Metagenomic Applications

The power of current sequencing platforms allows for multiple metagenomic applications, and more are being developed all the time.  RTLGenomics works to stay as relevant as we can be.  If you are looking for an application we do not list below, please contact us to ask if we can do it.

 

Microbial Diversity Analysis

The analysis of the microbiome using metagenomics has recently become one of the most important approaches for microbial identification and diversity studies. This is usually accomplished through PCR amplification followed by sequencing a portion of a phylogetically important genetic region (usually 16S ribosomal RNA gene for bacteria and ITS or 18S for fungi). The generated data are then compared to validated microbial sequencing databases. We have the capability to compare your results against databases curated in house for special applications, or against publicly accessible databases.
One of our specialties is the evaluation of microbial diversity using tagged or barcoded approaches. In fact, Research and Testing Laboratory pioneered many aspects of these approaches, as can be found in current literature. We have a wide variety of assays available, and are always ready to help develop custom assays.


environmental DNA (eDNA)

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eDNA is an excellent approach for non-invasive monitoring of species diversity.  This application allows for confirming the presence of rare or hard to quantify species, measuring general abundances, and tracking invasive species to name a few of its uses.  The use of DNA present in water or soil from sloughed cells does create some headaches for sample collection, but these are completely outweighed by the power of the analysis. Contact us for more information.


DIET ANALYSIS

Using an approach similar to eDNA, diet analysis looks for markers specific to prey or forage species in the feces or gut contents of consumers.  Because feces often has high levels of inhibitors, and the target DNA fragments are short, this technique can be tricky and requires special protocols for DNA extraction and amplification.  However, the molecular approach is a much more robust approach than the standard physical examination of fecal material or gut contents. This is because many prey and forage species are completely broken down in digestion leaving the hard to digest portions of other species as the sole component for physical examinations.  This ends up biasing results of dietary analyses toward these hard to digest species.  Contact us and let us help you build a less biased profile of what your organism of interest is consuming.  


MHC Analysis

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Major Histocompatibility Complex (MHC) is a multigene family part of the adaptive immune system.  MHC codes for cell surface proteins that function in the T-cell system.   Host-pathogen arms races and sexual selection have both been suggested as mechanisms for regulation and evolution of MHC.  Previous methods for sequencing MHC relied on cloning MHC amplicons and sequencing the clones.  Next Generation Sequencing methods have eliminated the need to clone samples before sequencing and allow for generation of many more reads per sample.  Contact us for more information on sequencing your MHC project.