Scientist (Microbiologist/Biotechnologist)


Dr. Soumya Ghosh, PDF (Thompson Rivers University-Canada), Ph.D (Stellenbosch University-South Africa), Department of Biological Sciences, Faculty of Sciences, Thompson Rivers University, Kamloops, British Columbia, Canada. (India Contact) +91-706-3038772 Email:


Microbial ecology studies is my research area, which encompasses microbial diversity, interaction and population dynamics. I have worked in universities in Germany, Netherlands, South Africa, India and recently completed my  postdoctoral work at Thompson Rivers University, Canada. My research publications have 397 citations ( and I am keen to work on the microbial metagenomics of different matrixes encompassing both the taxonomical and functional profiling (bioprospecting of enzymes, antibiotics).

During my postdoctoral tenure in the laboratory of Prof. Naowarat Cheeptham at the Biology faculty at Thompson Rivers University, Kamloops, Canada since 15th April, 2016. I was working on a project to identify the biological control agents against White Nose Syndromes of bats. WNS syndrome is an invasive bat disease caused by Pseudogymnoascus destructans (Pd). The study involved successful isolation/purification followed by screening of cultivated microbiome (natural environment/caves/bat swabs) and natural products for anti-Pd activities. Presently, we have several microbial positive candidates as well as natural products. Apart from my original research project on WNS. To be highlighted, apart from my principle postdoctoral project at Thompson Rivers University, Canada, I was also engaged in a number of other projects. Among them one of my significant contributions was in the Canadian Professional Meat Cutting – A textbook for Industry Practitioners and those interested in a career in The Meat Industry where I typically isolated the meat borne pathogens from spoilt meat. I am also involved in a number other projects. The projects involved, cave microbial diversity studies (16S-/ITS-based molecular identification), screening of cave microbiome against multidrug resistance strains and testing them for biomineralization as a way to explain the underlying mechanism involved in speleogenesis in caves. During my postdoctoral studies, up till now, I have published 3 research articles: 1 review article in Biochemical Pharmacology, 3 research articles in Diversity, Antibiotics and Journal of Experimental Microbiology and Immunology. Additionally, 2 research articles are recently been submitted and under review to Frontiers in Microbiology and Journal of Microbiological Methods. My postdoctoral supervisor and I were also intensely engaged in writing grant applications. During this period of 1 year we have applied to Bat Conservation Internal Small Grants Program (BCI-SGP), Human Frontier Science Programme-Long Term Fellowships (HSFP-LTF), Banting Postdoctoral Fellowship, Natural Sciences and Engineering Research Council of Canada- Research Tools and Instruments Grants Programme (NSERC-RTI), NSERC- Discovery Grants, United States Fish Wildlife Service (USFWS)- Small grants and lastly the USFWS- Bats for the Future Fund (BFF). In the last year we have received the grant from UFWS-BFF. Simultaneously, I have also co-supervised 2 honors, 3 directed studies and 7 research volunteers’ students for their thesis preparation during this period (2016-2017). These students were thoroughly involved in all my research studies that involved learning of molecular microbiological techniques relevant for microbial ecology studies and bioprospecting of novel genes possessing antimicrobial activities.

After coming back to India, I was immediately engaged as a visiting faculty at a college in Rajasthan where I was dealing with the courses in Microbiology. Presently, I am still collaborating with my postdoctoral lab in Canada, writing my postdoctoral articles and concurrently giving online courses in Microbiology, Biochemistry, Microbial biotechnology to the undergraduate (B.Sc.) and post graduate (M.Sc.) students in India.


Professional engagements


Visiting faculty             (10.08.2017  –    30.03.2018); Kuchaman College, Kuchaman City (Nagaur),

Rajasthan, India.


Post-doctoral               (15.04.2016 – 02.08.2017); Laboratory of Dr. Naowarat (Ann) Cheeptham at Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, British Columbia, Canada. (Funded by US Fisheries and Wildlife Service)


Ph.D.                           (09.03.2011 – 05.03.2015) specialized in Biotechnology/Wine Biotechnology, Institute for Wine Biotechnology, Stellenbosch University, South Africa.


Research Fellow         (01.08.2008-15.6.2010) Department of Systems Biology, Technical University Munich, Munich, Germany.


Research Fellow         (01.11.2005-31.07.2008) Center for Plant Molecular Biology (ZMBP), Eberhard Karls University of Tübingen, Tübingen, Germany.


Research Fellow         (01.01.2005-30.10.2005) Biological Center, University of Groningen, Groningen, The Netherlands.


Project Assistant         (13.11.2003-31.12.2004) Institute of Microbial Technology (Council of Scientific and Industrial Research), Chandigarh, India.


Senior Research         (01.07.2003-30.09.2003) Post Graduate Institute of Medical Education and

Fellow                         Research, Chandigarh, India.


Junior Research          (30.04.2001-30.04.2003) Department of Environmental Sciences, University of

Fellow                         Pune, (Presently renamed as Savitribai Phule Pune University), Pune, India.





Ph.D.                            (09.03.2011 – 05.03.2015) specialized in Biotechnology/Wine Biotechnology, Institute for Wine Biotechnology, Stellenbosch University, South Africa. The Ph.D. thesis submitted on 12th December, 2014, PhD thesis defended on 2nd February, 2015 and PhD awarded on 5th March, 2015. Title: Metagenomic screening of cell wall hydrolases, their anti-fungal activities and potential role in wine fermentation.


Biologie-                      (01.11.2005-29.09.2006), Department of Developmental Genetics, Center for Plant

Diplomarbeit               Molecular Biology (ZMBP) Eberhard Karls University of Tübingen, Germany (Grade: gut 2,0/good 2.0).


Certificate course in    (25th May, 2005) Cursus Stralingsbescherming getuigschrift,

Radiation                      Groningen University, The Netherlands.


Certificate                     (12th June, 2006) Certificate for the knowledge of imparting and guiding into workplace in Radiation protection, Eberhard Karls University of Tübingen, Germany.


M.Sc. Zoology             (10.06.99-15.05.01) in Developmental biology, Department of Zoology,

University of Pune (Presently renamed as Savitribai Phule Pune University),                                  Pune, India (Percentage: 62.7%; Grade: First class).


B.Sc. Microbiology      (15.05.1996-28.06.99) in Microbiology, Department of Microbiology, University

of Pune (Presently renamed as Savitribai Phule Pune University), Pune, India (Percentage: 60.31%; Grade: First class).



