Metagenomic microbial community profiling using unique clade-specific marker genes

Metagenomic shotgun sequencing data can identify microbes populating a microbial community and their proportions, but existing taxonomic profiling methods are inefficient for increasingly large datasets. We present an approach that uses clade-specific marker genes to unambiguously assign reads to mi...

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Detalles Bibliográficos
Autores principales: Segata, Nicola, Waldron, Levi, Ballarini, Annalisa, Narasimhan, Vagheesh, Jousson, Olivier, Huttenhower, Curtis
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2012
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3443552/
https://www.ncbi.nlm.nih.gov/pubmed/22688413
http://dx.doi.org/10.1038/nmeth.2066
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author Segata, Nicola
Waldron, Levi
Ballarini, Annalisa
Narasimhan, Vagheesh
Jousson, Olivier
Huttenhower, Curtis
author_facet Segata, Nicola
Waldron, Levi
Ballarini, Annalisa
Narasimhan, Vagheesh
Jousson, Olivier
Huttenhower, Curtis
author_sort Segata, Nicola
collection PubMed
description Metagenomic shotgun sequencing data can identify microbes populating a microbial community and their proportions, but existing taxonomic profiling methods are inefficient for increasingly large datasets. We present an approach that uses clade-specific marker genes to unambiguously assign reads to microbial clades more accurately and >50× faster than current approaches. We validated MetaPhlAn on terabases of short reads and provide the largest metagenomic profiling to date of the human gut
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spelling pubmed-34435522013-02-01 Metagenomic microbial community profiling using unique clade-specific marker genes Segata, Nicola Waldron, Levi Ballarini, Annalisa Narasimhan, Vagheesh Jousson, Olivier Huttenhower, Curtis Nat Methods Article Metagenomic shotgun sequencing data can identify microbes populating a microbial community and their proportions, but existing taxonomic profiling methods are inefficient for increasingly large datasets. We present an approach that uses clade-specific marker genes to unambiguously assign reads to microbial clades more accurately and >50× faster than current approaches. We validated MetaPhlAn on terabases of short reads and provide the largest metagenomic profiling to date of the human gut 2012-06-10 /pmc/articles/PMC3443552/ /pubmed/22688413 http://dx.doi.org/10.1038/nmeth.2066 Text en http://www.nature.com/authors/editorial_policies/license.html#terms Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http://www.nature.com/authors/editorial_policies/license.html#terms
spellingShingle Article
Segata, Nicola
Waldron, Levi
Ballarini, Annalisa
Narasimhan, Vagheesh
Jousson, Olivier
Huttenhower, Curtis
Metagenomic microbial community profiling using unique clade-specific marker genes
title Metagenomic microbial community profiling using unique clade-specific marker genes
title_full Metagenomic microbial community profiling using unique clade-specific marker genes
title_fullStr Metagenomic microbial community profiling using unique clade-specific marker genes
title_full_unstemmed Metagenomic microbial community profiling using unique clade-specific marker genes
title_short Metagenomic microbial community profiling using unique clade-specific marker genes
title_sort metagenomic microbial community profiling using unique clade-specific marker genes
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3443552/
https://www.ncbi.nlm.nih.gov/pubmed/22688413
http://dx.doi.org/10.1038/nmeth.2066
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