Laboratory Profile: The Institute for Microbial Biotechnology and Metagenomics Laboratory at the University of Western Cape

Laboratory Profile: The Institute for Microbial Biotechnology and Metagenomics Laboratory at the University of Western Cape

Description

The Institute for Microbial Biotechnology and Metagenomics (IMBM, http://imbm.co.za/) was established by the University of the Western Cape (UWC) in September 2007 and is based within the Department of Biotechnology. The Institute is led by the Director, Professor Marla Trindade. The Institute is recognised as one of the leading research units at UWC and considered a global competitor in microbial biotechnology and metagenomics, and as such hosts the prestigious DST/NRF SARChI research chair in Microbial Genomics.  In alignment with the UWC’s strategic decision to intensity its contribution to innovation and economic growth, the Institute became the first of its kind to create a position to drive the commercialisation of the numerous opportunities with commercial potential in the pipeline at the IMBM.  To this end Dr Anita Burger was appointed as Research and Innovation Manager in April 2016.  She focuses on the establishment of collaborative linkages with national and international industries to identify products/processes for further development and the commercialisation thereof.

The Institute’s research encompasses a number of disciplines including microbiology, (meta)genomics, molecular biology, enzymology, ecology, bioinformatics and analytical chemistry, and researchers employ and develop modern and leading-edge technologies. Through a number of international and national collaborations, and the expertise and know-how that the Institute has, the Institute has generated extensive collections of bacterial isolates which serve as a valuable source for the development of novel bio-products and processes for a number of industries. The largest collection contains over 3000 marine invertebrate-associated bacteria from the South African coast. The collection also includes over 300 thermophilic bacteria, 100 psychrotrophic bacteria and 100 actinomycetes, and a number of metagenomic libraries and environmental DNA preparations sampled from a number of extreme and indigenous South African environments. The genomes from these isolates or metagenomes are largely unexplored, and therefore harbour great potential for the discovery of novel compounds.  The Institute’s focus areas include enzymes for industrial use (the Institute has bacterial collections from a selection of harsh environments such as extreme temperatures, high salt, high metal), as well as high-value biochemicals (including functional polymers and biosurfactants), pharmaceutical/nutraceutical/cosmeceutical, food & beverage and agricultural products, as well as the use of engineered or natural whole-cell biocatalysts for a number of processes including remediation strategies for different wastewater streams such as from mines, wine cellars and olive plants.

The IMBM team comprises of a total of 14 academic, administrative and technical staff members and about 40 post-graduate students per year. The majority (75%) of the students are MSc and PhD students, with a minimum of five Hons and five postdoctoral students per year.

 

History of the Lab

The Institute originated from the Advanced Research Centre for Applied Microbiology (ARCAM) which was established by Professor Don Cowan in 2001. In 2007, the UWC approved the elevation of ARCAM to Institute status.  The Institute has a history of European Union(EU)-funded collaborations on the identification of novel microorganisms from extreme habitats, microbial molecular ecology of pristine and polluted South African environments, metagenomics gene discovery, genomics and genome analysis, bioprospecting for new bioresources, as well as an interest in microbial-based technologies for bioenergy and biofuels.

 

Equipment

The IMBM laboratory is located in the new, state-of-the-art, Life Science Building (LSB) at the University of the Western Cape. The laboratory has “well founded” status including equipment such as high performance liquid chromatography (HPLC), AKTA protein purification system, Cary 50 spectrophotometer, Q-Pix2 automated colony picker, Nanodrop spectrophotometer, Qubit DNA/RNA fluorometer, Beckman Avanti J-26 XPI centrifuge, 96-well plate reader, Biorad denaturing gradient electrophoresis system, Biorad CHEF gel electrophoresis system, Labconco freeze drier, Labconco vacuum drier, IKA rotary evaporator, four -80C freezers, a range of incubators, microfuges and -20C freezers as well as a wide range of small allied equipment. The IMBM laboratory also accommodates the Next Generation Sequencing Facility which is fully equipped with all the standard molecular biological equipment as well as the Illumina MiSeq benchtop sequencer, Roche GS Junior Benchtop sequencer, Roche LightCycler LC480 (96 well plate only), Anatech BioAnalyser for DNA and RNA quantification, Hydroshear for shearing nucleic acids, Beckman centrifuge, UV PCR cabinet, and an externally ventilated hood. The Institute provides a wide range of software and tools for the analysis of the various data generated, and collaborates closely with the South African National Bioinformatics Institute (SANBI) also based in the Life Science building for major bioinformatics and computational needs.

 

Safety equipment and protocols

General Lab Health and Safety protocols are followed. All researchers wear protective clothing at all times and goggles when working with hazardous chemicals. Researchers must work with hazardous chemicals in extraction hoods. There is a UV PCR cabinet for DNA work.

 

Usage

The laboratory is a PLS2 laboratory. Equipment is used for molecular biology, microbiology, biotechnology and allied research areas. There are no facilities within the Institute to work with mammalian cells.

Any collaborator or partner, whether national or international, is welcome to enquire about the use of the lab. In addition, training of researchers or technology developers can be considered on a case by case basis. Anyone wanting to use equipment will be trained on its proper use. Specific training is offered on the Q-Pix (colony picker), MiSeq, LC480.

 

Discoveries

It would be a long list of important discoveries that have been made in the laboratory. As one example, in 2013 a new research focus in marine biotechnology with a strategic focus on the development of marine microbe-derived drug compounds for the treatment of a number of diseases was established. This was triggered by the invitation to participate as the lead African partner in the EU-FP7 PharmaSea project which involves 24 international institutions (academic and pharmaceutical industry; represented by world-leading experts in the respective and multiple disciplines). The project is focused on the entire pipeline from microbial discovery through to development of natural products for preclinical evaluation, for the treatment of infection, inflammation, and central nervous diseases. In the laboratory’s specific contribution, both culture based approaches as well as cutting edge (meta)genomic strategies are employed to identify novel biosynthetic gene clusters and metabolites from bacterial symbionts associated with novel marine invertebrates endemic to South Africa. A collection of over 3300 bacterial isolates from the marine invertebrates has been established, several of which represent novel species & genera, and hundredsof these display a range of antimicrobial activity, including potent activity against known pathogens and multidrug resistant infectious agents (including Tuberculosis), as well as anti-inflammation and anti-neurological activities. A number of the activities associated with South African marine biodiversity have been identified as potential candidates, particularly for anti-inflammation development. Thus far the genomes of more than 10 of the biologically active isolates have been sequenced, and the novel genetic diversity in the secondary metabolite pathways alone is astounding. This provides confidence that these encode new compounds which have not previously been identified, and may represent novel drug leads for the treatment of a range of diseases. In addition to the ongoing bioassay screening against a wide panel of diseases, these sequenced organisms are being targeted for evaluation of their activities for treating anti-fungal anti-TB, and anti-drug resistant bacterial infections as well as anti-inflammation.

 

Contact details

Dr Anita Burger, Research and Innovation Manager, Email: alburger@uwc.ac.za, Tel +27 21 959 2083, Skype: anitaburgerbiosafety