Assembly and Annotation of <named-content content-type="genus-species">Pneumocystis jirovecii</named-content> from the Human Lung Microbiome

ABSTRACT Pneumocystis jirovecii is a fungus that causes Pneumocystis pneumonia in immunosuppressed patients and has been closely associated with AIDS since the beginning of the AIDS epidemic. Because in vitro cultivation of P. jirovecii is not possible, progress has been hindered in our understandin...

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Autores principales:	Melanie T. Cushion, Scott P. Keely
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2013
Materias:	Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/9833b0ee5c8e4641bb95914a04842d85
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spelling	oai:doaj.org-article:9833b0ee5c8e4641bb95914a04842d852021-11-15T15:40:30ZAssembly and Annotation of <named-content content-type="genus-species">Pneumocystis jirovecii</named-content> from the Human Lung Microbiome10.1128/mBio.00224-132150-7511https://doaj.org/article/9833b0ee5c8e4641bb95914a04842d852013-05-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.00224-13https://doaj.org/toc/2150-7511ABSTRACT Pneumocystis jirovecii is a fungus that causes Pneumocystis pneumonia in immunosuppressed patients and has been closely associated with AIDS since the beginning of the AIDS epidemic. Because in vitro cultivation of P. jirovecii is not possible, progress has been hindered in our understanding of its life cycle, mode of transmission, metabolic function, and genome. Limited amounts of P. jirovecii can be obtained from infected patients, but the occurrence of bacteria, other fungi, and human cells in clinical samples presents new challenges for whole-genome sequencing and downstream bioinformatic analysis. In a recent article, Cissé et al. used cell immunoprecipitation enrichment together with whole-genome amplification to generate sufficient quantities of DNA for Roche 454 and Illumina sequencing [O. H. Cissé, M. Pagni, and P. M. Hauser, mBio 4(1):e00428-12, 2012, doi:10.1128/mBio.00428-12]. In addition, a bioinformatic pipeline was devised to sort and assemble lung microbiome reads, thereby generating an 8.1-Mb P. jirovecii genome comprised of 356 contigs with an N50 (median length of all contigs) of 41.6 kb. Knowledge of this genome will open new avenues of research, including the identification of nutritional requirements for in vitro cultivation as well as the identification of new and novel drug and vaccine targets.Melanie T. CushionScott P. KeelyAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 4, Iss 2 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiology QR1-502
spellingShingle	Microbiology QR1-502 Melanie T. Cushion Scott P. Keely Assembly and Annotation of <named-content content-type="genus-species">Pneumocystis jirovecii</named-content> from the Human Lung Microbiome
description	ABSTRACT Pneumocystis jirovecii is a fungus that causes Pneumocystis pneumonia in immunosuppressed patients and has been closely associated with AIDS since the beginning of the AIDS epidemic. Because in vitro cultivation of P. jirovecii is not possible, progress has been hindered in our understanding of its life cycle, mode of transmission, metabolic function, and genome. Limited amounts of P. jirovecii can be obtained from infected patients, but the occurrence of bacteria, other fungi, and human cells in clinical samples presents new challenges for whole-genome sequencing and downstream bioinformatic analysis. In a recent article, Cissé et al. used cell immunoprecipitation enrichment together with whole-genome amplification to generate sufficient quantities of DNA for Roche 454 and Illumina sequencing [O. H. Cissé, M. Pagni, and P. M. Hauser, mBio 4(1):e00428-12, 2012, doi:10.1128/mBio.00428-12]. In addition, a bioinformatic pipeline was devised to sort and assemble lung microbiome reads, thereby generating an 8.1-Mb P. jirovecii genome comprised of 356 contigs with an N50 (median length of all contigs) of 41.6 kb. Knowledge of this genome will open new avenues of research, including the identification of nutritional requirements for in vitro cultivation as well as the identification of new and novel drug and vaccine targets.
format	article
author	Melanie T. Cushion Scott P. Keely
author_facet	Melanie T. Cushion Scott P. Keely
author_sort	Melanie T. Cushion
title	Assembly and Annotation of <named-content content-type="genus-species">Pneumocystis jirovecii</named-content> from the Human Lung Microbiome
title_short	Assembly and Annotation of <named-content content-type="genus-species">Pneumocystis jirovecii</named-content> from the Human Lung Microbiome
title_full	Assembly and Annotation of <named-content content-type="genus-species">Pneumocystis jirovecii</named-content> from the Human Lung Microbiome
title_fullStr	Assembly and Annotation of <named-content content-type="genus-species">Pneumocystis jirovecii</named-content> from the Human Lung Microbiome
title_full_unstemmed	Assembly and Annotation of <named-content content-type="genus-species">Pneumocystis jirovecii</named-content> from the Human Lung Microbiome
title_sort	assembly and annotation of <named-content content-type="genus-species">pneumocystis jirovecii</named-content> from the human lung microbiome
publisher	American Society for Microbiology
publishDate	2013
url	https://doaj.org/article/9833b0ee5c8e4641bb95914a04842d85
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Assembly and Annotation of <named-content content-type="genus-species">Pneumocystis jirovecii</named-content> from the Human Lung Microbiome

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