Positions

Overview

  • Dr. Bej is a retired professor from the Department of Biology. He is a Credentialed Course Instructor Faculty at the Department of Criminal Justice. He has studied microbial gene regulation and the development and applications of molecular methods for the rapid diagnosis of pathogens at the University of Louisville, Louisville, KY. His current research interest encompasses the study of microbiome science to understand the structure, function, and applications of the microbial network in the (1) gut ecosystems of laboratory model animals, (2) Antarctic cold ecosystems, and (3) forensic investigations. Currently, he is studying the forensic microbiome in collaboration with colleagues at the Department of Criminal Justice (Forensic Science), and the microbiome structure and function in the Gulf of Mexico coastal ecosystems. He has published numerous research papers, review articles, and book chapters. He is the lead editor of a book titled "Polar Microbiology: The Ecology, Biodiversity and Bioremediation Potential of Microorganisms in Extremely Cold Environments" (Taylor & Francis Publisher). Dr. Bej has established active research collaborations with colleagues in the U.S. and worldwide. He is a recipient of the President’s and the Dean’s Award for Excellence in Teaching at UAB, NASA Faculty Fellowship, Honorary Member of the Golden Key International Honor Society, and the Tawani/NASA Exobiology Antarctic Scientific Research Expedition. He serves as Editor of the Elsevier Journal of Microbiological Methods and also on the editorial board of several microbiology journals.
  • Selected Publications

