Asim Kumar Bej

(1) Extremophiles: Microorganisms thrive in all ecosystems including “extreme habitats” where they have adapted to cope with environmental parameters often considered inimical for others to maintain life functions. Given that in as much as over 70% of the earth maintains near or below freezing temperatures, the cold ecospheres constitute the largest “physical extreme” for microbial communities to exist, manifest adaptive attributes and drive key biological, geochemical and physical processes. Among all cold ecosystems, the ice-covered Antarctic continent offers the extreme cold, dry and windy conditions posing challenges to the inhabiting microorganisms. We are using the culture-based methodologies and culture-independent NextGen Sequencing Technology and Bioinformatics tools to study microbiota in various Antarctic ecosystems to understand the cellular and genetic mechanisms that support the functional communities, energy acquisition from ultraoligotrophic conditions and bioprospecting from their secondary metabolites. See some of the research publications that have resulted from this research: Koo et al., 2017a, 2017b; 2014; Huang et al., 2012; 2013; Mojib et al., 2011a; 2011b; 2013; 2010.

(2) Gut Microbiota: Collective microbial community or “microbiota,” particularly associated with human and animal gut systems has recently spurred significant interest in our understanding of their role in maintaining almost all aspects of host health. Such association is considered a product of coevolution that has been occurring for 500 million years, suggesting a mutual selection of certain key microbial members that persist in the gut environment. Additionally, certain microbial taxa have been observed as consistent, and often heightened, in the guts of host species regardless of geographical location, alluding to the existence of a “core” gut microbiota. We are using NextGen Sequencing Technology and Bioinformatics tools to study the composition of gut microbiota of model organisms and role in the nutrient cycling that benefit the host health as well as in maintaining the trophic structure of the inhabiting ecosystems. See some of the research publications that have resulted from this research: Hakim et al., 2015; Hakim et al., 2016; Koo et al., 2017.

(3) Microbial Pathogens: The infections by antibiotic resistant Vibrio and other foodborne pathogens have been increasing worldwide at an alarming rate. This trend is in-line with the rise of many other multidrug resistant strains of deadly human pathogens, and has become a concern to governments, healthcare professionals and industries. We are interested in two categories of research investigations: (a) rapid detection of antibiotic-resistant, pathgenic strains of vibrios and other foodborne pathogens using state-of-the-art molecular technologies; and (b) exploring compunds from natural sources (bioprospecting) that potentially manifest effective antimicrobial function against this and other pathogens. See some of the research publications from students in the lab related to this research: Mojib et al., 2010; Ward and Bej, 2006; Rizvi et al., 2006; Paniker and Bej, 2005;

• Molecular Genetics
• Principles of DNA Technology

• George Green (2019-present)
• Joseph Hakim (M.S., 2013-2015; Ph.D., 2015-2019)
• Hyunmin Koo (M.S., 2011-2013; Ph.D., 2013-2018)

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• Hakim JA, Schram JB, Galloway AW, Morrow CD, Crowley MR, Watts SA, Bej AK. 2019. The Purple Sea Urchin Strongylocentrotus purpuratus Demonstrates a Compartmentalization of Gut Bacterial Microbiota, Predictive Functional Attributes, and Taxonomic Co-Occurrence. Microorganisms 7(2):35.
• Hakim JA, Morrow CD, Watts SA, Bej AK. 2019. High-throughput amplicon sequencing datasets of the metacommunity DNA of the gut microbiota of naturally occurring and laboratory aquaculture green sea urchins Lytechinus variegatus. Data in brief. 2019 Oct 1;26:104405.
• Koo H, Hakim JA, Morrow CD, Crowley MR, Andersen DT, Bej AK. 2018. Metagenomic Analysis of Microbial Community Compositions and Cold-Responsive Stress Genes in Selected Antarctic Lacustrine and Soil Ecosystems. Life (Basel, Switzerland). 2018 Jul;8(3).
• Koo H, Hakim JA, Morrow CD, Andersen DT, Bej AK. 2018. Metagenomic profile of lithobiont communities of the Untersee Oasis, Antarctica. In Methods in Microbiology volume 45 "Microbiology of atypical environments,” Gurtler V and Trevors J (editors).
• Koo H, Mojib N, Hakim JA, Hawes I, Tanabe Y, Andersen DT, Bej AK. 2017. Microbial Communities and Their Predicted Metabolic Functions in Growth Laminae of a Unique Large Conical Mat from Lake Untersee, East Antarctica. Frontiers in Microbiology. 8: 1347.
• Koo H, Hakim JA, Morrow CD, Eipers PG, Davila A, Andersen DT, Bej AK. 2017. Comparison of two bioinformatics tools used to characterize the microbial diversity and predictive functional attributes of microbial mats from Lake Obersee, Antarctica. Journal of Microbiological Methods.
• Koo H, Hakim JA, Powell ML, Kumar R, Eipers PG, Morrow CD, Crowley M, Lefkowitz EJ, Watts SA and Bej AK. 2017. Metagenomics approach to the study of the gut microbiome structure and function in Zebrafish Danio rerio fed with gluten formulated diet. Journal of Microbiological Methods 135, 69-76.
• Hakim JA, Koo H, Kumar R, Lefkowitz EJ, Morrow CD, Powell ML, Watts SA, and Bej AK. 2016. The gut microbiome of the sea urchin, Lytechinus variegatus, from its natural habitat demonstrates selective attributes of microbial taxa and predictive metabolic profiles. FEMS Microbiology Ecology, 92(9), fiw146.
• Koo H, Strope BM*, Kim EH*, Shabani AM*, Kumar R, Crowley MR, Andersen DT and Bej AK. 2016. Draft Genome Sequence of Janthinobacterium sp. Ant5-2-1 Isolated from a Proglacial Lake Podprudnoye in Schirmacher Oasis of East Antarctica. Genome Announcements, 4(1), e01600-15, PMID: 26798103. (*=Undergraduates)
• Hakim JA, Koo H, Dennis LN, Kumar R, Ptacek T, Morrow CD, Lefkowitz EJ, Powell ML, Bej AK and Watts SA. 2015. An abundance of Epsilonproteobacteria revealed in the gut microbiome of the laboratory cultured sea urchin, Lytechinus variegatus. Frontiers in Microbiology, 6(1047).
• Huang J, Mojib N, Rakesh R. Goli**, Watkins S*, Waites K, Ravindra R, Andersen DT, and Bej AK. 2012. Antimicrobial activity of PVP from an Antarctic bacterium, Janthinobacterium sp. Ant5-2, on multi-drug and methicillin resistant Staphylococcus aureus. Natural Products and Bioprospecting 2(3):104-110. (*=Undergraduate; **=High School)
• Gangwar M, Waters AM*, Bej G*, Bej AK, Mojib N. 2013. Detection of Total and Pathogenic Salmonella in Shellfish Using Real-time Multiplexed PCR Assay Targeting invA and spvB. Food Analytical Methods 6(3):922-932. (*=Undergraduate)
• Mojib N, Andersen DT, Bej AK. 2011. Structure and function of a cold shock domain fold protein, CspD, in Janthinobacterium sp. Ant5-2 from East Antarctica. FEMS Microbiology Letters 319:106-114.
• Mojib N, Nasti TH, Andersen DT, Attigada VR, Hoover RB, Yusuf N, Bej AK. 2011. The antiproliferative function of violacein-like purple violet pigment (PVP) from an Antarctic Janthinobacterium sp. Ant5-2 in UV-induced 2237 fibrosarcoma. International Journal of Dermatology 50:1223-1233.