ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition
Identifieur interne : 001913 ( Main/Curation ); précédent : 001912; suivant : 001914ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition
Auteurs : David Koslicki [États-Unis] ; Saikat Chatterjee [Suède] ; Damon Shahrivar [Suède] ; Alan W. Walker [Royaume-Uni] ; Suzanna C. Francis [Royaume-Uni] ; Louise J. Fraser [Royaume-Uni] ; Mikko Vehkaper [Royaume-Uni] ; Yueheng Lan [République populaire de Chine] ; Jukka Corander [Finlande]Source :
- PLoS ONE [ 1932-6203 ] ; 2015.
Descripteurs français
- KwdFr :
- ADN bactérien (), ADN bactérien (génétique), ARN ribosomique 16S (génétique), Algorithmes, Analyse de regroupements, Analyse de séquence d'ADN, Bactéries (), Bactéries (génétique), Fèces (microbiologie), Humains, Internet, Microbiote (génétique), Métagénomique (), Reproductibilité des résultats, Réaction de polymérisation en chaîne.
- MESH :
English descriptors
- KwdEn :
- Algorithms, Bacteria (classification), Bacteria (genetics), Cluster Analysis, DNA, Bacterial (chemistry), DNA, Bacterial (genetics), Feces (microbiology), Humans, Internet, Metagenomics (methods), Microbiota (genetics), Polymerase Chain Reaction, RNA, Ribosomal, 16S (genetics), Reproducibility of Results, Sequence Analysis, DNA.
- MESH :
- chemical , chemistry : DNA, Bacterial.
- classification : Bacteria.
- genetics : Bacteria, DNA, Bacterial, Microbiota, RNA, Ribosomal, 16S.
- methods : Metagenomics.
- microbiology : Feces.
- Algorithms, Cluster Analysis, Humans, Internet, Polymerase Chain Reaction, Reproducibility of Results, Sequence Analysis, DNA.
Abstract
Estimation of bacterial community composition from high-throughput sequenced 16S rRNA gene amplicons is a key task in microbial ecology. Since the sequence data from each sample typically consist of a large number of reads and are adversely impacted by different levels of biological and technical noise, accurate analysis of such large datasets is challenging.
There has been a recent surge of interest in using compressed sensing inspired and convex-optimization based methods to solve the estimation problem for bacterial community composition. These methods typically rely on summarizing the sequence data by frequencies of low-order
An open source, platform-independent implementation of the method in the Julia programming language is freely available at
Url:
DOI: 10.1371/journal.pone.0140644
PubMed: 26496191
PubMed Central: 4619776
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PMC:4619776Le document en format XML
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term>
<term>Bacteria (classification)</term>
<term>Bacteria (genetics)</term>
<term>Cluster Analysis</term>
<term>DNA, Bacterial (chemistry)</term>
<term>DNA, Bacterial (genetics)</term>
<term>Feces (microbiology)</term>
<term>Humans</term>
<term>Internet</term>
<term>Metagenomics (methods)</term>
<term>Microbiota (genetics)</term>
<term>Polymerase Chain Reaction</term>
<term>RNA, Ribosomal, 16S (genetics)</term>
<term>Reproducibility of Results</term>
<term>Sequence Analysis, DNA</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>ADN bactérien ()</term>
<term>ADN bactérien (génétique)</term>
<term>ARN ribosomique 16S (génétique)</term>
<term>Algorithmes</term>
<term>Analyse de regroupements</term>
<term>Analyse de séquence d'ADN</term>
<term>Bactéries ()</term>
<term>Bactéries (génétique)</term>
<term>Fèces (microbiologie)</term>
<term>Humains</term>
<term>Internet</term>
<term>Microbiote (génétique)</term>
<term>Métagénomique ()</term>
<term>Reproductibilité des résultats</term>
<term>Réaction de polymérisation en chaîne</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA, Bacterial</term>
</keywords>
<keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Bacteria</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Bacteria</term>
<term>DNA, Bacterial</term>
<term>Microbiota</term>
<term>RNA, Ribosomal, 16S</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN bactérien</term>
<term>ARN ribosomique 16S</term>
<term>Bactéries</term>
<term>Microbiote</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Metagenomics</term>
</keywords>
<keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Fèces</term>
</keywords>
<keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Feces</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Algorithms</term>
<term>Cluster Analysis</term>
<term>Humans</term>
<term>Internet</term>
<term>Polymerase Chain Reaction</term>
<term>Reproducibility of Results</term>
<term>Sequence Analysis, DNA</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>ADN bactérien</term>
<term>Algorithmes</term>
<term>Analyse de regroupements</term>
<term>Analyse de séquence d'ADN</term>
<term>Bactéries</term>
<term>Humains</term>
<term>Internet</term>
<term>Métagénomique</term>
<term>Reproductibilité des résultats</term>
<term>Réaction de polymérisation en chaîne</term>
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<front><div type="abstract" xml:lang="en"><sec id="sec001"><title>Motivation</title>
<p>Estimation of bacterial community composition from high-throughput sequenced 16S rRNA gene amplicons is a key task in microbial ecology. Since the sequence data from each sample typically consist of a large number of reads and are adversely impacted by different levels of biological and technical noise, accurate analysis of such large datasets is challenging.</p>
</sec>
<sec id="sec002"><title>Results</title>
<p>There has been a recent surge of interest in using compressed sensing inspired and convex-optimization based methods to solve the estimation problem for bacterial community composition. These methods typically rely on summarizing the sequence data by frequencies of low-order <italic>k</italic>
-mers and matching this information statistically with a taxonomically structured database. Here we show that the accuracy of the resulting community composition estimates can be substantially improved by aggregating the reads from a sample with an unsupervised machine learning approach prior to the estimation phase. The <italic>aggregation of reads</italic>
is a <italic>pre-processing</italic>
approach where we use a standard K-means clustering algorithm that partitions a large set of reads into subsets with reasonable computational cost to provide several vectors of first order statistics instead of only single statistical summarization in terms of <italic>k</italic>
-mer frequencies. The output of the clustering is then processed further to obtain the final estimate for each sample. The resulting method is called Aggregation of Reads by K-means (ARK), and it is based on a statistical argument via mixture density formulation. ARK is found to improve the fidelity and robustness of several recently introduced methods, with only a modest increase in computational complexity.</p>
</sec>
<sec id="sec003"><title>Availability</title>
<p>An open source, platform-independent implementation of the method in the Julia programming language is freely available at <ext-link ext-link-type="uri" xlink:href="https://github.com/dkoslicki/ARK">https://github.com/dkoslicki/ARK</ext-link>
. A Matlab implementation is available at <ext-link ext-link-type="uri" xlink:href="http://www.ee.kth.se/ctsoftware">http://www.ee.kth.se/ctsoftware</ext-link>
.</p>
</sec>
</div>
</front>
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</author>
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</author>
<author><name sortKey="Tiedje, Jm" uniqKey="Tiedje J">JM Tiedje</name>
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<author><name sortKey="Wilm, A" uniqKey="Wilm A">A Wilm</name>
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<author><name sortKey="Lay, C" uniqKey="Lay C">C Lay</name>
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<biblStruct><analytic><author><name sortKey="Cheng, L" uniqKey="Cheng L">L Cheng</name>
</author>
<author><name sortKey="Walker, Aw" uniqKey="Walker A">AW Walker</name>
</author>
<author><name sortKey="Corander, J" uniqKey="Corander J">J Corander</name>
</author>
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</TEI>
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