    Academic Article

    Year Title Altmetric
    2022 High-throughput amplicon sequencing datasets of the metacommunity DNA of the gut microbiota of Zebrafish Danio rerio fed diets with differential quantities of protein and fat contentsData in Brief.  42. 2022
    2021 Microbial composition and genes for key metabolic attributes in the gut digesta of sea urchins lytechinus variegatus and strongylocentrotus purpuratus using shotgun metagenomicsCurrent Issues in Molecular Biology.  43:978-995. 2021
    2021 The Gut Microbiota of Naturally Occurring and Laboratory Aquaculture Lytechinus variegatus Revealed Differences in the Community Composition, Taxonomic Co-Occurrence, and Predicted Functional AttributesApplied and Environmental Microbiology.  1:201-224. 2021
    2019 High-throughput amplicon sequencing datasets of the metacommunity DNA of the gut microbiota of naturally occurring and laboratory aquaculture green sea urchins Lytechinus variegatusData in Brief.  26. 2019
    2019 The purple sea urchin strongylocentrotus purpuratus demonstrates a compartmentalization of gut bacterial microbiota, predictive functional attributes, and taxonomic co-occurrenceMicroorganisms.  7. 2019
    2018 Metagenomic analysis of microbial community compositions and cold-responsive stress genes in selected antarctic lacustrine and soil ecosystemsLife.  8. 2018
    2018 Microbial Community Composition and Predicted Functional Attributes of Antarctic Lithobionts Using Targeted Next-Generation Sequencing and Bioinformatics ToolsMethods in Microbiology.  45:243-290. 2018
    2017 Comparison of two bioinformatics tools used to characterize the microbial diversity and predictive functional attributes of microbial mats from Lake Obersee, AntarcticaJournal of Microbiological Methods.  140:15-22. 2017
    2017 Microbial communities and their predicted metabolic functions in growth laminae of a unique large conical mat from Lake Untersee, East AntarcticaFrontiers in Microbiology.  8. 2017
    2017 Metagenomics approach to the study of the gut microbiome structure and function in zebrafish Danio rerio fed with gluten formulated dietJournal of Microbiological Methods.  135:69-76. 2017
    2016 The gut microbiome of the sea urchin, Lytechinus variegatus, from its natural habitat demonstrates selective attributes of microbial taxa and predictive metabolic profilesFEMS Microbiology Ecology.  92. 2016
    2016 Metagenomic data of the bacterial community in coastal Gulf of Mexico sediment microcosms following exposure to Macondo oil (MC252)Data in Brief.  6:89-93. 2016
    2016 Distribution of cold adaptation proteins in microbial mats in Lake Joyce, Antarctica: Analysis of metagenomic data by using two bioinformatics toolsJournal of Microbiological Methods.  120:23-28. 2016
    2016 Draft genome sequence of Janthinobacterium sp. Ant5-2-1, isolated from Proglacial Lake Podprudnoye in the Schirmacher Oasis of East AntarcticaGenome Announcements.  4. 2016
    2015 Bacterial community shift in the coastal Gulf of Mexico salt-marsh sediment microcosm in vitro following exposure to the Mississippi Canyon Block 252 oil (MC252)3 Biotech.  5:379-392. 2015
    2015 An abundance of Epsilonproteobacteria revealed in the gut microbiome of the laboratory cultured sea urchin, Lytechinus variegatusFrontiers in Microbiology.  6. 2015
    2014 Comparative analysis of bacterial community-metagenomics in coastal Gulf of Mexico sediment microcosms following exposure to Macondo oil (MC252)Antonie van Leeuwenhoek: international journal of general and molecular microbiology.  106:993-1009. 2014
    2014 Draft genome sequence of Hymenobacter sp. strain IS2118, isolated from a freshwater lake in Schirmacher Oasis, Antarctica, reveals diverse genes for adaptation to cold ecosystemsGenome Announcements.  2. 2014
    2014 Draft genome sequence of Pseudomonas sp. strain Ant30-3, a psychrotolerant bacterium with biodegradative attribute isolated from AntarcticaGenome Announcements.  2. 2014
    2013 Detection of Salmonella in Shellfish Using SYBR Green™ I-Based Real-Time Multiplexed PCR Assay Targeting invA and spvBFood Analytical Methods.  6:922-932. 2013
    2013 Detection of phage infection in the bacterial population of Lake Untersee (Antarctica)Microbiology (Russian Federation).  82:383-386. 2013
    2013 UV and cold tolerance of a pigment-producing Antarctic Janthinobacterium sp. Ant5-2Extremophiles.  17:367-378. 2013
    2013 [The discovery of phages in the bacterial population in lake Untersee (Antarctica)].Microbiology (Russian Federation).  82:366-369. 2013
    2013 Bacterial diversity of the rock-water interface in an East Antarctic freshwater ecosystem, Lake Tawani(P)Aquatic Biosystems.  9. 2013
    2013 Bacterial diversity within five unexplored freshwater lakes interconnected by surface channels in East Antarctic Dronning Maud Land (Schirmacher Oasis) using amplicon pyrosequencingPolar Biology.  37:359-366. 2013
