RESEARCH INTERESTS
Molecular Microbial Ecology, Marine Microbial Ecology, Aquatic Microbial Ecology, Environmental Microbiology, Evolution and comparative genomics of pathogenic bacteria, Evolutionary and phylogenetic analyses of bacteria, , , , etc.
PRESENT POSITION
JSPS Postdoctoral Fellow, Marine Microbiology Laboratory, Ocean Research Institute, The University of Tokyo, Japan. Since October 01, 2006.
PRESENT ACTIVITIES: Whole genome sequencing of a marine Pseudomonas aeruginosa, comparative phylogenetic and physiological analysis of marine Pseudomonads e.g., P. aeruginosa and P. putida. Phylogenetic analyses of nucleotide sequences, culture independent microbial ecological analyses etc.
ACADEMIC QUALIFICATIONS
Doctor of Natural Environmental Studies (Marine Microbiology)
PhD from the Marine Microbiology Division of Ocean Research Institute of the University of Tokyo Japan. Awarded on 29th September, 2006. Title of the PhD dissertation was “Isolation, identification and phylogeny of marine Pseudomonas aeruginosa”.
Master of Science (Limnology)
One year Master of Science (MSc) degree from the Department of Botany, University of Dhaka, Dhaka-1000, Bangladesh. 1996. Obtained First Class (Grade A, marks 67.0%) and secured third position. A one-year thesis was carried out in the Department of Botany, University of Dhaka and Environmental Microbiology Laboratory, Laboratory Sciences Division, International Center for Diarrhoeal Disease Research, Bangladesh (ICDDR, B). Thesis topic was “Helioplankton Dynamics and Physico-chemical Limnology of Four Ponds in Matlab, Chandpur”. In M. Sc. Course, major subject studied were Microbiology, Molecular genetics and Limnology.
Bachelor of Science (Botany)
Three years Bachelor of Science (BSc) degree, from the Department of Botany, University of Dhaka, Dhaka-1000, Bangladesh. 1994. Obtained First Class (Grade A, marks 64.0%) and secured Second position. Major studied subjects were Microbiology, Genetics, Limnology and Ecology.
BRIEF DESCRIPTION OF PHD THESIS:
CHAPTER 1.
Isolation of Pseudomonas aeruginosa from the open ocean and their genotypic and phenotypic comparison with freshwater, clinical and animal isolates.
P. aeruginosa were isolated from the open ocean. This is the first report of isolation of this important bacterium from the open ocean. A comparative phenotypic and genotypic analysis was carried out with the strains from freshwater, clinical and animal sources. Ocean P. aeruginosa was found to be unique regarding their genotypic patterns. Multidrug resistant P. aeruginosa are present in the open ocean. P. aeruginosa showed patchy distribution in the ocean. Please see the publication (Khan et al., 2007).
CHAPTER 2:
Growth, survival and viable but non-culturability of open ocean Pseudomonas aeruginosa in comparison with freshwater and clinical isolates.
Microcosms were prepared in the laboratory using deionized water and artificial seawater with (0 to 7%) or without NaCl, at different pH (4 to 9), at various temperatures (-20 to 35ºC) and growth and survival responses were observed in a comparison basis. Ocean, river and clinical P. aeruginosa were used in this study. Viable and non-culturable state was observed for all P. aeruginosa at stressful conditions. All P. aeruginosa can survive at high NaCl and pH level. Ocean P. aeruginosa preferred higher NaCl and pH for their growth and survival. All strains were capable of entering into VBNC state at high NaCl condition. VBNC P. aeruginosa were resuscitated at favorable conditions. A manuscript from this study in preparation.
CHAPTER 3.
Phylogenetic analyses and MLST typing of ocean P. aeruguinosa.
It revealed that the oceanic P. aeruginosa are unique and they have unique strain types among other P. aeruginosa. While phylogenetic trees were drawn from the sequence data of various genes (at least seven), it was found that marine P. aeruginosa were in different lineages which indicates that P. aeruginosa had multiple evolution in the open ocean. A manuscript from this study was submitted to AEM and now in review.
