Metagenomic microbial community profiling using unique clade-specific marker genes
Top Cited Papers
Open Access
- 10 June 2012
- journal article
- research article
- Published by Springer Nature in Nature Methods
- Vol. 9 (8) , 811-814
- https://doi.org/10.1038/nmeth.2066
Abstract
MetaPhlAn (metagenomic phylogenetic analysis) allows the rapid and accurate identification of microbial species and higher clades from shotgun sequencing data. Metagenomic shotgun sequencing data can identify microbes populating a microbial community and their proportions, but existing taxonomic profiling methods are inefficient for increasingly large data sets. 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 our metagenomic phylogenetic analysis tool, MetaPhlAn, on terabases of short reads and provide the largest metagenomic profiling to date of the human gut. It can be accessed at http://huttenhower.sph.harvard.edu/metaphlan/ .Keywords
This publication has 38 references indexed in Scilit:
- A framework for human microbiome researchNature, 2012
- PhymmBL expanded: confidence scores, custom databases, parallelization and moreNature Methods, 2011
- Taxonomic metagenome sequence assignment with structured output modelsNature Methods, 2011
- Bifidobacterium animalis subsp. lactis fermented milk product reduces inflammation by altering a niche for colitogenic microbesProceedings of the National Academy of Sciences, 2010
- Search and clustering orders of magnitude faster than BLASTBioinformatics, 2010
- Vaginal microbiome of reproductive-age womenProceedings of the National Academy of Sciences, 2010
- Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov modelsNature Methods, 2009
- A core gut microbiome in obese and lean twinsNature, 2008
- Use of simulated data sets to evaluate the fidelity of metagenomic processing methodsNature Methods, 2007
- Basic Local Alignment Search ToolJournal of Molecular Biology, 1990