Feb 3, 2015

Metagenomic profiling of known and unknown microbes with microbeGPS

PloS One
Martin S Lindner, Bernhard Y Renard

Abstract

Microbial community profiling identifies and quantifies organisms in metagenomic sequencing data using either reference based or unsupervised approaches. However, current reference based profiling methods only report the presence and abundance of single reference genomes that are available in databases. Since only a small fraction of environmental genomes is represented in genomic databases, these approaches entail the risk of false identifications and often suggest a higher precision than justified by the data. Therefore, we developed MicrobeGPS, a novel metagenomic profiling approach that overcomes these limitations. MicrobeGPS is the first method that identifies microbiota in the sample and estimates their genomic distances to known reference genomes. With this strategy, MicrobeGPS identifies organisms down to the strain level and highlights possibly inaccurate identifications when the correct reference genome is missing. We demonstrate on three metagenomic datasets with different origin that our approach successfully avoids misleading interpretation of results and additionally provides more accurate results than current profiling methods. Our results indicate that MicrobeGPS can enable reference based taxonomic profiling of...Continue Reading

  • References28
  • Citations10

References

Mentioned in this Paper

Cerebellar Decompression Injury
Mycoplasma pneumoniae
Genome
Pathogenic Organism
Genomic Stability
Metagenome
Environment
Ncbi Taxonomy
Profile (Lab Procedure)
Metagenomics

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