RESPONSIBILITIES AND ACTIVITIES
Isolation and identification of marine Pseudomonads by classical and molecular techniques,
Serotyping, Antibiotyping, PCR, Multiplex PCR, DGGE, PFGE, MLST (multilocus sequence typing), Sequencing of 16S, Its, gyrB, rpoD, rpoB, pvdS, acsA, aroE, nuoD, mutL, trpE, ppsA etc. by ABI (Applied Biosystems) genetic analyzers, phylogenetic analyses of nucleotide sequences,
Motility analyses, Hemolytic activities, Proteolytic activities, Microcosm study for the physiological status of marine P. aeruginosa especially viable but non-culturable state and resuscitation for: NaCl stress, Temperature stress, Variable pH in artificial seawater, Variable pH in deionized water.
DNA-DNA hybridization.
EX WORK EXPERIENCES
From May 1997 to April 2003:
Worked as a Research Officer in the Environmental Microbiology Laboratory of International Center for Diarrhoeal Disease Research, Bangladesh (ICDDR,B) from may 1997 to April 2003. During my tenure in ICDDR,B I have successfully completed assignments which was given to me. The projects in which I was involved were as follows:
A. "Epidemiology and Ecology of Vibrio cholerae in Bangladesh." From July 1996 to June 2002. This Project was funded by NIH, USA, and collaborated with University of Maryland Biotechnology Institute, USA, Johns Hopkins University, USA, Emory University, USA and ICDDR,B.
B. " A simple water filtration project for cholera intervention by removing plankton" from August 1998 to July 2002. Funded by NIH, USA, collaborated with University of Maryland Biotechnology Institute, USA and ICDDR,B.
C. “Genomic assessment of phenotypic plasticity in an aquatic bacterium (Vibrio cholerae ), from October 2001 to March 2003” funded by NSF, USA, collaborated with Dartmouth College, Hanover, USA ,University of Maryland Biotechnology Institute, USA and ICDDR,B
D. “Infectious diseases risk management in Mozambique and Bangladesh” from October 2002 to March, 2003. This project is funded by DFID and UNICEF and a collaborative research among ICDDR,B, Loughborough University, UK and Environmental Health Division, Mozambique.
RESPONSIBILITIES in ICDDR,B
Laboratory studies
Microbiological analysis e.g. PCR, Culture, Colony Blot, and Dot Blot Hybridization etc for identification of V. cholerae from environmental samples. DFA for identification and enumeration of V. cholerae in various environmental samples e.g. water, plankton, sediments and aquatic plants.
Monitoring of various physicochemical parameters of water e.g. Dissolved Oxygen (DO), Biological Oxygen Demand (BOD), Dissolved Carbondioxide (DCO2), Salinity, Conductivity, Hardness, Alkalinity, TDS, Chlorides, Nitrate Nitrogen (NO3-N), soluble reactive phosphorous (SRP), Soluble Reactive Silicon (SRS) etc. following standard procedures. Identification and enumeration of phytoplankton collected from various aquatic ecosystems of some rural areas of Bangladesh. Carried out the seasonal variation and dynamics of different types of phytoplankton in the fresh water environments of Bangladesh as well as in the marine environment of Bay of Bengal.
Field studies
Collection of various environmental samples e.g. Water, Phytoplankton, Zooplankton, Sediments, Aquatic Plants etc. for Microbiological, chemical, taxonomical and other laboratory analyses following standard procedures. Monitoring of various physicochemical parameters e.g. Water Temperature, Air Temperature, Water Depth, Dissolved oxygen, Conductivity, Salinity, pH, Total Dissolved Solids, etc following standard procedures.
Others:
Written scientific and technical articles, papers, reports on the results of laboratory and field based analyses of the projects. Supervised students and junior staffs in the laboratory as well as in the fields.
Prepared requisitions and played role on purchasing various local and overseas materials uses for the projects. Attended project management meetings. Please see the publication lists.
