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CONSTAX: a Tool for Improved Taxonomic Gdanetz et al. BMC Bioinformatics (2017) 18:538 DOI 10.1186/s12859-017-1952-x METHODOLOGY ARTICLE Open Access CONSTAX: a tool for improved taxonomic resolution of environmental fungal ITS sequences Kristi Gdanetz1†, Gian Maria Niccolò Benucci2*† , Natalie Vande Pol3 and Gregory Bonito2 Abstract Background: One of the most crucial steps in high-throughput sequence-based microbiome studies is the taxonomic assignment of sequences belonging to operational taxonomic units (OTUs). Without taxonomic classification, functional and biological information of microbial communities cannot be inferred or interpreted. The internal transcribed spacer (ITS) region of the ribosomal DNA is the conventional marker region for fungal community studies. While bioinformatics pipelines that cluster reads into OTUs have received much attention in the literature, less attention has been given to the taxonomic classification of these sequences, upon which biological inference is dependent. Results: Here we compare how three common fungal OTU taxonomic assignment tools (RDP Classifier, UTAX, and SINTAX) handle ITS fungal sequence data. The classification power, defined as the proportion of assigned OTUs at a given taxonomic rank, varied among the classifiers. Classifiers were generally consistent (assignment of the same taxonomy to a given OTU) across datasets and ranks; a small number of OTUs were assigned unique classifications across programs. We developed CONSTAX (CONSensus TAXonomy), a Python tool that compares taxonomic classifications of the three programs and merges them into an improved consensus taxonomy. This tool also produces summary classification outputs that are useful for downstream analyses. Conclusions: Our results demonstrate that independent taxonomy assignment tools classify unique members of the fungal community, and greater classification power is realized by generating consensus taxonomy of available classifiers with CONSTAX. Keywords: taxonomy classifiers, RDP, SINTAX, UPARSE, UNOISE, ITS, mycobiome, fungal microbiome Background been used to describe fungal communities [1] over the Next-generation sequencing technologies and high- past 25 years [2]. The ITS region, comprising the ITS1, performance computers define the culture-independent 5.8S, and ITS2 segments, was recently selected as the era of microbial ecology. High-throughput sequencing of formal DNA barcode for fungi [3–5], although there is DNA barcode marker regions, namely the bacterial 16S a lack of consensus regarding which ITS (ITS1 or ITS2) rRNA gene or fungal internal transcribed spacer (ITS) to utilize as a barcode [6–8]. It remains unclear which ribosomal regions, have allowed researchers to characterize of the ITS primer sets has the best resolution for fungal complex microbial communities at a depth not previously diversity, and papers targeting either ITS segment have possible with culture-based methods. Hypervariable regions been published at near equal frequencies [8–10]. of the 16S rRNA gene have been extensively studied and Pipelines for processing fungal ITS amplicon datasets adopted by researchers to describe prokaryotic microbial such as CLOTU [11], CloVR-ITS [12], PIPITS [1], and communities, and a mix of ribosomal markers have others [13] are available in the literature, but most of the tool-development effort has been towards generating * Correspondence: [email protected] nearly automated pipelines for filtering, trimming, and †Equal contributors 2 clustering of amplicon reads into operational taxonomic Department of Plant, Soil, & Microbial Sciences, Michigan State University, East Lansing, Michigan 48824, USA units (OTUs). Less emphasis has been placed on assigning Full list of author information is available at the end of the article taxonomy to representative OTU sequences in a dataset. © The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Gdanetz et al. BMC Bioinformatics (2017) 18:538 Page 2 of 9 Linnaean taxonomy provides a controlled vocabulary that organisms [22, 27, 28]. Since only a small fraction of mi- communicates ecological, biological or geographic infor- crobial species estimated to be on the planet have been mation. Linking OTUs to functionally meaningful names, described, taxonomic classification is not a trivial task and which typically depends upon species-level resolution, is no algorithm is 100% precise. Several types of classifica- key to addressing biological and ecological hypotheses. tion errors are possible, as