MAPPING MICROBIAL DIVERSITY

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 Our current project is located in a U.S. National Marine Sanctuary that is managed by NOAA. Critical ecological knowledge about the health of the sanctuary food web will inform conservation practices. An additional goal is to screen the vast resource of bacterial genomes to identify novel gene clusters that have a high potential to identify natural products to improve public health. We are generating unique DNA libraries that possess key genes coding for secondary metabolites, including antibiotics.  

We recently sampled sediment microbes along the Otago Shelf of South Island New Zealand. Sediment microbial diversity in this region may prove to be especially high. This opportunity allows further development of designated marine protected areas and the search for natural product potential. The Otago canyon offshore East Coast, South Island allows for sampling at various depths as shown in the sun-illuminated digital elevation photo in FAQs below. Depth range 100m (red) to 2000m (purple).  

 We have published articles in Scientific Reports and Marine Genomics that investigates the microbial biodiversity in the Stellwagen Bank National Marine Sanctuary (SBNMS).   Quantification of sequenced samples showed the strain Streptomyces scabrisporus NF3 to have high potential for secondary metabolites. These results enable preliminary identification of the SBNMS sites with the highest potential for harboring secondary metabolite biosynthetic gene clusters with respect to Streptomyces (NF3) genomics regions 

We have made progress with genomic and culture based methods to identify key strains of Streptomyces in our ocean sediment samples. We include undergraduate and graduate students in this endeavor, which has contributed to their success as scientists: https://www.youtube.com/watch?v=jGf-H0vVTVs

https://www.mdpi.com/2077-1312/12/11/2076

This work is ongoing so keep an eye on out for updates.

On the horizon we have an exciting project underway.  Strains isolated from marine bacteria with the highest concentration of secondary metabolites are being targeted, which contribute to the majority of bioactive compounds and yield non-ribosomal peptide synthases, a valuable drug source product [Owen et al. 2013]. MMI's strategy focuses on the identification of novel biosynthetic pathways of microorganisms living in the ocean environment to develop a drug discovery program. 

PIPELINE DEVELOPMENT. Computational analysis of biosynthetic gene clusters (BGCs).  

Owen et al. 2013. Mapping gene clusters within arrayed metagenomics libraries to expand the structural diversity of biomedically relevant natural products.   

    Ocean Facts  

Over 70% of the Earth’s surface is covered by the ocean and vast areas remain unexplored. This biodiverse environment is home to 34% of known phyla.  It is estimated that less than 1% of these microorganisms have been cultured and characterized in the laboratory. The remaining 99 % likely possess unique genetic diversity [2].  This new frontier has revealed a novel “unculturable world” in which community structure is more readily classified directly from environmental samples.  Enzymes isolated from marine microbes have a range of diverse biochemical functions and characteristics that have allowed microbial communities to adapt and thrive for millennia.  This genetic diversity translates to chemical diversity that harbor unique chemical compounds that may lead to natural product discovery.  Advancements in next generation sequencing have led to improved metagenomic techniques that significantly improve scientists' ability to delineate undiscovered microorganisms [3].  

2. PNAS. 110:11797-11802.[8] Allen E, Banfield JF. 2005. Community genomics in microbial ecology and evolution. Nature reviews Microbiology 3: 489-498. 

3. Zeyaullah M, Kamli MR, Islam B, Atif M, Benkhayal FA, Nehal M, Rizvi MA, Ali A. 2009. Metagenomics An advanced approach for noncultivable micro-organisms. Biotech Mol Biol Rev. 4(3):49-54.