    2013 The molecularly crowded cytoplasm of bacterial cells: Dividing cells contrasted with viable but non-culturable (VBNC) bacterial cellsCurrent Issues in Molecular Biology.  15:1-6. 2013
    2012 Antimicrobial activity of PVP from an Antarctic bacterium, Janthinobacterium sp. Ant5-2, on multi-drug and methicillin resistant Staphylococcus aureusNatural Products and Bioprospecting.  2:104-110. 2012
    2012 Bacterial gene expression at low temperaturesExtremophiles.  16:167-176. 2012
    2011 The antiproliferative function of violacein-like purple violet pigment (PVP) from an Antarctic Janthinobacterium sp. Ant5-2 in UV-induced 2237 fibrosarcomaInternational Journal of Dermatology.  50:1223-1233. 2011
    2011 Structure and function of a cold shock domain fold protein, CspD, in Janthinobacterium sp. Ant5-2 from East AntarcticaFEMS Microbiology Letters.  319:106-114. 2011
    2010 Antimycobacterial activity in vitro of pigments isolated from Antarctic bacteriaAntonie van Leeuwenhoek: international journal of general and molecular microbiology.  98:531-540. 2010
    2010 Multiplexed real-time PCR amplification of tlh, tdh and trh genes in Vibrio parahaemolyticus and its rapid detection in shellfish and Gulf of Mexico waterAntonie van Leeuwenhoek: international journal of general and molecular microbiology.  98:279-290. 2010
    2010 Multiplexed real-time PCR amplification of tlh, tdh and trh genes in Vibrio parahaemolyticus and its rapid detection in shellfish and Gulf of Mexico water.Antonie van Leeuwenhoek: international journal of general and molecular microbiology.  98:279-290. 2010
    2010 Detection, expression and quantitation of the biodegradative genes in Antarctic microorganisms using PCRAntonie van Leeuwenhoek: international journal of general and molecular microbiology.  97:275-287. 2010
    2010 Occurrence and distribution of capB in Antarctic microorganisms and study of its structure and regulation in the Antarctic biodegradative Pseudomonas sp. 30/3Extremophiles.  14:171-183. 2010
    2009 Erratum: Spirochaeta dissipatitropha sp. nov., an alkaliphilic, obligately anaerobic bacterium, and emended description of the genus Spirochaeta Ehrenberg 1835 (International Journal of Systematic and Evolutionary Microbiology (2009) vol. 59 (1798-1804) 10.1099/ijs.0.016733-0)International Journal of Systematic and Evolutionary Microbiology.  59:2646. 2009
    2009 Spirochaeta dissipatitropha sp. nov., an alkaliphilic, obligately anaerobic bacterium, and emended description of the genus Spirochaeta Ehrenberg 1835International Journal of Systematic and Evolutionary Microbiology.  59:2646-2646. 2009
    2009 Spirochaeta dissipatitropha sp. nov., an alkaliphilic, obligately anaerobic bacterium, and emended description of the genus Spirochaeta Ehrenberg 1835.International Journal of Systematic and Evolutionary Microbiology.  59:1798-1804. 2009
    2009 Spirochaeta dissipatitropha sp. nov., an alkaliphilic, obligately anaerobic bacterium, and emended description of the genus Spirochaeta Ehrenberg 1835International Journal of Systematic and Evolutionary Microbiology.  59:1798-1804. 2009
    2007 Thermococcus thioreducens sp. nov., a novel hyperthermophilic, obligately sulfur-reducing archaeon from a deep-sea hydrothermal ventInternational Journal of Systematic and Evolutionary Microbiology.  57:1612-1618. 2007
    2007 Tsukamurella spongiae sp. nov., a novel actinomycete isolated from a deep-water marine spongeInternational Journal of Systematic and Evolutionary Microbiology.  57:1478-1481. 2007
    2007 Erratum: Multiplex PCR detection of clinical and environmental strains of Vibrio vulnificus in shellfish (Canadian Journal of Microbiology (2004) 50, (911-922))Canadian Journal of Microbiology.  53:671. 2007
    2006 Analysis of aggregative behavior of Pseudomonas sp. 30-3 isolated from Antarctic soilSoil Biology and Biochemistry.  38:3152-3157. 2006
    2006 Detection of pandemic Vibrio parahaemolyticus O3:K6 serovar in Gulf of Mexico water and shellfish using real-time PCR with Taqman® fluorescent probesFEMS Microbiology Letters.  262:185-192. 2006
    2006 Trichococcus patagoniensis sp. nov., a facultative anaerobe that grow at -5 °C, isolated from penguin guano in Chilean PatagoniaInternational Journal of Systematic and Evolutionary Microbiology.  56:2055-2062. 2006
    2006 Detection of Vibrio parahaemolyticus in shellfish by use of multiplexed real-time PCR with TaqMan fluorescent probesApplied and Environmental Microbiology.  72:2031-2042. 2006
    2005 Real-time PCR detection of Vibrio vulnificus in oysters: Comparison of oligonucleotide primers and probes targeting vvhAApplied and Environmental Microbiology.  71:5702-5709. 2005
    2005 Characterization of Arthrobacter nicotinovorans HIM, an atrazine-degrading bacterium, from agricultural soil New ZealandFEMS Microbiology Ecology.  52:279-286. 2005
    2005 Carnobacterium pleistocenium sp. nov., a novel psychrotolerant, facultative anaerobe isolated from permafrost of the Fox tunnel in AlaskaInternational Journal of Systematic and Evolutionary Microbiology.  55:473-478. 2005
