::714-1f71489e5-69f6-4e6b-90a6-c6b1d3fecec7virtual::714-1f71489e5-69f6-4e6b-90a6-c6b1d3fecec7virtual::714-1TEXTu807569.pdf.txtu807569.pdf.txtExtracted texttext/plain3332https://repositorio.uniandes.edu.co/bitstreams/fe852591-3604-432a-a5a9-578b6a24fd83/download60b3b6c9e1f25fe7f17ac6edef11d9ebMD54THUMBNAILu807569.pdf.jpgu807569.pdf.jpgIM Thumbnailimage/jpeg23130https://repositorio.uniandes.edu.co/bitstreams/9a756714-1752-4fe6-8e78-009bd087e7fc/downloaddea88fe8ebabd77ef5b16a6d32278c32MD55ORIGINALu807569.pdfapplication/pdf3264909https://repositorio.uniandes.edu.co/bitstreams/5df0f557-a6c0-4b98-8f18-765d9adc2c30/downloada0572d1ee0441ed075a14df2bf19b26eMD511992/39990oai:repositorio.uniandes.edu.co:1992/399902024-03-13 11:47:13.576http://creativecommons.org/licenses/by-nc-sa/4.0/open.accesshttps://repositorio.uniandes.edu.coRepositorio institucional Sénecaadminrepositorio@uniandes.edu.co