CINECA IRIS Institutional Research Information System
IRIS is the IT solution to facilitate the collection and management of data and activities related to research product.
EnglishMetagenomic characterization of microbial communities has the potential to become a tool to identify pathogens in human samples. However, software tools able to extract strain-level typing information from metagenomic data are needed. Low-throughput molecular typing schema such as Multilocus Sequence Typing (MLST) are still widely used and provide a wealth of strain-level information that is currently not exploited by metagenomic methods. We introduce MetaMLST, a software tool that reconstructs the MLST loci of microorganisms present in microbial communities from metagenomic data. Tested on synthetic and spiked-in real metagenomes, the pipeline was able to reconstruct the MLST sequences with >98.5% accuracy at coverages as low as 1X. On real samples, the pipeline showed higher sensitivity than assembly-based approaches and it proved successful in identifying strains in epidemic outbreaks as well as in intestinal, skin and gastrointestinal microbiome samples.
Zolfo, M.; Tett, A.; Jousson, O.; Donati, C.; Segata, N. (2017). MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples. NUCLEIC ACIDS RESEARCH, 45 (2): e7. doi: 10.1093/nar/gkw837 handle: http://hdl.handle.net/10449/35720
| Citation: | Zolfo, M.; Tett, A.; Jousson, O.; Donati, C.; Segata, N. (2017). MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples. NUCLEIC ACIDS RESEARCH, 45 (2): e7. doi: 10.1093/nar/gkw837 handle: http://hdl.handle.net/10449/35720 |
| Internal authors: | |
| Organization unit: | Unit of Computational Biology # CRI |
| Authors: | Zolfo, M.; Tett, A.; Jousson, O.; Donati, C.; Segata, N. |
| Title: | MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples |
| Journal: | NUCLEIC ACIDS RESEARCH |
| Issue Date: | 2017 |
| Scientific Disciplinary Area: | Settore BIO/19 - Microbiologia Generale |
| Keywords ENG: | Metagenomics Population genetics Microbiology |
| Language: | English |
| IF: | With Impact Factor ISI |
| Publication status: | Published |
| Nature of content: | Articolo in rivista/Article |
| Digital Object Identifier (DOI): | http://dx.doi.org/10.1093/nar/gkw837 |
| EU grant: | 7° Programma quadro (FP7) |
| EU grant agreement number: | 618833 |
| Appears in Collections: | 01 - Journal article |
Files in This Item:
| File | Description | Type | License | |
|---|---|---|---|---|
| 2017 NAR.pdf | N/A |  | Open AccessView/Open |
Copyright © 2020