    2004 Detection of pathogenic Vibrio spp. in shellfish by using multiplex PCR and DNA microarraysApplied and Environmental Microbiology.  70:7436-7444. 2004
    2004 Multiplex PCR detection of clinical and environmental strains of Vibrio vulnificus in shellfishCanadian Journal of Microbiology.  50:911-922. 2004
    2004 Rapid Detection of Vibrio vulnificus in Shellfish and Gulf of Mexico Water by Real-Time PCRApplied and Environmental Microbiology.  70:498-507. 2004
    2004 Real-time PCR quantification of Vibrio parahaemolyticus in oysters using an alternative matrixJournal of Food Protection.  67:2424-2429. 2004
    2003 Desulfonatronum thiodismutans sp. nov., a novel alkaliphilic, sulfate-reducing bacterium capable of lithoautotrophic growthInternational Journal of Systematic and Evolutionary Microbiology.  53:1327-1332. 2003
    2003 Tindallia californiensis sp. nov., a new anaerobic, haloalkaliphilic, spore-forming acetogen isolated from Mono Lake in CaliforniaExtremophiles.  7:327-334. 2003
    2003 Detection of pathogenic bacteria in shellfish using multiplex PCR followed by CovaLink™ NH microwell plate sandwich hybridizationJournal of Microbiological Methods.  53:199-209. 2003
    2003 Molecular based methods for the detection of microbial pathogens in the environmentJournal of Microbiological Methods.  53:139-140. 2003
    2003 Spirochaeta americana sp. nov., a new haloalkaliphilic, obligately anaerobic spirochaete isolated from soda Mono Lake in CaliforniaInternational Journal of Systematic and Evolutionary Microbiology.  53:815-821. 2003
    2003 PCR detection of a newly emerged pandemic Vibrio parahaemolyticus O3:K6 pathogen in pure cultures and seeded waters from the Gulf of MexicoApplied and Environmental Microbiology.  69:2194-2200. 2003
    2003 Oyster-to-oyster variability in levels of Vibrio parahaemolyticusJournal of Food Protection.  66:125-129. 2003
    2002 Cold tolerance of Pseudomonas sp. 30-3 isolated from oil-contaminated soil, AntarcticaPolar Biology.  25:5-11. 2002
    2002 Evaluation of PCR amplification-based detection of heat-killed Escherichia coli and cell-free DNA in shellfishMolecular biology today : the online journal of molecular biology.  3:85-90. 2002
    2002 Molecular analysis of Vibrio parahaemolyticus isolated from human patients and shellfish during US Pacific north-west outbreaksLetters in Applied Microbiology.  34:155-161. 2002
    2001 Response and tolerance of toxigenic Vibro cholerae O1 to cold temperaturesAntonie van Leeuwenhoek: international journal of general and molecular microbiology.  79:377-384. 2001
    2000 Cluster analysis of AP-PCR generated DNA fingerprints of Vibrio vulnificus isolates from patients fatally infected after consumption of raw oystersLetters in Applied Microbiology.  30:258-262. 2000
    2000 Adaptive response to cold temperatures and characterization of cspA in Salmonella typhimurium LT2Antonie van Leeuwenhoek: international journal of general and molecular microbiology.  77:13-20. 2000
    2000 Cold-tolerant alkane-degrading Rhodococcus species from AntarcticaPolar Biology.  23:100-105. 2000
    1999 Detection of total and hemolysin-producing Vibrio parahaemolyticus in shellfish using multiplex PCR amplification of tl, tdh and trhJournal of Microbiological Methods.  36:215-225. 1999
    1999 Adaptive response to cold temperatures in Vibrio vulnificusCurrent Microbiology: an international journal.  38:168-175. 1999
    1998 Detection of microbial pathogens in shellfish with multiplex PCRCurrent Microbiology: an international journal.  37:101-107. 1998
    1998 Optimization of the arbitrarily-primed polymerase chain reaction (AP-PCR) for intra-species differentiation of Vibrio vulnificusJournal of Microbiological Methods.  33:181-189. 1998
    1998 Detection of Giardia in environmental waters by immuno-PCR amplification methodsCurrent Microbiology: an international journal.  36:107-113. 1998
    1998 Growth, survival and characterization of CspA in Salmonella enteritidis following cold shockCurrent Microbiology: an international journal.  36:29-35. 1998
    1996 Detection of Viable Vibrio cholerae by Reverse-Transcriptase Polymerase Chain Reaction (RT-PCR)Molecular Biotechnology.  5:1-10. 1996
    1995 Molecular cloning of a cDNA encoding putative molt-inhibiting hormone from the blue crab, callinectes sapidusBiochemical and Biophysical Research Communications.  209:1126-1131. 1995
    1994 Adaptive acid tolerance response (ATR) in Aeromonas hydrophilaMicrobiology.  140:1731-1736. 1994
    1994 Detection of Salmonella spp. in oysters by PCRApplied and Environmental Microbiology.  60:368-373. 1994
    1993 Detection of Salmonella spp. in Oysters Using Polymerase Chain Reactions (PCR) and Gene ProbesJournal of Food Science.  58:1191-1197. 1993
    1993 Suicidal genetic elements and their use in biological containment of bacteriaAnnual Review of Microbiology.  47:139-166. 1993