Publications: (Total number of Citations as per Google scholar is 397)


Published in Peer reviewed journals: 7; Submitted and under revision: 2; In preparation: 3; Conference proceedings: 6; Scientific manual: 1; Review of article: 1; Posters: 12


Peer Reviewed Journals:


Björn C.Willige, Soumya Ghosh, Carola Nill, Melina Zourelidou, Esther M.N. Dohmann, Andreas Maier,Claus Schwechheimer; The DELLA Domain of GA INSENSITIVE Meditates the Interaction with the GA INSENSITIVE DWARFIA Gibberellin Receptor of Arabidopsis; The Plant Cell, Vol. 19:4, 1209-1220, April 2007 (IF: 8.688); Citations: 384


Soumya Ghosh, Bahareh Bagheri, Horatio Herbert Morgan, Benoit Divol and Mathabatha Evodia Setati; Assessment of wine microbial diversity using ARISA and cultivation-based techniques; Annals of Microbiology, Vol. 65:4, 1833-1840, January 2015 (IF: 1.122); Citations: 6


Soumya Ghosh, Nomeda Kuisiene, Naowarat Cheeptham; Cave microbiomes for drug discovery: reality or pipe dream?; Biochemical Pharmacology, Vol. 134, 18-34, June 2017 (DOI: 10.1016/j.bcp.2016.11.018 (Special issue: Antibiotics-Meeting the Challenges of 21st Century Health Care Part II) Invited manuscript (IF: 5.009) Citations: 4


Soumya Ghosh; Metagenomic screening of cell wall hydrolases, their anti-fungal activities and potential role in wine fermentation, SUNScholar Research Repository, Stellenbosch University, 2015-04; Citation: 1


Robyn L McArthur, Soumya Ghosh and Naowarat Cheeptham; Improvement of protocols for the screening of biological control agents against white-nose syndrome; The Journal of Experimental Microbiology and Immunology+ ; Vol. 2, 1-7, June 2017; Citations: 2


Soumya Ghosh, Robyn McArthur, Zhi Chao Guo, Rory McKerchar, Kingsley Donkor, Naowarat Cheeptham; Evidence for anti-Pseudogymnoascus destructans (Pd) activity of propolis; Antibiotics Vol. 7 (2), 1-12, December 2017; doi:10.3390/antibiotics7010002 (Special Issue “Top 35 of Antibiotics Travel Awards 2017”) Invited manuscript (Cite Score 2016 (Scopus): 1.65)


Soumya Ghosh, Elise Paine, Rob Wall, Gabrielle Kam, Tanna Lauriente, Pet-Chompoo Sangarmangkang, Derrick Horne, Naowarat Cheeptham; In situ cultured bacterial diversity from the Iron Curtain Cave, Chilliwack, British Columbia, Canada; Diversity Vol. 9(3), 36; August, 2017 (DOI:10.3390/d9030036) (Special issue “Microbial Diversity in Caves”) Invited manuscript  (Cite Score 2016 (Scopus): 2.03)®ion=stream&module=stream_unit&version=latest&contentPlacement=1&pgtype=sectionfront


Soumya Ghosh, Emma Persad, Tin Yung Shiue, Cindy Lam, Lauren G. Mascibroda, Michael B. Sherman, Thomas Smith, Naowarat Cheeptham; Isolation and Characterization of a Microviridae G4 Bacteriophage against Multi-Drug Resistant Escherichia coli 15-318; Journal of Microbiological Methods (IF: 1.790) (Submitted and under revision)


Jessica Thandara Gosse, Soumya Ghosh, Christopher Boddy and Naowarat Cheeptham; Whole genome sequencing and metabolomics study of Streptomyces species, ICC1 and ICC4, identified from the Iron Curtain Cave, Chilliwack, British Columbia, Canada; Frontiers in Microbiology (IF: 4.076) (Submitted and under revision)


Soumya Ghosh, Benoit Divol and Mathabatha Evodia Setati; Whole metagenomic shotgun sequencing of grape must biome (manuscript in preparation intended to be submitted in Frontiers in Microbiology; IF: 4.076)


Soumya Ghosh, Benoit Divol and Mathabatha Evodia Setati; Phenotypic and genetic screening for extracellular hydrolytic enzymes and antifungal activity in selected non-Saccharomyces wine yeasts (manuscript in preparation and intended to be submitted in Applied Environmental Microbiology; IF: 3.807)


Contribution in manual(s):


Dr. Soumya Ghosh, Timothy Crowe and Kamal Grewal-Choudhury

Canadian Professional Meat Cutting – A textbook for Industry Practitioners and those interested in a career in The Meat Industry.  Chapter 2: Professionalism. Pages 30, 63-66.

Meat is one of the highest nutritious sources for food borne diseases/illness. This chapter specifically focused on the food related illness caused due to poor sanitation and food hygiene and the pathogens that are common to the meat industry. I was specifically involved in purifying the meat pathogens such as Salmonella spp., Clostridium spp., Staphylococcus spp., Listeria monocytogenes and Candida albicans (Yeast) from spoilt meat and imaging them for this text book.



Naowarat Cheeptham, Soumya Ghosh, Robyn McArthur, Cori Lausen; Anti-Pd activity: Can environmental microorganisms be used against Pseudogymnoascus destructans, the causative agent of white nose syndrome?  Invasive Species Research Conference, 20th -22nd June, 2017, TRU, Kamloops, British Columbia, Canada


Evodia Setati, Bahar Bagheri, Soumya Ghosh, Benoit Divol, Florian Bauer; Taxonomic and functional diversity of the grape must ecosystem; Second International Conference on Metagenomics, 2nd June – 5th June, 2013, Pretoria, South Africa


Ursula Andong, Soumya Ghosh, Evodia Setati, Dan Jacobson, Florian Bauer; Structural diversity of yeast associated with grapes in biodynamically and conventionally managed vineyards; South African Society for Microbiology, Conference programme, 6th -9th November, 2011, Cape Town, South Africa