From January 1996 to April 1997:
Worked as a Field Biologist in Canadian International Development Agency (CIDA), Bangladesh from January 1996 to April 1997. Duty stations were 16 remote rural Thana’s of Northeast region of Bangladesh. My duties and responsibilities were collection of plants from various environments e.g., wetlands, homesteads, agricultural lands and fellow lands. Identification and enumeration of their abundance were in my study. Economic important of all those plants were also analyzed.
BRIEF DESCRIPTION OF MASTER’S THESIS:
One-year thesis in Limnology under the supervision of Prof. Moniruzzaman Khondker, Department of Botany, University of Dhaka and Environmental Microbiology Lab., LSD, ICDDR, B. Thesis topic was " Helioplankton dynamics and physicochemical limnology of four ponds in Matlab, Bangladesh." Four village ponds of Matlab, Chandpur, Bangladesh were selected for the study. Samples of water, phytoplankton, zooplankton, aquatic plants, sediments etc. were collected every fifteen days interval. Both Phytoplankton and Zooplankton were studied. Abundance, density, diversity, seasonality of plankton was carried out. Various biophy6sicochemical parameters of water were monitored. The parameters were Dissolved Oxygen, Dissolved Carbon Dioxide, Salinity, Alkalinity, Acidity, pH, Hardness, Total Dissolved Solids, Conductivity, Nitrate Nitrogen, Soluble Reactive Phosphorus, Soluble Reactive Silicon, Chloride, Chlorophyll, and Phaeopigments etc.
Computer literacy and software’s used
MS Word, Word perfect, Excel, Power point, Adobe Illustrator, Adobe Photoshop, SPSS, MEGA, ATGC, Split tree, etc.
ACADEMIC AWARDS AND DISTINCTIONS
1. Awarded JSPS (Japanese Society of Promotion of Science) postdoctoral fellowship for two years from October 2006 to September 2008.
2. Awarded UNESCO-MIRCEN fellowship for three months from January 16, 2002 to April 18, 2002, in the laboratory of Prof. Rita R. Colwell, In the Center of Marine Biotechnology, University of Maryland, Baltimore, Maryland, USA. Training includes molecular characterization of Viable but Non-culturable toxigenic Vibrio cholerae from various environmental samples using PCR, colony blot hybridization, dot blot hybridization, Hybridization with radioactive and non-radioactive probes etc.
3. Dean awards (this award is given for outstanding academic performances, sincerity and regularity at graduation level.)
4. University scholarships (based on overall academic performances during undergraduate and graduate study in the university.
REVIEWER FOR INTERNATIONAL JOURNALS
The ISME Journal
Microbial Ecology
Journal of Rapid Methods and Automation Microbiology
PUBLICATIONS
IN JOURNALS
1. Khan, N.H., Ishii, Y., Kimata-Kino, N., Esaki, H., Nishimura, M. and Kogure, K. (2007). Isolation of Pseudomonas aeruginosa from open ocean and comparison with freshwater, clinical and animal isolates. Microbial Ecology, 53: 173-186.
2. Khan, N.H. and Kogure, K. Multilocus Sequenc Typing and Phylogenetic analyses of marine Pseudomonas aeruginosa (in review).
3. Khan, N.H. and Kogure, K. Growth, survival and viable but non-culturability of open ocean Pseudomonas aeruginosa in comparison with freshwater and clinical isolates (In preparation).
4. Khan, N.H., Ishii, Y. and Kogure, K. Antimicrobial susceptibility of open ocean Pseudomonas aeruginosa in comparison with freshwater, clinical and animal isolates (In preparation).
5. Khan, N.H. Ahsan, M. and Kogure, K. Phylogenetic comparison of marine Pseudomonas putida with clinical and terrestrial isolates (In preparation).
