PhyloTrac is an application for the visualization and analysis of PhyloChip microarrays. The PhyloChip is a popular 16S rRNA gene microarray for microbial surveys, and has been successfully used to study the microbial diversity of several interesting environments. However, its adoption has been limited by a lack of accessible analysis software. PhyloTrac fills this need and is the first desktop application providing end-to-end PhyloChip analysis. It standardizes the PhyloChip probe intensity and OTU classification scoring routines, and provides rich, interactive visualizations of the results through several integrated displays. PhyloTrac is freely available for non-commercial users and for all major computer desktop operating systems. The integration of a popular microarray platform with a dedicated analysis application provides a comprehensive and easy-to-use microbial survey toolkit.

Since it was first proposed as a universal phylogenetic marker of life on earth, sequence analysis of the small subunit ribosomal RNA (16S rRNA) gene has become the gold-standard for assessing the microbial diversity within environmental samples. This molecular nucleic acid-based approach provides the means to study microbes in their natural surroundings, typically by cloning and sequencing a few hundred 16S rRNA genes from the ~1 trillion generated from a PCR amplification. Although species richness may be roughly predicted by extrapolation of these very few observations, reproducible discovery of species composition may require >10000 sequencing reactions per sample (Dunbar 2002). As it is currently practiced, cloning and sequencing the 16S rRNA gene pool of environmental microbial communities is an essential but inefficient process, where the most abundant phylotypes or species mask less abundant but potentially significant members.

As an alternative approach to sampling by cloning 16S rRNA genes, hybridization of target sequences to an array of 16S rRNA probes, permits a much greater number of molecules to be sampled compared to the hundreds or thousands in a typical environmental clone library, and consequently leads to a more complete assessment of the diversity present. After a first generation prototype was validated (Wilson 2002, DeSantis 2006), Gary Andersen’s Laboratory at Lawrence Berkeley National Laboratory (LBNL) designed a second generation of the PhyloChip intended for widespread use (DeSantis 2007, Brodie 2007). Manufactured by Affymetrix the high-density oligonucleotide microarray containing 500,000 probes is a reliable tool for the comprehensive identification, detection and quantification of all known prokaryotic 16S rRNA gene sequences (Bacterial and Archeal). The PhyloChip targets the variation in the 16S rRNA gene of over 30,000 database sequences totaling almost 9,000 distinct taxonomic groups. These groups are assayed by a set of 11 or more pairs of perfectly matching and mismatching probes, making the PhyloChip highly sensitive and specific. The PhyloChip has been applied to a wide variety of environments including urban aerosols, uranium contaminated subsurface soil and water, and the human lung. In each case, it was demonstrated and validated to reveal a much broader diversity than typical 16S rRNA gene clone library. Because of its capability, low cost, and high-throughput processing, the technology is revolutionizing the field of microbial ecology and metagenomics by providing a broader picture of microbial diversity in a rapid and low-cost way.

PhyloTrac is freely available for academic users, and runs on Macintosh OS X Windows and Linux workstations.

Welcome to PhyloTrac