The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes
Open accessAbstract
New microbial genomes are constantly being sequenced, and it is crucial to accurately determine their taxonomic identities and evolutionary relationships. Here we report PhyloPhlAn, a new method to assign microbial phylogeny and putative taxonomy using >400 proteins optimized from among 3,737 genomes. This method measures the sequence diversity of all clades, classifies genomes from deep-branching candidate divisions through closely related subspecies and improves consistency between phylogenetic and taxonomic groupings. PhyloPhlAn improved taxonomic accuracy for existing and newly sequenced genomes, detecting 157 erroneous labels, correcting 46 and placing or refining 130 new genomes. We provide examples of accurate classifications from subspecies (Sulfolobus spp.) to phyla, and of preliminary rooting of deep-branching candidate divisions, including consistent statistical support for Caldiserica (formerly candidate division OP5). PhyloPhlAn will thus be useful for both phylogenetic assessment and taxonomic quality control of newly sequenced genomes. The final phylogenies, conserved protein sequences and open-source implementation are available online. Sequencing whole microbial genomes has become standard practice and methods to examine their phylogenetic relationships need to match the increasing demand. Segata et al. present a new computational pipeline that allows fast and accurate taxonomic assignment of microbial species.
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Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
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Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach
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Self-citationToward Automatic Reconstruction of a Highly Resolved Tree of Life
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“While no one taxonomy is perfect, this represents a well-accepted microbial categorization, as it has been extensively manually curated, and its genomic and phenotypic bases are well-established 36 .”
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Cited by
Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P., & Tyson, G. W. (2015) · Genome Research · doi:10.1101/gr.186072.114 · Cited by 12,496
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
Parks, D. H., Chuvochina, M., Waite, D. W., Rinke, C., Skarshewski, A., Chaumeil, P.-A., & Hugenholtz, P. (2018) · Nature Biotechnology · doi:10.1038/nbt.4229 · Cited by 3,603
Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis
Scher, J. U., Sczesnak, A., Longman, R. S., Segata, N., Ubeda, C., Bielski, C., Rostron, T., Cerundolo, V., Pamer, E. G., Abramson, S. B., et al. (2013) · eLife · doi:10.7554/elife.01202 · Cited by 2,047
Self-citationSpecies-level functional profiling of metagenomes and metatranscriptomes
Franzosa, E. A., McIver, L. J., Rahnavard, G., Thompson, L. R., Schirmer, M., Weingart, G., Lipson, K. S., Knight, R., Caporaso, J. G., Segata, N., et al. (2018) · Nature Methods · doi:10.1038/s41592-018-0176-y · Cited by 1,693
Self-citationPasolli, E., Asnicar, F., Manara, S., Zolfo, M., Karcher, N., Armanini, F., Beghini, F., Manghi, P., Tett, A., Ghensi, P., et al. (2019) · Cell · doi:10.1016/j.cell.2019.01.001 · Cited by 1,591
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Metadata
- Authors
- Segata, N., Börnigen, D., Morgan, X. C., & Huttenhower, C.
- Venue
- Nature Communications
- Published
- 2013-08-14
- Volume
- 4
- Issue
- 1
- Pages
- 2304-2304
- ISSN
- 2041-1723 (ISSN-L)
- OpenAlex
- W2116913446
- Cited by
- 849
- References
- 9
- FWCI
- 13.72
- Type
- journal article
- Language
- en
- Open access
- bronze
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