Soumya Ghosh, Björn Willige, Carola Nill, Melina Zourelidou, Esther Dohmann, Andreas Maier, Claus Schwechheimer; Interaction of the Arabidopsis GA receptor GID1a with the growth repressor GAI; 3rd Tri-National Arabidopsis Meeting, 26th -29th September, 2006, Tubingen, Germany
Claus Schwechheimer, Björn Willige, Soumya Ghosh, Carola Nill, Melina Zourelidou,Esther Dohmann, Andreas Maier , Erika Isono, Katja Schwager; Regulated development by regulated proteolysis; 3rd Tri-National Arabidopsis Meeting, 26th -29th September, 2006, Tübingen, Germany


Nandakumar K, Soumya Ghosh, Apte A.A, Bhavasar SN, Bodhankar SL, Gore M, Jagdale R, Ghole VS; Simmulatory study for the maintenance of efficacy and satiety in the laboratory animals; 55th Indian Pharmaceutical Congress, 19-21st December, 2003, Chennai, India




Soumya Ghosh, Robyn McArthur, Naowarat Cheeptham; Bacteria isolated from Bush Lake and Timber Lake, British Columbia, Canada exhibit antagonistic activities against Pseudogymnoascus destructans, the causative agent of white-nose syndrome; 17th International Congress of Speleology (17th ICS), Speleo 2017, 23rd July – 29th July, 2017, Sydney, Australia (Extended Abstract published)


Soumya Ghosh, Elise Paine, Rob Wall, Gabrielle Kam, Tanna Lauriente, Pet-Chompoo Sangarmangkang, Derrick Horne, Naowarat Cheeptham; Cultivable bacterial diversity from Iron Curtain Cave in Canada; 17th International Congress of Speleology (17th ICS), Speleo 2017, 23rd – 29th July, 2017, Sydney, Australia (Extended Abstract published)


Aaron Wong, Soumya Ghosh, Naowarat Cheeptham, Karen J. Vanderwolf; Screening of New Brunswick Subterranean Microorganisms for Antimicrobial Activity against MDR strains and anti-Pd activity; CSM conference, 20th -23rd June, 2017, Waterloo, Ontario, Canada


Vincent Yu, Soumya Ghosh, Kirk Safford, Naowarat Cheeptham; Screening of cave microorganisms isolated from White Rabbit Cave and   a newly discovered cave “Over The Hill” for antimicrobial activity; Canadian Society of Microbiologists Annual Conference, 20th -23rd June, 2017, University of Waterloo, Waterloo, Ontario, Canada


Robyn McArthur, Soumya Ghosh, Cori Lausen, and Naowarat Cheeptham; Inhibition of Pseudogymnoascus destructans, the causative agent of white-nose syndrome, by environmental microorganisms; Canadian Society of Microbiologists Annual Conference, 20th -23rd June, 2017, University of Waterloo, Waterloo, Ontario, Canada


Soumya Ghosh, Robyn McArthur, Sierra Grand, Wadiah Mubarak, Gabrielle Kam, Tanna Lauriente, Aaron

Wong, Cori Lausen and Naowarat Cheeptham; Examining potential biological controls exhibiting anti-Pd activity: bee propolis, viral proteins, and microorganisms from caves and other environments, mistletoe and bat wings.White Nose Syndrome Workshop, 2017, 23rd -25th May, 2017, Nashville, Tennessee, USA


Soumya Ghosh, Evodia Setati, Benoit Divol; Using metagenomics to explore the functional potential of the wine microbiome; 18th Biennial Conference of the South African Society of Microbiology (SASM), 24th – 27th November, 2013, Bela Bela, South Africa


Soumya Ghosh, Ursula-Claire Andong, Benoit Divol and Evodia Setati; Construction of a wine metagenomic library from fermenting wine must; 23rd – 30th October, 2011, EMBL school for Metagenomics, Ruprecht – Karls – Universität Heidelberg, Heidelberg, Germany


Rene Richter, Björn Willige, Soumya Ghosh, Carola Nill, Melina Zourelidou, Esther Dohmann, Andreas Maier, Claus Schwechheimer; Functional analysis of GA regulated genes; September, 2008, 5th Tri-National Arabidopsis Meeting, Zürich, Switzerland


Björn Willige, Soumya Ghosh, Carola Nill, Melina Zourelidou, Esther Dohmann, Andreas Maier, Claus Schwechheimer; The DELLA domain of GAI is sufficient for the interaction with the GA receptor; 4th Tri-National Arabidopsis Meeting, 12th- 15th September, 2007, Vienna, Austria


Melina Zourelidou, Andreas Maier, Esther Dohmann, Soumya Ghosh, Hanbing Li, Carola Kuhnle and Claus Schwechheimer; A GAI-interacting protein kinase regulates plant growth and development; Keystone meeting, 9th-11th July, 2006, Silverthorne, USA


Soumya Ghosh, Till Roeneberg, Martha Merrow; Light reception in Neurospora crassa – A second novel input pathway; The 14th European Ph.D. school for Chronobiology, 5th -10th, 2005, Groningen, The Netherlands


Review of article(s):


Isolation and Identification of Sediment derived Actinomycetes through Molecular Characterization of 16s rRNA Technique (International Journal of Biology, Add: 1120 Finch Avenue West, Suite 701-309, Toronto, ON., M3J 3H7, Canada;


Supervision experiences at Thompson Rivers University, Kamloops, BC, Canada


Co-supervision of undergraduate students:


Summer undergraduate research trainees (May, 2017)

Monique Nijer (Third year Biology, University of British Columbia, Okanagan, Canada)

Brandon Hayashi (Third Year Biology, Thompson Rivers University, Kamloops, BC, Canada)

Julianna Bissonnette (Third Year Biology, Thompson Rivers University, Kamloops, BC, Canada


Winter undergraduate research trainees (January, 2017)

Sierra Grand (Third Year Biology, University of Victoria, Victoria, BC, Canada

Wadiah Mubarak (Third Year Biology, Thompson Rivers University, Kamloops, BC, Canada

(This project is in collaboration with Prof. Christopher Boddy from University of Ottawa, Canada; Manuscript in preparation)




Summer Directed studies students (May, 2017)

Gabriella Kam UREAP fellow (Fourth Year Biology, Thompson Rivers University, Kamloops, BC, Canada)

Richenda McFarland UREAP fellow (Fourth Year Biology, Thompson Rivers University, Kamloops, BC, Canada)


Summer undergraduate research trainees (April, 2016-2017)


Pet-Chompoo Sangarmangkang, Summer undergraduate research trainee

9.05.2016 – 10.06.2016 4th year Undergraduate student (Biology Science Department, University of British Columbia, Vancouver, BC, Canada)

