Microbiome Analysis Platform
Advances in Next-Generation Sequencing technologies have transformed our capacity to investigate and understand the microbiome of several environments. For Dairy Sciences we now know that diverse microbial communities inhabit the bovine rumen, intestinal tract, and mammary gland – and that some of members of these communities are found in all three sites! At the Microbiome Analysis Platform, we have the expertise to help design your strategy, the technology to help characterize the bacterial composition of samples at high-throughput capacities, and the resources to preform “down-stream” experiments to help determine the biological relevance of the correlations you find.
Design your Approach
Designing your experimental approach to your microbiome study is the most difficult and critical part of your study. We can help! But first, we suggest reading the following articles:
Try to stay up-to-date by reading blogs and watching tutorials from leaders in the field!
Nucleic Acid Extraction Equipment
The QIAcube automates 12 parallel DNA extractions. Kits are available to extract DNA from milk, rumen, and fecal samples on this kit. It is a good choice for medium-throughput projects (i.e. 100-500 samples)
The QIAcube HT automates 96 parallel DNA extractions. Kits are available to extract DNA fecal samples on this kit. It is a good choice for high-throughput projects (i.e. >500 samples)
The Maxwell RSC automates 16 parallel DNA or RNA extraction and purification reactions, and kits are available extract DNA or RNA from a variety of sample types. Good for fecal samples or bacterial cultures for whole genome sequencing.
DNA Sequencing Equipment
The Illumina MiSeq provides high-coverage bi-directional short read sequencing up to 300bp. This technology is good for sequencing bacterial genomes and 16S rRNA targeted amplicon sequencing – or low diversity shot-gun metagenomics.
The Oxford Nanopore MinION provides affordable long-read sequencing which is excellent for closing bacterial genomes or for long-read metagenomics projects.
Culture-Dependent Microbiome Experiments
Microbial growth facilities
We have microbiological facilities for obtaining and maintaining isolates including incubators, anaerobic chambers, and biological safety cabinets.
The DasBox allows for simulation and manipulation of novel microbiome configurations, or in vitro challenge studies.