mPUMA: a computational approach to microbiota analysis by de novo assembly of operational taxonomic units based on protein-coding barcode sequences

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DOIResolve DOI: http://doi.org/10.1186/2049-2618-1-23
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TypeArticle
Journal titleMicrobiome
ISSN2049-2618
Volume1
Issue1
Article number23
Pages17
SubjectOperational taxonomic unit; Automated sequence analysis pipeline; 60 kDa chaperonin; Cpn 60; Microbial profiling; Microbiota; Microbiota analysis
AbstractBACKGROUND: Formation of operational taxonomic units (OTU) is a common approach to data aggregation in microbial ecology studies based on amplification and sequencing of individual gene targets. The de novo assembly of OTU sequences has been recently demonstrated as an alternative to widely used clustering methods, providing robust information from experimental data alone, without any reliance on an external reference database. RESULTS: Here we introduce mPUMA (microbial Profiling Using Metagenomic Assembly, http://mpuma.sourceforge.net), a software package for identification and analysis of protein-coding barcode sequence data. It was developed originally for Cpn 60 universal target sequences (also known as Gro EL or Hsp 60). Using an unattended process that is independent of external reference sequences, mPUMA forms OTUs by DNA sequence assembly and is capable of tracking OTU abundance. mPUMA processes microbial profiles both in terms of the direct DNA sequence as well as in the translated amino acid sequence for protein coding barcodes. By forming OTUs and calculating abundance through an assembly approach, mPUMA is capable of generating inputs for several popular microbiota analysis tools. Using SFF data from sequencing of a synthetic community of Cpn 60 sequences derived from the human vaginal microbiome, we demonstrate that mPUMA can faithfully reconstruct all expected OTU sequences and produce compositional profiles consistent with actual community structure. CONCLUSIONS: mPUMA enables analysis of microbial communities while empowering the discovery of novel organisms through OTU assembly.
Publication date
PublisherBioMed Central
LanguageEnglish
AffiliationAquatic and Crop Resource Development; National Research Council Canada
Peer reviewedYes
Identifier2049-2618-1-23
NPARC number23000568
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Record identifier955b5ec2-0dcb-40d9-bd9c-f420ff33cf75
Record created2016-08-02
Record modified2016-08-02
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