    1992 Applications of the polymerase chain reaction in environmental microbiologyGenome Research.  1:151-159. 1992
    1992 MONITORING MICROBIAL PATHOGENS AND INDICATOR MICROORGANISMS IN WATER USING THE POLYMERASE CHAIN-REACTION AND GENE PROBE METHODSACS National Meeting Book of Abstracts.  204:8-ENVR. 1992
    1992 Maintenance and killing efficiency of conditional lethal constructs in Pseudomonas putidaJournal of Industrial Microbiology and Biotechnology.  10:79-85. 1992
    1992 Applications of the polymerase chain reaction in environmental microbiologyGenome Research.  1:151-159. 1992
    1992 Differentiation of Giardia duodenalis from other Giardia spp. by using polymerase chain reaction and gene probesJournal of Clinical Microbiology.  30:74-78. 1992
    1992 Molecular approaches for environmental monitoring of microorganismsBioTechniques: the journal of laboratory technology for bioresearch.  12:706-717. 1992
    1991 Response of microbial populations to environmental disturbanceMicrobial Ecology: an international journal.  22:249-256. 1991
    1991 Erratum: Detection of Escherichia coli and Shigella spp. in water by using the polymerase chain reaction and gene probes for uid (Applied and Environmental Microbiology 57 (1013-1017))Applied and Environmental Microbiology.  57:2445. 1991
    1991 CORRECTIONApplied and Environmental Microbiology.  57:2445-2445. 1991
    1991 Detection of bacterial mRNA using polymerase chain reactionBioTechniques: the journal of laboratory technology for bioresearch.  10:48-49. 1991
    1991 Acquisition of mitochondrial DNA by a transformation vector for Ustilago violaceaGene.  98:135-140. 1991
    1991 Amplification of nucleic acids by polymerase chain reaction (PCR) and other methods and their applicationsCritical Reviews in Biochemistry and Molecular Biology.  26:301-334. 1991
    1991 Detection of Escherichia coli and Shigella spp. in water by using the polymerase chain reaction and gene probes for uidApplied and Environmental Microbiology.  57:1013-1017. 1991
    1991 Detection of Giardia cysts by using the polymerase chain reaction and distinguishing live from dead cystsApplied and Environmental Microbiology.  57:3456-3461. 1991
    1991 Detection of coliform bacteria and Escherichia coli by multiplex polymerase chain reaction: Comparison with defined substrate and plating methods for water quality monitoringApplied and Environmental Microbiology.  57:2429-2432. 1991
    1991 Detection of viable Legionella pneumophila in water by polymerase chain reaction and gene probe methodsApplied and Environmental Microbiology.  57:597-600. 1991
    1991 Effect of introducing genetically engineered microorganisms on soil microbial community diversityFEMS Microbiology Letters.  86:169-176. 1991
    1991 Effect of introducing genetically engineered microorganisms on soil microbial community diversityFEMS Microbiology Letters.  86:169-175. 1991
    1991 Polymerase chain reaction-gene probe detection of microorganisms by using filter-concentrated samplesApplied and Environmental Microbiology.  57:3529-3534. 1991
    1990 Introduction and maintenance of prokaryotic DNA in Ustilago violaceaJournal of Industrial Microbiology and Biotechnology.  5:355-363. 1990
    1990 A high efficiency transformation system for the basidiomycete Ustilago violacea employing hygromycin resistance and lithium-acetate treatmentGene.  86:135. 1990
    1990 Detection of Legionella with polymerase chain reaction and gene probe methodsMolecular and Cellular Probes.  4:175-187. 1990
    1990 Detection of coliform bacteria in water by polymerase chain reaction and gene probesApplied and Environmental Microbiology.  56:307-314. 1990
    1990 Microbial degradation of quinoline and methylquinolinesApplied and Environmental Microbiology.  56:345-351. 1990
    1990 Multiplex PCR amplification and immobilized capture probes for detection of bacterial pathogens and indicators in waterMolecular and Cellular Probes.  4:353-365. 1990
    1989 Preparation of protoplasts of Ustilago violacea for transformation and pulse-field electrophoresis.BioTechniques: the journal of laboratory technology for bioresearch.  7. 1989
    1989 A high efficiency transformation system for the basidiomycete Ustilago violacea employing hygromycin resistance and lithium-acetate treatmentGene.  80:171-176. 1989
    1989 Approaches for monitoring and containing genetically engineered microorganisms released into the environmentEnvironmental Engineering Science.  6:135-144. 1989
    1988 Model suicide vector for containment of genetically engineered microorganismsApplied and Environmental Microbiology.  54:2472-2477. 1988
    1988 Recovery of DNA from soils and sediments.Applied and Environmental Microbiology.  54:2908-2915. 1988
    1984 Effects of desiccation on the ventral nerve cord-neurosecretory system of tropical earthworm, Metaphire peguana (Rosa, 1890)Proceedings: Animal Sciences.  93:43-47. 1984