Tanna Lauriente, Summer undergraduate research trainee

(9.05.2016 – 29.07.2016) 2nd year Undergraduate student (Department of Biological Sciences, Thompson Rivers University, Kamloops, BC, Canada)

Gabriella Kam, Summer undergraduate research trainee

(17.05.2016 – 29.07.2016) 2nd year Undergraduate student (Department of Biological Sciences, Thompson Rivers University, Kamloops, BC, Canada)

(The manuscript has been published in Diversity. The further studies of this project are recently being completed in collaboration with Prof. Christopher Boddy from University of Ottawa, Canada; Manuscript submitted and under revision in Frontiers in Microbiology)


During this tenure they were involved in conducting screening of limestone cave bacteria isolated from Iron Curtain Cave, Chilliwack BC for their antimicrobial activities. Seventy-one bacterial isolates were grown at 3 different temperatures (8°C, 15°C, 25°C), at respective culture media (R2A, Actinomyces HiVeg™ Broth, Hickey-Tresner (HT) and V8 original)  and tested against Pseudogymnascus destructans (Pd), the causative fungal agent for White Nose Syndrome.  Simultaneously, these isolates were also screened against various multidrug resistant bacterial strains such E. coli 15-318, E. coli 15-124 and E. coli 15-102 along with E. coli normal strains. Staphylococcus aureus, S. aureus MRSA43300, Pseudomonas aeruginosa, Serratia marcescens and Candida albicans were also used as test strains. We have successfully isolated two bacterial isolates that have shown antimicrobial activities. The # 4 (as designated bacterial strain) exhibited against MDR strains of E. coli 15-124, 15-102, 15-318, pathogenic strain of Pseudomonas along with non-resistant strain of Staphylococcus aureus and E. coli. Conversely, the #1 has showed antimicrobial activities against E. coli 15-102 and 15-124 bacterial strains only. Notably, all the antimicrobial activities were only observed when the isolates were grown at 8°C in V8 and HT media (for #4) and R2A media (for  #1). In order to identify the origin of the antimicrobial activities of the potential bacterial candidates the supernatant of these cultured bacteria were heat-treated and tested for their antimicrobial potential in comparison to the un-treated samples.  For the molecular phylogeny studies of these 71 bacterial isolates, genomic DNA extractions were performed followed by PCR-amplification of 16S rRNA gene and the PCR-products were sent for sequencing for identification.

Concurrently, over the past several years the Reed’s laboratory of TRU has been conducting research with senior undergraduate students. The research involves expanding the list of known applications of a particular organic chemistry reaction methodology. As a consequence of this research a number of organic compounds were synthesized and characterized, the majority of which , have not been reported in the literature. Moreover, none of these compounds, that are known, have not reported as having been tested for antimicrobial activities. Here, in collaboration with the Cheeptham’s laboratory with these above mentioned undergraduate students, we demonstrate the initial investigations of a group of structurally related compounds for the antimicrobial activities against all the pathogenic/normal bacterial and fungal strains that have come out to exhibit the indicated activities against multi-drug resistant E.coli strains with no activities against the non-resistant E. coli strain.

Lastly, we re-confirmed the result obtained for the antimicrobial activities by 6 bacterial isolates retrieved from the White Rabbit Cave, BC, Canada. They were tested against MDR strains of E. coli 15-124, 15-102, 15-318, E. coli non-resistant strain, S. marcescens, S. aureus MRSA43300 and C. albicans strains.


Fall undergraduate research trainees


Richenda McFarland and Jess Dio (1.09.2016 – 30.04.2017)

They are working on 2 caves, Rock n’ 2 veg cave and Rodent Heaven Rodent Hell Cave, soil samples. They are currently isolating microbes (yeast, fungi and bacteria) from these samples. Following the isolation, the microbial isolates will be tested for their antimicrobial activities against the MDR bacterial strains, pathogenic bacterial/yeast strains. Concurrently, the microbial isolates will also be tested for enzymatic characteristics such as Chitinases, β-Glucosidases, β-1,4-cellulases, β-1,3-1,6- glucanases, acid proteases and pectinases. The microbial isolates that will exhibit antagonistic and enzymatic properties will identified molecularly by their phylogenetic markers and thereafter, the phylogenetic relatedness between the species will also be established.


Tin Yung Shiue (1.10.2016 – 31.12.2016)

This project is in collaboration with Prof. Thomas Smith, University of Texas Medical Branch at Galveston, Department of Biochemistry and Molecular Biology, Texas, US. (The manuscript has been submitted and currently under review in Journal of Microbiological Methods)

Bacteriophages screened from the sewage water samples exhibited lytic activities against different bacterial strains. Shiue collected sewage water sample (untreated influent) from the Kamloops Waste Water Treatment center, Kamloops, BC, Canada. The water sample was filter sterilized using 0.22 µm filter. Eleven microorganisms including non-resistant bacterial strains (Escherichia coli, Staphylococcus aureus), multidrug resistant bacterial strains (E. coli 15-102, E. coli 15-124, E. coli 15-102, S. aureus MRSA-43300), bacteria (Serratia marcescens, Pseudomonas aeruginosa, Agrobacterium vitis) and fungal strains (Candida albicans, Pseudogymnoascus destructans) were selected as target organisms for the screen for the bacteriophages from the filtered sewage water sample. Seeded agar assay technique was implemented for the screening. The test microorganisms at a final cell concentration of 106 – 108 cells/mL were mixed with 12 mL of sewage water sample and incubated for 10-30 mins at room temperature.  The incubation for P. destructans was performed at 15°C for overnight. All the incubated cells were then mixed with 60 mL of molten nutrient (bacteria) and Sabouraud dextrose (Fungi) agar and poured in the petri plates. The media plates were kept for incubation over night at 37°C (bacteria), 25°C (Candida) while P. destructans was incubated at 15°C for 10 days. Significant difference in the plaques count were observed between the E. coli 15-318 (437 plaques) and E. coli non-resistant strains (8 plaques).   Eleven plaques were observed with S. marcescens cells. None of the other bacterial and fungal strains were found to host the phage particles.  Further, the bacteriophages are being isolated, purified and molecularly identified (phage nucleotide sequencing) to elucidate the viral diversities associated to each of these bacterial isolates. This is a distinctive study conducted in order to reveal the viruses as alternative potentials to fight against emerging and existing multidrug resistant infectious diseases.


