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Metagenomics: The genomic analysis of assemblages of organisms.
 JoVE Environment

Unraveling the Unseen Players in the Ocean - A Field Guide to Water Chemistry and Marine Microbiology

1Department of Biology, San Diego State University, 2Scripps Institution of Oceanography, University of California San Diego


JoVE 52131

Here, we present a comprehensive protocol to assess the organic and inorganic nutrient availability and the abundance and structure of microbial and viral communities in remote marine environments.

 JoVE Immunology and Infection

Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics'

1Department of Microbial and Environmental Genomics, The J. Craig Venter Institute


JoVE 3899

Single Virus Genomics (SVG) is a method to isolate and amplify the genomes of single virons. Viral suspensions of a mixed assemblage are sorted using flow cytometry onto a microscope slide with discrete wells containing agarose, thereby capturing the virion and reducing genome shearing during downstream processing. Whole genome amplification is achieved using multiple displacement amplification (MDA) resulting in genomic material that is suitable for sequencing.

 JoVE Biology

Large Insert Environmental Genomic Library Production

1Department of Microbiology and Immunology, University of British Columbia - UBC


JoVE 1387

Construction of a fosmid library with environmental genomic DNA isolated from the vertical depth continuum of a seasonally hypoxic fjord is described. The resulting clone library is picked into 384-well plates and archived for downstream sequencing and functional screening by the application of an automated colony picking system.

 JoVE Biology

The Green Monster Process for the Generation of Yeast Strains Carrying Multiple Gene Deletions

1Department of Synthetic Biology and Bioenergy, J. Craig Venter Institute, 2Department of Microbial and Environmental Genomics, J. Craig Venter Institute, 3Donnelly Centre & Department of Molecular Genetics, University of Toronto, 4Lunenfeld Research Institute, Mt Sinai Hospital


JoVE 4072

The Green Monster method enables the rapid assembly of multiple deletions marked with a reporter gene encoding green fluorescent protein. This method is based on driving yeast strains through repeated cycles of sexual assortment of deletions and fluorescence-based enrichment of cells carrying more deletions.

 JoVE Biology

A High Throughput Screen for Biomining Cellulase Activity from Metagenomic Libraries

1Microbiology and Immunology, University of British Columbia - UBC


JoVE 2461

This protocol describes a high throughput screen for cellulolytic activity from a metagenomic library expressed in Escherichia coli. The screen is solution based and highly automated, and uses one-pot chemistry in 384 well microplates with the final readout as an absorbance measurement.

 JoVE Immunology and Infection

Separation of Single-stranded DNA, Double-stranded DNA and RNA from an Environmental Viral Community Using Hydroxyapatite Chromatography

1Department of Microbial and Environmental Genomics, The J. Craig Venter Institute, 2Department of Synthetic Biology and Bioenergy, The J. Craig Venter Institute


JoVE 3146

We describe an efficient method to separate single-stranded DNA, double-stranded DNA and RNA molecules from environmental viral communities. Nucleic acids are fractionated using hydroxyapatite chromatography with increasing concentrations of phosphate-containing buffers. This method permits the isolation of all viral nucleic acid types from environmental samples.

 JoVE Biology

Extraction of High Molecular Weight DNA from Microbial Mats

1Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina


JoVE 2887

We provide an improved protocol for extracting high molecular weight DNA from hypersaline microbial mats. Microbial cells are separated from the mat matrix prior to DNA extraction and purification. This enhances the concentrations, quality, and size of the DNA. The protocol may be used for other refractory samples.

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