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Nucleic Acids Res. 2013 Dec;41(22):e205. doi: 10.1093/nar/gkt1070. Epub 2013 Nov 7.

High-resolution microbial community reconstruction by integrating short reads from multiple 16S rRNA regions.

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Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel, Toyota Technological Institute at Chicago, Chicago, IL 60637, USA, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel, Microsoft Research, Cambridge, MA 02142, USA, FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA and Department of Mathematics and Computer Science, The Open University of Israel, Raanana 43537, Israel.


The emergence of massively parallel sequencing technology has revolutionized microbial profiling, allowing the unprecedented comparison of microbial diversity across time and space in a wide range of host-associated and environmental ecosystems. Although the high-throughput nature of such methods enables the detection of low-frequency bacteria, these advances come at the cost of sequencing read length, limiting the phylogenetic resolution possible by current methods. Here, we present a generic approach for integrating short reads from large genomic regions, thus enabling phylogenetic resolution far exceeding current methods. The approach is based on a mapping to a statistical model that is later solved as a constrained optimization problem. We demonstrate the utility of this method by analyzing human saliva and Drosophila samples, using Illumina single-end sequencing of a 750 bp amplicon of the 16S rRNA gene. Phylogenetic resolution is significantly extended while reducing the number of falsely detected bacteria, as compared with standard single-region Roche 454 Pyrosequencing. Our approach can be seamlessly applied to simultaneous sequencing of multiple genes providing a higher resolution view of the composition and activity of complex microbial communities.

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