Fall Directed studies students

Aaron Wong and Vincent Yu (1.09.2016 – 30.04.2017)

Aaron is engaged in cultivating the microbial isolates (Fungi/yeast/bacteria) from Berryton Cave, Underground lake Cave, and Dorchester Cave while Vincent is isolating from the White Rabbit below Hare’s Breathe entrance rope drop (White Rabbit Cave), Acoustic mud tube room and a newly discovered cave ‘Over the Hill’. The microbial isolates will be tested for their potential antimicrobial activities against the MDR bacterial strains, bacterial and yeast pathogens. Furthermore, they will be tested for their potential enzymatic activities such as Chitinase, β-Glucosidase, β-1,4-cellulase, β-1,3-1,6- glucanase, acid proteases and pectinases. The microbial isolates that will exhibit the antimicrobial and enzymatic activities will be subjected to molecular identification using the 16S rRNA gene (bacterial identification) or the 5.8S-ITS regions (fungal/yeast identification) as phylogenetic markers. A phylogenetic relatedness will be constructed with the closest microorganisms. This study will also identify potential microorganism/s that will exhibit both enzymatic and antimicrobial activities simultaneously. Therefore, an attempt will be made to establish a link between these two properties for the specific microbial isolate.


Keegan Koning (1.09.2016 – 30.04.2017)

Wild mushrooms have been part of the human diet for centuries because of their nutritional and organoleptic characteristics and purported medicinal properties. Keegan study includes collections of healthy mushrooms (stems and caps) of Pink Oyster Mushroom (Pleurotus djamor), Golden Oyster Mushroom (Pleurotus citrinopileatus), substrate mycelia and compost soil samples from ‘What The Fungus (WTF) Mushroom Farm’ in Summerland, B.C. Mushroom. Furthermore, he will test the to evaluate the antagonistic and enzymatic potential of mushrooms, fungal/yeast isolates, mushroom’s cellular exudates and extracts against multi-drug resistant organisms (MDROs) and substrates respectively.

Co-supervision of Honors students:


Robyn McArthur (1.09.2016 – 30.04.2017)

Robyn is conducting studies to test propolis (bee glue) and fungal isolates from unique environments for their ability to inhibit the growth of Pseudogymnoascus destructans (Pd). Fungal samples are collected from cave soil and swab samples, local mushroom farms, forests, herbariums and horticulture stations which are cultivated and purified.  Pd spores are harvested and laid on the Sabouraud Dextrose Agar media plates to create fungal lawns. She implemented the plug-inhibition assay where the fungal isolates will be spotted on the Pd lawn and potential candidate will be identified as the zone of inhibition around its colony. Further, the potential candidate will be characterized for its antimicrobial properties and subsequently sequenced (ITS-5.8S region) to determine its Geno-species identification. This research aims to find a biological control agent against Pd, the fungus that causes white-nose syndrome in bats. (The Propolis manuscript has been published in Antibiotics)


Rory McKerchar (1.04.2016 – 30.04.2017)

Rory is working with 3 different cave bacteria strains (strain number 1, 4, pm58b) previously shown to display anti-microbial and-biofilm activities. While the strain 1 and 4 has been isolated from Iron Curtain Cave, BC, pm58b being isolated from a volcanic cave in Wells Gray provincial park, BC. He is attempting to grow these bacteria under fermentative conditions in order to extract the secondary metabolites responsible for these activities. In order to achieve this, he aims to clean up, separate, and identify some of these metabolites using thin layer chromatography and LC-MS. In addition to this he also determine if these metabolites are proteinaceous or thermo-labile in nature by attempting to deactivate them with heat. Therefore, the overall goal of this project is to determine the chemical characteristics of these compounds, allowing for easier detection, facilitating further investigation of these compounds as potential pharmaceuticals agents.


Collaborative project:

Intersection between Science and Art (Breastfeeding ART EXPO Major Community Artworks)

The goal of this project is to collage both scientific and artistic perspectives while looking more closely at human breast milk. As a collective group, TRU microbiologists Dr. Naowarat Cheeptham and I along with artist Maureen Smith began to wonder about and determine what bacteria might be associated with human milk and with creating a healthy gut microbiome. Both the scientific and artistic process are being utilized to create a public work that will tour with the exposition. I contributed in isolating the fresh human breast milk donated by the nursing mothers. The milk sample were spread platted on the Nutrient Agar, Sabouraud Dextrose Agar, Blood Agar, and Chocolate Agar media plates and incubated at 37°C overnight. Following the incubation the morphologically identical colonies were visualized. The colonies were picked and were Gram stained and microscopic images were made using the DCM 130E digital camera for microscope. Furthermore, these scanning electron micrographs were also made of these isolated colonies. Apart from these the physical contents such as casein were also elucidated. All these images will be enlarged for display at the Expo. At the end, all these images will be compiled into an art piece incorporating various components.


Research Experiences


Postdoctoral project: Finding effective biological control options against Pd.

(Cave Microbiomes Laboratory, Department of Biological Sciences, Thompson Rivers University, British Columbia, Canada) (Funded by US Fisheries and Wildlife Service)

Cave habitats have proved to be an exceptional matrix for diverse microbes to thrive and therefore become a focus of microbial ecology studies since many years. Not only that, they have shown to harbour microorganisms that display peculiar enzymatic/antimicrobial activities, not found in other places. At the other end, a few investigations have also indicated that bats inhabiting the caves of North-Eastern America, West and British Columbia, are thoroughly affected by the White Nose Syndrome, a fungal disease that has drastically diminished the bats’ population, posing a major environmental threat in Canada. Thereby, various research laboratories are focussed on identifying antagonistic microbe/s to this deadly fungus, named Pseudogymnoascus destructans (Pd). Considering all these research gaps surrounding this disease, my postdoctoral study was unique in its own way and therefore encompassed diverse areas (cave microbial diversities, metagenomics, bioprospecting) and has rightly intended to retrieve potential microorganism/s exhibiting antagonistic effect (biological control) against Pd. Not only that, it will give enormous opportunity to identify and isolate antimicrobial bioactive compounds relevant for various pharmaceutical and biotechnological industries. Additionally, the techniques optimized, the scientific data retrieved and the inferences drawn from this research could be implemented in similar studies possibly conducted on the other understudied but nonetheless relevant matrices, ensuring a vast contribution in the progress of the microbial ecology research.