6. Huq, A., Sack, R.B., Nizam, A., Longini, I., Nair, G.B., Ali, A., Morris, J.G., Khan, N.H., Siddique, A.Q., Yunus, M., Albert, M.J., Sack, D.A. and Colwell, R.R. (2005). Critical factors influencing the occurrence of Vibrio cholerae in the environment of Bangladesh. Applied and Environmental Microbiology. 71: 4645-4654.(IF=3.81)
7. Welker, M, Khan, S., Haque, M.M., Islam, S., Khan, N.H., Chorus, I. and Fastner, J. (2005). Microcystins (cyanobacterial toxins) in surface waters of rural Bangladesh: Pilot study. Journal of Water and Health. 03.5: 325-338
8. Islam, M.S., Talukder, K. A., Khan, N. H., Mahmud, Z. H., Rahman, M. Z., Nair, G. B., Siddique, A. K. M., Yunus, M., Sack, D. A., Sack, R. B., Huq, A and Colwell, R. R. (2004). Clonal variation in toxigenic Vibrio cholerae O1 in the aquatic environment. Microbiology and Immunology. 48: 773-777 (IF=1.44).
9. M.S. Islam, S. Mahmuda, M.G. Morshed, H.B.M. Bakht, N. H. Khan, R.B. Sack, and D.A. Sack (2004). Role of cyanobacteria in the persistence of Vibrio cholerae O139 in saline microcosms. Canadian Journal of Microbiology 50:127-131 (IF=1.12)
10. Colwell RR, Huq A, Islam MS, Aziz KM, Yunus M, Khan N.H., Mahmud A, Sack RB, Nair GB, Chakraborty J, Sack DA, Russek-Cohen E (2003). Reduction of cholera in Bangladeshi villages by simple filtration. Proc Natl Acad Sci, 100(3):1051-5 (IF=11.27).
11. Islam MS, Golder M, Morshed GM, Khan N.H., Islam MR and Sack RB.(2002) Involvement of the hap gene (mucinase) in the survival of Vibrio cholerae O1 in association with the blue-green alga, Anabaena sp. Canadian Journal of Microbiology, 48(9): 793-800.(IF=1.12).
12. Islam, M.S., Siddika, A., Khan, N.H., Golder, M.M., Sadique, M.A., Kabir, A.N.M.H., Huq, A. and Colwell, R.R. (2001). Microbiological analysis of tube-well water in a rural area of Bangladesh. Applied and Environmental Microbiology. Vol.67 (7), pp.3328-3330. (IF=3.81)
13. Islam, M.S., Hossain, M.A., Khan, S.I., Khan, N.H., Sack, R.B., Albert, M.J., Huq,A,And Colwell, R.R. (2001). Survival of Shigella dysentery type 1 on fomites. Journal of Health Population and Nutrition. 19:264-272 (IF=0.625).
14. Islam, M.S., A. Begum, S.I. Khan, M. A. Sadique, N.H. Khan, M.J. Albert, M.Yunus, A. Huq and R.R. Colwell. (2000). Microbiology of pond ecosystems in rural Bangladesh: Its public health implications. International Journal of Environmental Studies. Vol.58, pp.33-47.
ABSTRACTS
1. Khan, N. H., Mahbuba, A. and Kogure, K. (2008). Comparative Multilocus Sequence Analyses of marine, freshwater and clinical Pseudomonas putida. Annual Conference of Japanese Society of Bacteriology. March 24-26, 2008. Kyoto, Japan.
2. Khan, N. H., Mahbuba, A. and Kogure, K. (2008). Multilocus Sequence Analyses of marine, freshwater and clinical Pseudomonas putida. 108th ASM general meeting. Will be held on June 1 to 5, 2008. Boston, USA.
3. Khan, N.H. and Kogure, K. (2007). Multilocus Sequence Typing (MLST) and phylogeny of Marine Pseudomonas aeruginosa. ASM conferences: Pseudomonas 2007, August 26-30, 2007 was held in Seattle, Washington, USA.
4. H. Shinomiya, L. Nonaka, NH Khan, K. Kogure, Y. Ishii, Y. Asano and S. Suzuki (2007). Differences in genotype, serotype and pathogenecity between clinical and marine isolates of Pseudomonas aeruginosa. ASM conferences: Pseudomonas 2007, August 26-30, 2007 was held in Seattle, Washington, USA.
