Comparative metagenomic analysis of human gut microbiome composition using two different bioinformatic pipelines.
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.
CEINGE-Biotecnologie Avanzate, Via G. Salvatore, 80145 Naples, Italy ; Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via S. Pansini, 80131 Naples, Italy.
Valeria
V
D'Argenio
CEINGE-Biotecnologie Avanzate, Via G. Salvatore, 80145 Naples, Italy ; Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via S. Pansini, 80131 Naples, Italy.
Giorgio
0000-0002-5980-8704
G
Casaburi
CEINGE-Biotecnologie Avanzate, Via G. Salvatore, 80145 Naples, Italy ; Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via S. Pansini, 80131 Naples, Italy.
Vincenza
V
Precone
CEINGE-Biotecnologie Avanzate, Via G. Salvatore, 80145 Naples, Italy ; Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via S. Pansini, 80131 Naples, Italy ; IRCCS-Fondazione SDN, Via Gianturco, 80143 Naples, Italy.
Francesco
0000-0002-2346-3564
F
Salvatore
D001419:Bacteria / Q000145:classification / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D041981:Gastrointestinal Tract / Q000382:microbiology; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D054892:Metagenome; D056186:Metagenomics; D064307:Microbiota / Q000235:genetics*; D012336:RNA, Ribosomal, 16S / Q000235:genetics
D012336:RNA, Ribosomal, 16S