Ph.D. project: Metagenomic screening of cell wall hydrolases, their anti-fungal activities and potential role in wine fermentation (Citation: 1)

(Institute for Wine Biotechnology, Stellenbosch University, Stellenbosch, Western Cape, South Africa).


The grape and wine ecosystem contains fungi, bacteria and yeasts whose interactions contribute to the final wine product. While the non-Saccharomyces yeasts are dominant in the early stage of alcoholic fermentation, the later stage is always dominated by Saccharomyces cerevisiae. Although their presence in wine fermentation is often short-lived, the non-Saccharomyces yeasts are known to produce an array of extracellular hydrolytic enzymes which facilitate the extraction and release of aroma compounds, but might also play a role in microbial interactions.

The present study aimed to investigate the microbial diversity of grape juice and to evaluate the potential of non-Saccharomyces yeasts to produce hydrolytic enzymes and display anti-fungal properties. To capture the microbial diversity, culture-dependent (plating) and –independent (Automated Ribosomal Intergenic Spacer Analysis (ARISA)) techniques were used in parallel. The fungal and bacterial ARISA displayed a wider range of operational taxonomic units (OTUs) in comparison to cultivation-based technique, demonstrating that ARISA is a powerful culture-independent technique applicable to ecological studies in wine.

Some of the uncommon yeast isolates derived from our cultivation-based study were subjected to an enzymatic screening process. Hydrolases, such as chitinases, β-1,4-cellulases, β-1,3-1,6-glucanases, β-glucosidases, pectinases and acid proteases were specifically sought. Most of the yeast isolates exhibited chitinase, β-1,4-cellulase as well as β-1,3-1,6-glucanase activities. Only Metschnikowia chrysoperlae exhibited β-glucosidase activity. We also retrieved the partial chitinase gene sequences from M. chrysoperlae, Pichia burtonii, Hyphopichia pseudoburtonii that exhibited chitinase activity. Among the isolates, Pseudozyma fusiformata exhibited a strong antagonistic activity against the wine spoilage yeasts B. bruxellensis AWRI 1499 and B. anomalus IWBT Y105. Furthermore, we showed that the killer phenotype of P. fusiformata cannot be attributed to a viral encoded dsRNA.

Finally, two metagenomic approaches were employed in an attempt to explore the indigenous microbiome in a more holistic manner, where we adopted whole metagenome Roche GS-FLX 454-pyrosequencing and construction of a fosmid library. The whole metagenome sequencing revealed a wide range of hydrolytic enzymes that showed homology to enzymes from different fungal and non-Saccharomyces yeast species. Moreover, the metagenomic library screening resulted in the retrieval of 22 chitinase and 11 β-glucosidase positive fosmid clones originating from yeasts. Two clones of interest, BgluFos-G10 and ChiFos-C21, were subjected to next generation sequencing. BgluFos-G10 revealed 2 ORFs exhibiting homology to glycosyl hydrolase family 16 proteins whereas no ORFs encoding chitinase enzymes could be identified in the ChiFos-C21 clone. However, all the potential ORFs identified exhibited homology to a gene cluster from Clavispora lusitaniae ATCC 42720, suggesting that the cloned DNA fragments belonged to a yeast species closely related to C. lusitaniae or members of the family Metschnikowiaceae.

Overall, our study identified a variety of novel hydrolytic enzymes. However, retrieving the full gene sequences of these identified enzymes would be the immediate follow-up of our study. Moreover, the hydrolytic and antifungal activities exhibited by the yeast isolate could be of major interest in evaluating their potential as biocontrol agents against grapevine fungal pathogens and subsequently the wine spoilage yeasts. It would be interesting to evaluate as well the potential impact of these enzymes under wine making condition and could be our next step of investigation.


Technical Experiences:

Ø  Cultivation-based (Microbiological) techniques.

Ø  Function-based screening of the yeast isolates for hydrolytic enzymes/antimicrobial peptides.

Ø  Extraction of metagenomes from grape must/wine.

Ø  Non-cultivation based phylogenetic analysis techniques – Yeast and bacterial ARISA (Automated Ribosomal Intergenic spacer analysis) of the metagenomes extracted from wine.

Ø  Construction of wine yeast- ITS (Intergenic Spacer Analysis) and bacterial-16 S library.

Ø  Construction of wine metagenomic fosmid library.

Ø  Function-based screening of the metagenomic library for fungal cell wall degrading enzymes.

Post Master’s research:

Regulation of GA signaling cascade in Arabidopsis by post-translational modification of the GA receptor, Gibberellin Insensitive Dwarf 1A, GID1A (Research Fellow at Department of Plant Molecular Biology (ZMBP), Eberhard Karls University of Tübingen, Tübingen and Department of Systems Biology, Technical University Munich, Germany).


Gibberellic acid plays an important role in modulating diverse processes throughout plant growth and development such as seed germination, leaf expansion, stem elongation, apical dominance, floral development and fertility (Davies, 1995). The GIBBERELLIC ACID DWARF1 (GID1) GA receptor was originally identified in rice (Ueguchi-Tanaka et al., 2005) based on the rice gid1 mutant. The Arabidopsis thaliana genome encodes three highly homologous GID1 proteins, which are redundant GA receptors and the loss of all these three genes is required to obtain a GA insensitive dwarf plant (Willige et al., 2007).

A 2D gel analysis of an Arabidopsis GID1A overexpression line led to the identification of at least three distinguishable GID1A spots following immunoblotting. Based on this finding, I hypothesized that there are post-translational modifications of the GID1A protein and my project focused on this aspect of GID1A regulation. Using 1D isoelectric focussing, which allowed to separate protein samples on the basis of their pI and to compare several samples on a single gel, I was able to provide evidence for the in vivo phosphorylation of GID1A:GFP.