5. Khan, N.H. and Kogure, K. (2007). Multilocus Sequence Typing (MLST) of Marine Pseudomonas aeruginosa. 107th ASM general meeting, May 21 to 25, 2007 was held in Toronto, Canada.
6. Khan, N. H. and Kogure, K. (2007). Multilocus Sequence Typing (MLST) of marine Pseudomonas aeruginosa. Annual Conference of Japanese Society of Bacteriology. March 25-28, 2007. Osaka, Japan.
7. Khan, NH, Wada, K., Tsukamoto, K. and Kogure, K. (2006). Open ocean yet another reservoir of Pseudomonas aeruginosa. Spring meeting of Japanese Society of Oceanography, Yokohama City University, Kanazawa Hakkei, Kanagawa, Japan. March 26 to 30, 2006.
8. Khan, N.H. and Kogure, K. (2006). "Pseudomonas aeruginosa is present in marine environments." 7th Asia Pacific Marine Biotechnology Conference, Nov. 2-5, 2006. Kochi, India.
9. Khan, N. H. and Kazuhiro Kogure. (2005). Growth, survival and viable but non-culturability of open ocean Pseudomonas aeruginosa in comparison with freshwater and clinical isolates. Was presented in 105th ASM general meeting, Atlanta, June 05 to 09, 2005.
10. K. Wada, N. H. Khan, K. Tsukamoto and K. Kogure (2005). Phylogenetic relationships of Pseudomonas aeruginosa isolated from open ocean comparing to terrestrial and clinical strains. Presented in Dynamics of the Ocean Biosystems International Symposium, 15-18th November, Miraikan, Tokyo, Japan.
11. 岡本将志、Nurul Huda Khan、小松春伸、木暮一啓、後藤直正 (2004) パルスフィールド電気泳動法によって決定したPseudomonas aeruginosa（緑膿菌）海洋分離株のゲノムサイズ. Annual conference of Japanese Society of Bacteriology, April 2004 was held in Tokyo, Japan.
12. Khan, N. H., Y. Ishii, K. Yamaguchi, H. Esaki, N. Kimata, M. Nishimura and K. Kogure. (2004). Isolation of Pseudomonas aeruginosa from marine environments and comparison with clinical and animal isolates. 104th ASM general meeting held in May, 2004 in New Orleans, LA, USA.
13. Khan, N. H., Y. Ishii, H. Esaki, N. Kimata and K. Kogure. (2004). Isolation of Pseudomonas aeruginosa from marine environments and comparison with clinical and animal isolates. 10th ISME general meeting held in August, 2004 in Mexico.
14. Khan, N. H. Y. Ishii, N. Kimata, H. Esaki, M. Nishimura and K. Kogure. (2004). Pseudomonas aeruginosa is a common member of open ocean bacterial flora, 20th JSME general meeting held in November 21-23, 2004 in Sendai, Japan.
15. M.S. Islam, S. Mahmuda, M.G. Morshed, H.B.M. Bakht, N.H. Khan, R.B. Sack, and D.A. Sack Role of Cyanobacteria in Persistence of Vibrio cholerae O139 in Microcosms. 10th ASCODD conference organized by ICDDR,B held in Dhaka, Bangladesh, December 7-8, 2003.
16. Islam, M.S., Rahman, H., Saikat, S.Q., Moniruzzaman, S.M.,Khan. N.H., Huq, A.and Colwell, R.R. (2002).Preliminary observation on arsenic contamination of potable water in Bangladesh. 1st National Conference on Environmental Health in Bangladesh organized by Bangladesh Poribesh Andolon (BAPA) held at ICDDR,B on February 19-20, 2002.
17. Islam, M.S., Bakht, H.B.M., Siddika.A., Khan. N.H., Golder, M.M., Sadique, M.A., Kabir, A.N.M.H., Huq, A.and Colwell, R.R. (2002). Microbiological analysis of tube-well water in a rural area of Bangladesh. 1st National Conference on Environmental Health in Bangladesh.
organized by Bangladesh Poribesh Andolon (BAPA) held at ICDDR,B on February 19-20, 2002.