highlighted in Table 1. The Processing sequencing reads, in addition to taxonomy RDPC, UTAX, and SINTAX classifiers report a confi- assignment of sequences, can be completed using vari- dence value for the classification given to an OTU so that ous bioinformatics pipeline tools. The most popular are the user can set a cutoff value below which no name is Mothur [14], QIIME [15], and USEARCH [16]. There given. Even though a number of databases and tools have are a variety of algorithms to use for the taxonomy as- been developed to enable high-throughput analyses of en- signment step, which include: BLAST [17], Ribosomal vironmental sequences, researchers still need to solve the Database Project (RDP) Naïve Bayesian Classifier [18], problems caused by misidentified or insufficiently identi- UTAX [19], and SINTAX [20]. The RDP Classifier fied sequences [5]. Further, some poorly sampled fungal (RDPC) uses Bayesian statistics to find 8-mers that have lineages reduce the ability of a classifier to confidently as- higher probability of belonging to a given genus. Based sign OTUs to the correct fungal lineage regardless of the on these conditions, RDPC estimates the probability that classification algorithm used. an unknown query DNA sequence belongs to the genus This study tested whether established taxonomic classi- [18]. The UTAX algorithm looks for k-mer words in com- fiers for fungal ITS DNA sequences generate similar pro- mon between a query sequence and a known reference se- files of the fungal community. Specifically, we compared quence, and calculates a score of word counts. The score the power (proportion of assigned OTUs at a given level) is used to estimate confidence values for each of the taxo- and consistency (agreement of OTU assignment across nomic levels, which are then trained on the reference classifiers) of the RDPC, UTAX, and SINTAX classifica- database to give an estimate of error rates [19]. The tion algorithms. Power and consistency were compared SINTAX algorithm predicts taxonomy by using k-mer across i) ITS1 or ITS2 regions, ii) OTU-clustering ap- similarity to identify the top hit in a reference database, proaches, and iii) merged or single stranded reads. Fur- and provides bootstrap confidence for all ranks in the ther, we created a Python tool that functions prediction [20]. Local alignment, most commonly im- independently of OTU-picking method to merge tax- plemented in BLAST [17], is still occasionally used for onomy assignments from multiple classifier programs into taxonomy assignment of high-throughput sequence an improved consensus taxonomy, and generates several datasets. However use of BLAST to identify OTUs in output files that can be used for subsequent community amplicon-based microbiome datasets has low accuracy analysis. as demonstrated previously [20–22], and discussed by Wang et al. [18]. Methods The UNITE reference database is a curated database Data accessibility of all International Nucleotide Sequence Database Col- Sample origins, barcode regions, and accession numbers laboration (INSDC) fungal sequences, and is the most for all datasets used in the current study can be found in commonly used reference database for fungal amplicon Table 2. Implementation of the tool presented in this paper analyses [23–25]. Recently the Ribosomal Database requires users to download and install the following Project released the Warcup Fungal Database [26], a software: RDPC [https://github.com/rdpstaff/classifier], curated version of UNITE and INSDC. Apart from pre- USEARCH version 8 for UTAX, and USEARCH version viously published database comparisons which showed 9 or later for SINTAX [http://drive5.com/usearch/down- the accuracy of UNITE [23] and Warcup fungal data- load.html], R v2.15.1 or later [https://www.r-project.org], bases [26], all comparative studies of taxonomy classifiers Python version 2.7 [https://www.python.org]. Detailed in- of which we are aware, have analyzed only prokaryotic stallation and analysis instructions, including all custom Table 1 Types of classifications Present in the database? Taxon name given? Correct name given? Result Error Type Yes Yes Yes Good assignment True positive Yes Yes No Misclassification False positive Yes No No Underclassification False negative No Yes No Overclassification False negative No No No Good assignment True negative Gdanetz et al. BMC Bioinformatics (2017) 18:538 Page 3 of 9 Table 2 Sample origins, barcode regions, and accession numbers for datasets Dataset Gene Region Read Type Sample
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