In order to identify the potential phosphorylation site on GID1A, I employed the NetPhos 2.0 programme (Blom et al., 1999) that identified several potentially phosphorylated serine, threonine and tyrosine residues of the GID1A protein. To mimic the constitutively phosphorylated state (by replacing the threonine and serine residues by aspartic acid residues and tyrosine residues by glutamic acid residues) and constitutively non-phosphorylated state (substituting threonine and serine residues by alanine residues and tyrosine by leucine residues) of the GID1A protein, I generated a total of sixteen amino acid exchanged mutants each of 35S::GID1a:GFP and  pGBT9::GID1a. pGBT9::GID1a amino acid exchanged mutants were then used for qualitative and quantitative protein interaction studies with the DELLA repressor protein GAI in the absence and presence of GA. The mutant variants T40A, T40D, S120AS121A, Y155LY159L, Y155EY159E, S177A, S177D, T227AS229A, T227DS229D, T240A, T240D lost their yeast two-hybrid interaction whereas S120DS121D, Y247L, Y247E, Y298L & Y298E retained their interaction.

The 35S:GID1A::GFP wild type construct can rescue the gid1 triple mutant dwarf phenotype. To investigate whether the mutant variants can still rescue the gid1 phenoptype, I transformed Arabidopsis plants with the 35S::GID1A:GFP mutant constructs and subsequently crossed the transgenes into the gid1a +/-, gid1b -/-, gid1c -/-  background. I was able to show complementation of the gid1 double or triple knock out mutant lines with all sixteen GID1A:GFP mutants, which implies that the constitutive de-/phosphorylation on GID1A did not alter the in vivo functionality of the protein. In other words, the mutations on GID1A had no influence on the GA-dependent interaction of GID1A and GAI in planta.

Since many constructs had failed to interact in the yeast two-hybrid study, this was a surprising finding and may reflect differences between the yeast and plant system.

Furthermore, all 35S::GID1A:GFP mutant transgenic lines were analyzed using 1D IEF analysis to examine whether the mutation has any influence on the in vivo phosphorylation status of the protein. The transgenic lines T40A, T40D, S120AS121A, S120DS121D, Y298E Y298L, S177A and S177D transgenic lines showed some alterations in the band profile in compared to the GID1A:GFP control as depicted by the different calculated pI values. The IEF banding profile of S120AS121A, S120DS121D showed distinguishable band intensity, S120DS121D bands were more intense in comparison to S120AS121A with an equal loading control. Moreover, the yeast two-hybrid analysis of these two mutant variants also showed that the interaction was abolished in case of S120AS121A whereas it was intact in case of S120DS121D. However, further confirmation of this result is very much required. Also, one cannot rule out the possibility of existence of different phosphorylation sites on the GID1A protein other than the ones predicted at the beginning of this analysis.

GID1A is both nuclear and cytoplasmic localized (Willige et al., 2007), therefore it was very much intriguing to elucidate whether the mutation on GID1A had any effect on its localization. Imaging of the mutant GID1A:GFP proteins by confocal microscopy showed that the mutated protein was also localized in cytoplasm and in the nucleus as observed for the wild type GID1A:GFP protein.

Taken together my results suggest that phosphorylation could be a post-translational modification of the GID1A protein, however sites chosen for analysis were not found to modify the functionality of the protein in terms of its localization, abundance, except for S120AS120A, S120DS121D, S177A and S177D, and ability to complement the mutant phenotype.


Technical Experiences:

Ø  Isolation of genomic and plasmid DNA.

Ø  Gene cloning of PCR amplified fragment or restriction digested gene product in commercially available pGAD424 (+2) and pGBT9 yeast two-hybrid vectors, pGEX-4T-3 vector (specially used for protein purification), TOPO vector and pGEMT-Easy vector, ‘GATEWAY’ compatible vectors.

Ø  Preparation of electro competent and heat competent bacterial (E.coli).

Ø  Bacterial (E.coli) and yeast (Saccharomyces cerevisiae) gene transformation.

Ø  Preparation of gene mutants using site-directed mutagenesis technique.

Ø  Sequencing of DNA using the ABI PRISMÒ 377 3700 DNA sequencer.

Ø  Quantitative and qualitative yeast two-hybrid assay to check for protein-protein interaction/s

Ø  1D SDS PAGE and Western blotting.

Ø  Isoelectric focusing (IEF) one-dimensional protein gels to see for the posttranslational modification of proteins.

Ø  Protein concentration estimation from the crude protein extracts employing Bradford and Lowry methods.

Ø  Purification of IPTG inducible proteins from bacterial (E.coli) culture, grown at 37°C, in small and large scale.

Ø  Demonstration of the invitro protein-protein interactions study using recombinant proteins: Yeast-two-hybrid assay (quantitative and qualitative), protein blot overlay and protein pull-down assays.


Discovery of novel circadian clock components in light signaling pathways in Neurospora crassa (Research Fellow, Groningen University, The Netherlands.


Technical Experiences:

Ø  Culturing of Neurospora crassa on different growth media in the tubes.

Ø  Monitoring the conidiation of Neurospora crassa under different light conditions.

Ø  Documenting the hyphal growth of Neurospora crassa by photographing and

measuring their length by using software program, ImageJ.


Development of thermo tolerant and starch utilizing strains of S. cerevisiae with high ethanol productivity (Project Assistant, Institute of Microbial Technology, Chandigarh, India).


Technical Experiences:

Ø  Cloning and expression of glucoamylase gene from Saccharomyces diasticus into a alcohol producing strain, IMT37A (n).

Ø  Cloning and expression of alpha-amylase gene from Bacillus species into the high alcohol producing strain IMT37C (n).

Ø  Mating of these yeast strains containing glucoamylase gene and alpha-amylase gene and subsequently producing a diploid strain (2n), D2 (2n) and D5 (2n), capable of degrading starch into alcohol.

Ø  Measuring alcohol production and total sugar level by Potassium dichromate method and Anthrone method respectively.


Antimycobacterial activity of the Human Neutrophil Peptides (HNP-1) against MDR strains of mycobacterium and its role as antiresistance peptide (Senior Research Fellow, Post Graduate Institute of Medical Education and Research, Chandigarh, India).


Technical Experiences:

Ø  Animal Tissue Culture, T-cell proliferation assay, macrophage activation assay.

Ø  Protein purification (whole gel eletroelution, dialysis, concentration of protein by amicon technique and by centricon).

Ø  Enzyme assays.

Ø  Chromatography (affinity, ion-exchange, gel filtration and paper).


Simmulatory study for the maintenance of efficacy and satiety in the laboratory animals (Junior Research Fellow, Department of Environmental Science, University of Pune, (Presently renamed as Savitribai Phule Pune University), Pune, India.