    Chapter

    Year Title Altmetric
    2016 CRISPR-Cas System: A new Paradigm for Bacterial Stress Response Through Genome Rearrangement.  146-160. 2016
    2016 Metagenomic Analysis of Microbial Cold Stress Proteins in Polar Lacustrine Ecosystems.  837-844. 2016
    2011 Vibrio.  1073-1088. 2011
    2009 Vibrio.  485-500. 2009

    Research Overview

  • Dr. Bej's current research interests are (1) Microbiome Science; and (2) Microbial extremophiles in Antarctic cold and subzero environments.

    (1) Microbiome science: (a) Gut microbiome, metabolism, and disease in laboratory animal models; (b) Microbiome applications in forensic science.

    (2) Extremophiles: (a) Metagenomic study of extremophiles in polar ecosystems; (b) Gene structure, function, and regulation of cold adaption in enteric and Antarctic bacteria.
  • Teaching Overview

  • Dr. Bej taught molecular genetics and DNA technology courses in the past. He supervises graduate research students and provides professional services to academic and research organizations.

    Courses:
    BY 311/511 - Molecular Genetics (Past)
    BY 431/531 - Principles of DNA Technology (Past)
    BY 694/794 - Colloquium in Microbiology (Past)
    BY 210/501 - Genetics/Genetics for teachers (Past)
    BY 432/632/732 - Biological Information Resources (Online) (Past)
    BY 445/545 - Investigative Molecular Genetics (Past)
    BY 261 - Microbiology (Past)
    BY 494/695/795 - Extremophiles and Bioprospecting (Past)
  • Full Name

  • Asim Bej