Metagenomics is the study of the variation of species in a complex microbial sample. Using next generation sequencing it is possible to investigate microbial communities by sequencing the marker gene of choice (eg 16S) or sampled fragments of the whole genome or transcriptome without the need for culturing. Metagenomic sequence reads are typically generated on the Roche* 454 GS FLX* taking advantage of the long read lengths and deep sequencing capabilities.
- Discover new enzymes and ways to produce these
- Adventitious agents discovery
- Interaction of microbial communities with the host
- Viral quasi-species typing
- Diversity of species
- Discover non-culturable microbes
Microbial 16S Metagenomics
16S metagenomics can be used to investigate microbial communities by deep sequencing the marker gene of choice, the 16S. Depending on the application area, amplicons encompassing several variable regions of the 16S gene can be sequenced on the Roche 454 platform with FLX read lengths. This will generate clonal sequences allowing taxonomic identification down to the genus level.
A modular service is provided, typically comprising sequencing adapter ligation, sequencing and downstream bioinformatics. Services can be provided starting with DNA extraction for all substrates of human origin. Results are delivered in tabular form and also in ready-to-use format for analysis projects using the popular MEGAN classifier.
Metagenomics can be used to investigate genomics of relatively abundant microbes by sequencing sampled fragments of the whole genome or transcriptome. For a whole genome approach, the use of fosmid libraries is recommended to optimize assembly of large amounts of genomic content. The fosmids are sequenced in a pooled fashion with a Roche 454 3 kb mate-pair library to enable the original constructs to be separated out during assembly. For whole transcriptome sequencing, total RNA is used to synthesize non-polyA cDNA through random priming for sequencing on the Roche 454.
A variety of data analysis services are available depending on your requirements. Custom reports can be generated as well as result presentation and training with our scientists.
Data options include:
- Clustering data
- BlastN against a curated version of the RDP database
- Classification data
- Differential analysis
- Taxonomic assignment
Results are delivered via a secure FTP site or are shipped on a portable hard drive depending upon the size of the dataset.
Take The Next Step
To discuss your next project and receive a custom quote or to receive further information on the metagenomic sequencing service, please contact Beckman Coulter Genomics.
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