Abstract
BackgroundFor more than two decades microbiologists have used a highly conserved microbial gene as a phylogenetic marker for bacteria and archaea. The small-subunit ribosomal RNA gene, also known as 16 S rRNA, is encoded by ribosomal DNA, 16 S rDNA, and has provided a powerful comparative tool to microbial ecologists. Over time, the microbial ecology field has matured from small-scale studies in a select number of environments to massive collections of sequence data that are paired with dozens of corresponding collection variables. As the complexity of data and tool sets have grown, the need for flexible automation and maintenance of the core processes of 16 S rDNA sequence analysis has increased correspondingly.ResultsWe present WATERS, an integrated approach for 16 S rDNA analysis that bundles a suite of publicly available 16 S rDNA analysis software tools into a single software package. The "toolkit" includes sequence alignment, chimera removal, OTU determination, taxonomy assignment, phylogentic tree construction as well as a host of ecological analysis and visualization tools. WATERS employs a flexible, collection-oriented 'workflow' approach using the open-source Kepler system as a platform.ConclusionsBy packaging available software tools into a single automated workflow, WATERS simplifies 16 S rDNA analyses, especially for those without specialized bioinformatics, programming expertise. In addition, WATERS, like some of the newer comprehensive rRNA analysis tools, allows researchers to minimize the time dedicated to carrying out tedious informatics steps and to focus their attention instead on the biological interpretation of the results. One advantage of WATERS over other comprehensive tools is that the use of the Kepler workflow system facilitates result interpretation and reproducibility via a data provenance sub-system. Furthermore, new "actors" can be added to the workflow as desired and we see WATERS as an initial seed for a sizeable and growing repository of interoperable, easy-to-combine tools for asking increasingly complex microbial ecology questions.
Highlights
For more than two decades microbiologists have used a highly conserved microbial gene as a phylogenetic marker for bacteria and archaea
In the mid-1980 s, researchers began to sequence ribosomal RNAs from environmental samples in order to characterize the types of microbes present in those samples, (e.g., [9,10]). This general approach was revolutionized by the invention of the polymerase chain reaction (PCR), which made it relatively easy to clone and sequence rDNA in particular those for small-subunit ribosomal RNA
Researchers focused on the small subunit rRNA gene because of the ease with which it can be PCR amplified, and because it has variable and highly conserved regions, it is thought to be universally distributed among all living organisms, and it is useful for inferring phylogenetic relationships [14,15]
Summary
For more than two decades microbiologists have used a highly conserved microbial gene as a phylogenetic marker for bacteria and archaea. In the mid-1980 s, researchers began to sequence ribosomal RNAs from environmental samples in order to characterize the types of microbes present in those samples, (e.g., [9,10]) This general approach was revolutionized by the invention of the polymerase chain reaction (PCR), which made it relatively easy to clone and sequence rDNA (the genes for ribosomal RNA) in particular those for small-subunit ribosomal RNA (ss-rRNA). These studies revealed a large amount of previously undetected microbial diversity [1,11,12,13]. The general premise of these methods remains relatively unchanged from the initial experiments two decades ago and relies on straightforward molecular biology techniques and bioinformatics tools from ecology, evolutionary biology and DNA sequencing projects
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