Comparative Metagenomic Analysis of Human Gut Microbiome Composition Using Two Different Bioinformatic Pipelines. (25th February 2014)

• Record Type: Journal Article
• Authors: D'Argenio, Valeria; Casaburi, Giorgio; Precone, Vincenza; Salvatore, Francesco
• Other Names: Mahmood Qaisar Academic Editor.
• Is Part Of: BioMed research international. Volume 2014(2014)
• Publication Date: 2014-02-25
• Subjects: Medicine -- Periodicals; Biology -- Periodicals; Biotechnology -- Periodicals; Life sciences -- Periodicals; 610.5
• DOI: 10.1155/2014/325340
• Languages: English
• ISSNs: 2314-6133

Abstract

Abstract : Technological advances in next-generation sequencing-based approaches have greatly impacted the analysis of microbial community composition. In particular, 16S rRNA-based methods have been widely used to analyze the whole set of bacteria present in a target environment. As a consequence, several specific bioinformatic pipelines have been developed to manage these data. MetaGenome Rapid Annotation using Subsystem Technology (MG-RAST) and Quantitative Insights Into Microbial Ecology (QIIME) are two freely available tools for metagenomic analyses that have been used in a wide range of studies. Here, we report the comparative analysis of the same dataset with both QIIME and MG-RAST in order to evaluate their accuracy in taxonomic assignment and in diversity analysis. We found that taxonomic assignment was more accurate with QIIME which, at family level, assigned a significantly higher number of reads. Thus, QIIME generated a more accurate BIOM file, which in turn improved the diversity analysis output. Finally, although informatics skills are needed to install QIIME, it offers a wide range of metrics that are useful for downstream applications and, not less important, it is not dependent on server times.