Taxon Biosciences utilizes a variety of technologies to explore microbial diversity.  The general strategy is to perform deep diversity profiles of well selected sites.  Specific DNA sequences are then identified that correlate with any parameters of interest that characterize the sites such as low molecular weight gas, salinity, etc.  Rapid and quantitative assays for these indicator species are then developed for use in large area Bioindicator Surveys.

Sample Profiles

Taxon uses two complementary approaches to catalog microbial diversity from environmental samples.  The first strategy is a relatively high throughput method termed SARD (for Serial Analysis of Ribosomal DNA) while the second involves sequencing clones from 16S rRNA gene libraries.  This balance of strategies provides a high resolution compendium of the most abundant species as well as providing quantitative information on the microbial community members including low abundant genomes. 

SARD technology achieves high capacity sampling by virtue of the fact that only a short DNA sequence tag is identified.  The sequence tag is extracted from the V5 variable region of the 16S rRNA gene.  SARD sequence tags can be thought of as barcodes for specific taxa which can be quantitatively tracked among different samples.  While SARD sequence tags are short and are comprised of only 16 nucleotides (4 conserved and 12 variable residues), the potential information content of these tags are quite high (4¹², or 16,777,216 possible different sequences).

A further level of capacity is achieved through the concatenation of these SARD tags into long serial arrays prior to sequencing.  As a result, upwards of 40 tags can be identified in a single sequencing run.  Sample profiles consisting of about 10,000 SARD tags are routinely generated using Sanger dideoxy sequencing.  Recently, SARD concatemers were adapted to 454 Life Science's pyrosequencing technology.  This adaptation increased the number of tags identified per sample to 100,000-500,000 thereby considerably expanding the breadth of microbial surveys.

SARD is a patented technology developed by Taxon (U.S. Patent No. 6,613,520).

DNA Sequence Databases

Both 16S rRNA gene sequences and SARD tag sequences are compiled into databases.  The construction of these databases is an ongoing process as the technology is developed for new applications.  As of early 2007, Taxon’s Hydrocarbon-Associated Database contained about 22,000 16S rRNA gene clone sequences and over 2 million SARD tag sequences.

The utility of these databases is dependant upon several factors (1) the degree to which the samples are characterized by physical parameters allowing for increasingly complex correlations, (2) the size of the database providing high degrees of statistical significance, and (3) the strength of the analysis algorithms used for the data analysis.  The continued population of these databases as well as proprietary analysis algorithm development is an important aspect of Taxon’s technology.

Bioindicator Surveys

Genomic DNA sequences that correlate with desired parameters of various samples serve as the basis for high throughput quantitative assays.  This process involves developing quantitative PCR assays that utilize DNA sequence-specific probe set pairs.  These assays provide a cost effective means of conducting hundreds to thousands of assays with single molecule detection limits.

These Bioindicator Surveys are developed for different applications and generally consist of a number of probe sets used in combination.  For example, the current generation Hydrocarbon Bioindicator Survey consists of 9 probe sets.  The signals from the different probe sets are integrated to generate a final composite map

Copyright © 2008 Taxon Biosciences, Inc.