Technical Experiences:

Ø  Laboratory animal handling (rats, mice, guinea pigs, rabbit), drug formulation specifically the herbal drug preparation, administration of the drugs (i.v., i.p., oral and aerosol).

Ø  Estimation of various biochemical parameters like serum glucose, serum cholesterol, urine urea, blood urea nitrogen, muscle creatinine, serum albumin and total protein.

Ø  Monitoring the motor activity of animals recorded on alternate days using actophotometer.

Ø  Measuring the rectal temperature of the animals undergoing starvation.

Ø  Recording the ECG of the animals using polygraph (Biopac Student Laboratory, Model MP30, USA).


M.Sc. projects, {Department of Zoology, University of Pune, (Presently renamed as Savitribai Phule Pune University), India}.

Isolation of a genomic clone homologous to a transposable element from Anopheles



Technical Experiences:

Ø  Screening of genomic library.

Ø  Preparation of phage plates.

Ø  Plaque blotting.

Ø  Auto radiography.


Characterization of gut micro flora from a tropical midge- Chironomus ramosus


Technical Experiences:

Ø  Preparation of media: Luria broth, Nutrient broth.

Ø  Staining of the microorganisms using different microbial stains.


Metal induced oxidative stress in male reproductive system in mammals (Central Food Technological Research, Mysore, India).


Technical Experiences:

Ø  Isolation and detunication from adult male rat’s testis.

Ø  Culturing of Seminiferous tubules and invitro administration of different metals.

Ø  Lipid peroxidation assay for measuring the MDA levels as the oxidative stress parameter.

Assaying of the enzymatic antioxidants (catalase, abscorbic acid, SOD and GSH).


Symposium attended/participations/awards


Ø  Selected as the *Top* 35 of the Antibiotics Travel Awards 2017 from worldwide

Applications, MDPI AG St. Alban-Anlage 66, 4052 Basel, Switzerland.

Ø  Participated in the 180 second research challenge with the faculties at Thompson Rivers University, Kamloops, Canada 29th March, 2017.

Ø  Members of the ICS 17th International Congress of Speleology (17th ICS), Sydney Australia 23rd July – 29th July, 2017.

Microbiology Organizing Committee jointly with Prof. Hazel A. Barton, PhD, University of Akron, USA, Prof. Naowarat Cheeptham, PhD, Thompson Rivers University, Canada and Prof. Hongmei Wang, PhD, China University of Geosciences, China.

Ø  Macrowine 2014, Stellenbosch, South Africa, 7-10th September, 2014.

Ø  18th Biennial Conference of the South African Society of Microbiology (SASM), Bela Bela, South Africa, 24th – 27th November, 2013.

Ø  Mechanisms of Cell Behaviour, Fifth Symposium of SFB 446, Eberhard Karls University of Tübingen, Tübingen, Germany, 2nd -3rd May 2008.

Ø  3rd Tri-National Arabidopsis Meeting, Tübingen, Germany, 26th -29th September, 2006.

Ø  The 14th European school for Chronobiology Gröningen, The Netherlands, 05th – 10th June, 2005.



Computer proficiency


Ø  Operating system Mac and Windows.

Ø  Microsoft office (word, excel and power point).

Ø  Adobe Photoshop (CS2).

Ø  Adobe Illustrator (CS3).

Ø  UCSF, CHIMERA: For extensible protein modelling system.

Ø  Endnote 9.0.0 (bibliography manager).

Ø  DNA star: For nucleic acid sequence analysis (import/export, cloning, alignment, BLASTs and many other tools.

Ø  Leica software for confocal microscopy.

Ø  Image J software for measuring the hypocotyl length and the root angle.

Ø  ABI PRISM for DNA sequencing.

Ø  Gene mapper for ARISA (Automated Ribosomal Intergenic spacer analysis).

Ø  On internet: BLAST search on the Arabidopsis nucleic acid and protein database.


Languages known


Ø        English             Fluent spoken, excellent in writing.

Ø        German             Basic knowledge.

Ø        Bengali             Mother Tongue.

Ø        Hindi                 Fluent spoken, good in writing.

Ø        Marathi             Fluent spoken.


Extra-Curricular Activities

Sketching, painting, drawing and listening to music are my hobbies. Among the sports I love to play cricket and table tennis. Participated and won a number of prizes in Table Tennis. Apart from all these I am also fond of pets.



Dr. Naowarat (Ann) Cheeptham, Ph.D.

Post Doctoral supervisor,

Associate Professor of Microbiology,

Department of Biological Sciences,

Faculty of Science,

Thompson Rivers University,

805 TRU way, Kamloops, BC V2C 0C8, Canada

Email    :

Phone   : +1 250 371 5891 (official)

Fax       : + 1 250 828 5450

URL      :


Dr. Cesareo Saiz-Jimenez, Ph.D.

Research Professor (Microbiology),

Instituto de Recursos Naturales y Agrobiologia, Avenida de Reina Mercedes 10 (street),

41012 Sevilla, Spain

Email    :

Phone   : +34 954 624711(official)

Fax       : + 34 954 624002

URL      :


Dr. Rinaldo Camillo Bertossa, Ph.D.

Research Associate,

GELIFES, Molecular Neurobiology,

University of Groningen

P.O. Box 14

9750 AA Haren, The Netherlands

Fax:   +31 50 363 23 48

Tel.:   +31 50 363 21 25

e-mails: (private)


Dr. Dipesh Prema, Ph.D.

Lecturer of Chemistry,

Department of Physical Sciences,

Faculty of Science,

Thompson Rivers University,

805 TRU way, Kamloops, BC V2C 0C8, Canada

Email    :

Phone   : +1 250 828 5419 (official)

: +1 250 5724688 (mobile)


Dr. Mathabatha Evodia Setati, Ph.D.

Ph.D. supervisor,

Senior Researcher in Wine Biotechnology

Institute for Wine Biotechnology

Stellenbosch University

Private Bag X1,Matieland 7602, South Africa

Email    :

Phone   : +27 21 808 9203 (official)

: +27 828439644 (mobile)

Fax       : + 27 21 808 3701


Dr. Kingsley Donkor, Ph.D.

Full Professor of Chemistry,

Department of Chemistry,

Thompson Rivers University,

805 TRU way, Kamloops, BC V2C 0C8,


Email    :

Phone   : +1 250-828-5406 (official)

Fax       : +1 250-828-5450

URL      :

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