18. Islam, M.S., Khan, N.H., Khondker, M., Yunus, M., Rahman.M.A. Sadique, M.A., Huq, E., Albert, M.J., Sack, R.B., Huq, A. and Colwell, R.R. (1999). Blue green algal bloom formation in pond ecosystem and seasonality of cholera cases in an endemic area of Bangladesh. Eighth annual scientific conference (ASCON) in ICDDR, B held in February 12-13,1999.
IN PROCEEDINGS
1. M.S. Islam. S.B. Neogi, M.S. Islam, K.C. Bhattacharya, H.B.M. Bakht, N.H. Khan, K.M.A. Aziz, G.B. Nair and D.A. Sack. (2003). Experiences, information and knowledge in hygiene promotion, Bangladesh. Proceedings of 28th WEDC conference, Calcutta, India. November, 2002.
2. Islam, M.S., Khan, N.H., Khondker, M and Sack, R.B. (2002). Role of phytoplankton and zooplankton in the seasonality of cholera in Bangladesh. The thirty-seventh joint conference of US-Japan cooperative medical science program, cholera and other bacterial enteric infections panel. December 17-19, 2002.
3. Anwar Huq, Sirajul Islam, Estelle Russek-Cohen, Md.Yunus, Abdul Aziz, J. Chakraborty, Abdullah Al Mahmud, Nurul Huda Khan and Rita R. Colwell. (2001). A simple water filtration for cholera intervention. Was presented in 34th US-Japan cholera conference held on 17th to 19th January in Osaka, Japan.
4. M.S.Islam, N. H. Khan, M. .A. Rahman, M. A. Sadique, S. M. Moniruzzaman, A. H. Baqui, M. S. Hossain, A. K. Siddique, R. B. Sack, D.A.Sack, A.Huq and R.R.Colwell. (2000). Role of animate and inanimate objects in transmission of shigellae in index families elucidated by culture and flourescent antibody techniques.74th International Conference on Infectious Diseases. Fukuoka, Japan.
REPORT
1. Islam, M.S., Moniruzzaman, S.M., Khan, N.H.and Rahman, M.A. (1998). Abundance of indicator bacterial pollution in tube well water from Keraniganj and Dattapara, Dhaka. Report submitted to British Geological Survey (BGS)
REFEREES
1. Prof. Kazuhiro Kogure
Marine Microbiology Division, Ocean Research Institute, The University of Tokyo, 1-15-1 Minamidai, Nakano-ku, 164-8639 Tokyo, Japan, Phone: 81-3-5351-6485 (Lab.), Fax: 81-3-5351-6482, Email: kogure@ori.u-tokyo.ac.jp, http://www.ecosystem.ori.u-tokyo.ac.jp/microbiology/staffs.html
2. Prof. Rita R. Colwell
Distinguished University Professor, Center for Bioinformatics and Computational Biology, 296 Agriculture/Life Sciences Surge Building, Room 3103, University of Maryland, College Park, MD 20742, FAX: 301-314-6654, TEL: 301-405-9550
E-mail: rcolwell@umiacs.umd.edu , Colwell@umbi.umd.edu
3. Dr. G. Balakrish Nair, PhD, FNA, FNASc, FTWAS
Director, National Institute of Cholera and Enteric Diseases, P-33, CIT Scheme XM, Beliaghata, Kolkata - 700 010, India, Tel: +91-33-23701176, Fax: +91-33-23705066, Mobile: +919830553757
E-mail: nairgb@icmr.org.in; gbnair_2000@yahoo.com
4. Dr. Anwar Huq, Ph. D., FAAM
Maryland Pathogen Research Institute, Bioscience Research Building, Room 3132, University of Maryland College Park, Maryland 20742, USA, Phone: 1-301-405-7428, E-mail: huq@umd.edu
5. Prof. Moniruzzaman Khondker
Laboratory of Limnology, Department of Botany, University of Dhaka, Dhaka-1000, Bangladesh., Phone: 880-2-8615215 (Res.), 880-2-9661920-59, Ext, 6045 (Off.) , Fax: 880-2-8615583, Email: khondker@udhaka.net
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