Metaxa2 Diversity Tools: Easing microbial community analysis with Metaxa2
Institution:
1. Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, 413 46 Gothenburg, Sweden;2. Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Box 280, 171 77 Stockholm, Sweden;3. Leibniz-Institute of Freshwater Ecology and Inland Fisheries & Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Str. 6-8, 14195 Berlin, Germany;4. Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Gothenburg, Sweden;1. Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, 413 46 Gothenburg, Sweden;2. Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Box 280, 171 77 Stockholm, Sweden;3. Leibniz-Institute of Freshwater Ecology and Inland Fisheries & Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Str. 6-8, 14195 Berlin, Germany;4. Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Gothenburg, Sweden
Abstract:
DNA sequencing has become an integrated part of microbial ecology, and taxonomic marker genes such as the SSU and LSU rRNA are frequently used to assess community structure. One solution for taxonomic community analysis based on shotgun metagenomic data is the Metaxa2 software, which can extract and classify sequence fragments belonging to the rRNA genes. This paper describes the Metaxa2 Diversity Tools, a set of new open-source software programs that extends the capabilities of the Metaxa2 software. These tools allow for better handling of data from multiple samples, improved species classifications, rarefaction analysis accounting for unclassified entries, and determination of significant differences in community composition of different samples. We demonstrate the performance of the software tools on rRNA data extracted from different shotgun metagenomes, and find the tools to streamline and improve the assessments of community diversity, particularly for samples from environments for which few reference genomes are available. Finally, we establish that our resampling algorithm for determining community dissimilarity is robust to differences in coverage depth, suggesting that it forms a complement to multidimensional visualization approaches for finding differences between communities. The Metaxa2 Diversity Tools are included in recent versions (2.1 and later) of Metaxa2 (http://microbiology.se/software/metaxa2/) and facilitate implementation of Metaxa2 within software pipelines for taxonomic analysis of environmental communities.
