DNA Analysis and Characterization

 

EBPI Analytics is proud to offer microbial community characterization through our industrial partners. CENSUS (qPCR), Quantarray and Next Generation Sequencing (NGS) analysis are all available to provide profiles of microbial communities used to identify individual species of microbes present. These technologies are quite valuable for site managers and engineers to cost-effectively detect and quantify microbes responsible for damaging corrosion processes, targeted members of the microbial community deemed critical for bioremediation or track the source of unwanted bacterial contamination. 

• Evaluate the feasibility of natural attenuation measures for environmental contamination
• Analyze efficacy of enhanced bioremediation and determine if bioaugmentation is necessary
• Identify elevated levels of organisms responsible for specific contaminant breakdown (Chlorinated organics, BTEX, PAHs) to identify sensitive spill sites and monitor bioremediation
• Look for elevated levels of organisms responsible for corrosion in natural ressource infrastructure, predict early structural failures and promote proactive replacement strategies

 

CENSUS (qPCR)

CENSUS is based on a revolutionary molecular biological tool (MBT) called quantitative polymerase chain reaction (qPCR) whereby many copies of a specific gene are generated. As each gene copy is made, a fluorescent marker is released, measured, and used to quantify the number of target genes present in the sample. The gene copied during the process (target) is determined by short segments of DNA called “primers” which are added to the reaction mixture. In essence, qPCR is like a copy machine with a counter. The “primers” select which pages (target) of the book (DNA) are copied and the counter keeps a running total of how many pages were copied (number of target genes in the sample).

CENSUS Advantages

• Accurate — DNA is extracted directly from the sample eliminating the need to grow the bacteria thus circumventing biases associated with more traditional based approaches like plate counts.
• Specific — Target either the specific bacterial group (e.g. Dehalococcoides) or a specific gene encoding a desired function (e.g. reductive dechlorination).
• Rapid — Results are available within days (7–10 standard TAT) with rush service available.
• Sensitivity — Practical Detection Limits (PDL) as low as 100 cells per sample with a dynamic range over seven orders of magnitude.
• Flexibility — Analysis can be performed on a variety of sample types including water, soil, sediment, Bio-Traps®, and others.  
• Broad Applicability — CENSUS assays targeting a broad range of organisms and microbial functions.

 

QUANTARRAY

The QuantArray is a hybrid technology combining the highly parallel detection of DNA microarrays with the accurate and precise quantification of qPCR into a single platform.  The key to the approach is nanoliter fluidics for low volume, solution phase qPCR allowing simultaneous quantification of different gene targets and therefore more comprehensive site assessment.In many other respects, the QuantArray is the same as conventional qPCR with probes so you can expect the same level of accuracy and precision.  qPCR is a process whereby many copies of a specific gene are generated.  The gene copied during the process (target gene) is determined by short segments of DNA called “primers” and a “probe”.  As each gene copy is made, a fluorescent marker is released from the probe, measured and used to quantify the number of target genes present in the sample.Other methods like multiplex qPCR have been described that achieve some level of parallel quantification.  There is a fundamental difference between the QuantArray and multiplex qPCR however.  For multiplex qPCR, multiple primer sets are added to a reaction mixture to quantify multiple gene targets.  Unlike multiplex qPCR, the QuantArray employs discrete through-holes for individual qPCR reactions ensuring that reaction kinetics are not compromised.

 

NEXT GENERATION SEQUENCING (NGS)

While each NGS platform is unique, the overall steps and the underlying concepts are similar.  DNA is extracted from the sample and fragmented into a library of small segments that are amplified and subsequently sequenced in millions of parallel reactions.  The sequencing step is similar to previous methods – the bases of each DNA fragment are sequentially identified from light signals emitted as the complement to each fragment strand is re-synthesized.  The net result is a set of newly identified strings of nucleotides called “reads” that represent members of the microbial community present in the original sample.