ICBG Central Asia Project: Prokaryotic Microorganisms Associate Program (PMAP)
for more information send e-mail to icbg@aesop.rutgers.edu
The Prokaryotic Microorganisms Associate Program (PMAP) will investigate the untapped microbial diversity found in ecologically extreme habitats in Uzbekistan and Kyrgyzstan. The screening program of the PMAP will be structured so to promote economic opportunities and enhance research capacity in Uzbekistan and Kyrgyzstan via development of the infrastructure and knowledge base necessary to undertake bioprospecting and screening for development of therapeutic agents from microbial sources.
Bioprospecting will be carried out using two approaches. First, an Intensive Biodiversity Analysis (IBA) will be performed on samples obtained in Uzbekistan and Kyrgyzstan, from ecologically “extreme” habitats (i.e., extremes of pH, extremes of salinity, nutrient-poor habitats, habitats contaminated with xenobiotics from anthropogenic activities, etc.). The objective of the IBA approach is to screen for and isolate microbes that are abundant in the sample, but underrepresented in, or are absent from, extant culture collections. These individual microbial species or higher level taxa that have not been the subject of intensive investigation, because they are absent from or are underrepresented in extant microbial collections, represent potential sources of novel chemistry.
Genomic libraries will be constructed from uncultivated microorganisms from the ecologically “extreme” habitats in Uzbekistan and Kyrgyzstan. The objective of the IBA approach is to screen for and isolate the microbes determined by characterizating 16S rRNA target genes using Terminal Restriction Fragment Length Polymorphism (TRFLP) analysis. This rapid, simple approach will allow for the detection of those members that are abundant in the sample, but are underrepresented in, or are absent from, extant culture collections. The basic assumption of this approach is that there is much more biodiversity in natural habitats than that represented by culturable microorganisms from those environments and that the power of genomic science can be used to identify genes encoding potential new antimicrobials. For genomic library construction, these large-fragment DNA libraries constructed in a variety of vectors and analyzed for expression in several heterologous hosts will allow us to identify novel enzymatic activities and to isolate families of novel bioactive small molecules encoded by this environmental DNA. This is based on the premise that gene clusters needed for biosynthesis of novel metabolites can be cloned and expressed from nucleic acids obtained from environmental samples, even in the absence of the ability to cultivate a microorganism from the sample. The expected outcome from both bioprospecting approaches is the isolation of microbes and consortia (or genes cloned from the source environmental materials containing these microbes and consortia) with novel chemistries from which bioactive compounds can be elicited and extracted for evaluation in the pre-clinincal screening programs. It is anticipated that 1000 different CFU’s will be isolated using a variety of culturing media and 1000 large genomic fragments will be cloned per month. These microbial isolates/consortia or cloned fragments will then be screened for antimicrobial activity against a variety of model or pathogenic microorganisms.
PUBLICATIONS (IN .PDF FORMAT):
Boris Wawrik, Lee Kerkhof, Gerben J. Zylstra, and Jerome J. Kukor. 2005. Identification of Unique Type II Polyketide Synthase Genes in Soil. Appl. Environ. Microbiol. 71: 2232-2238.