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  1. Science & Research (NCTR)

Carl Cerniglia Ph.D.

Director, Division of Microbiology

Dr. Carl Cerniglia123

Carl Cerniglia, Ph.D.
(870) 543-7121

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About  |  Publications  |  Division Scientists


Dr. Carl Cerniglia is the Director of the Division of Microbiology at NCTR, and is a senior biomedical research service scientist for FDA. He has been employed at NCTR since 1980. He is also an adjunct professor in the Department of Pharmacology and Toxicology at the University of Arkansas Medical Sciences, Little Rock. He received his Ph.D. in microbiology from North Carolina State University in 1976. After leaving N.C. State, he was a National Cancer Institute fellow at the University of Texas at Austin from 1975 to 1980.

Dr. Cerniglia is active in a variety of government and academic committees and national and international review panels. Since 1994 he has served as an advisor and expert reviewer at the World Health Organization (WHO) on antimicrobial residues in foods. Dr. Cerniglia was elected as a fellow in the American Academy of Microbiology in 1985 and is a past chairman of the Applied and Environmental Microbiology Gordon Research Conference, as well as the Applied and Environmental Microbiology Section of the American Society for Microbiology (ASM). He has served as a member of the editorial boards for:

  • Applied and Environmental Microbiology
  • Environmental Toxicology and Water Quality
  • Journal of Industrial Microbiology and Biotechnology
  • Journal of Microbiological Methods
  • Journal of Toxicology and Environmental Health.
  • Microbial Ecology
  • World Journal of Microbiology and Biotechnology.

His research has resulted in over 400 technical publications, 39 book chapters, and numerous review articles. He also co-edited a book on "Microbial Transformation and Degradation of Toxic Organic Chemicals." His research has been frequently highlighted in the scientific and popular press. Dr. Cerniglia has made more than 400 invited presentations at national and international conferences and meetings and was also an ASM Foundation of Microbiology lecturer. Dr. Cerniglia’s research achievements have been recognized by national and international awards from:

  • American Academy of Microbiology
  • American Pharmaceutical Association
  • American Society for Microbiology
  • Department of Health and Human Services (HHS)
  • Food and Drug Administration
  • International Society of Toxicity Testing.

Dr. Cerniglia's awards include:

  • "WHO Silver Medal Award" for outstanding scientific contribution to the Joint Expert Committee on Food Additives
  • "FDA Award Merit"
  • "HHS Outstanding Leader Award" in providing mentoring, training and career advancement opportunities to employees in a diverse workforce
  • "Distinguished Alumnus Award" from North Carolina State University.

Research Interests

Dr. Cerniglia's main areas of research at NCTR are food safety/biosecurity and methods development, 2) human microbiome-host interactions, and 3) microbial transformation of drugs as models of mammalian metabolism. He also holds a focus on metabolism biochemistry, genetics of polycyclic aromatic hydrocarbon metabolism, and the biodegradation of priority pollutants in the environment. His principal research at NCTR involves studying the importance of the human gastrointestinal microbiota in the metabolism and activation/detoxification of xenobiotic compounds. Dr. Cerniglia’s research division has been advancing methodologies to evaluate the impact of veterinary-drug residues in food on the human intestinal microbiota.

In addition, his research division has also been well-recognized for leading efforts in the biodegradation of priority pollutants in the environment. Dr. Cerniglia has conducted research in the division in the elucidation of metabolic pathways of polycyclic aromatic hydrocarbons (PAHs) degradation. Using state-of-the-art analytical chemistry, metabolism, genomics, proteomics, and bioinformatics approaches he has furthered our understanding of the environmental fate of these toxic compounds in the environment. Dr. Cerniglia’s leadership in the elucidation of biodegradative pathways has been recognized by the American Academy of Microbiology by his selection as an expert panel member for a workshop on environmental issues related to the Deepwater Horizon oil spill. 
Dr. Cerniglia leads a research team that is addressing critical knowledge gaps in the microbiome field using in vitro, in vivo, and ex vivo models. They are also using germ-free, gnotobiotic, and human microflora-associated mice to determine if acute and/or chronic exposure of test compounds would affect the microbiome.

There are special food-safety concerns for the residues of antimicrobial drugs, since therapeutic doses of antimicrobials can cause adverse effects on the human-intestinal microbiota. Changes to the normal intestinal microbiota due to antimicrobial exposure can lead to reduced colonization resistance. This can allow colonization by enteric pathogens, such as Salmonella spp., Campylobacter spp. and Escherichia coli ― and can lead to increased susceptibility to other bacterial infections. In addition, continuous exposure to veterinary antimicrobials may also exert a selective pressure on the intestinal microbiota, favoring the growth of microorganisms with natural or acquired antibiotic resistance. For these reasons, FDA is currently concerned about the possibility that the consumption by humans of small quantities of veterinary antimicrobials residues in food might adversely alter the normal human-intestinal microbiota. To assess the safety of ingested antibiotic residues to the consumer, national and international committees have evaluated data on the chemical, pharmacological, toxicological, and antimicrobial properties of veterinary drugs. They based their evaluations on studies of experimental animals and observations in humans. Dr. Cerniglia’s research team has provided critical data and scientific methodology for use in harmonizing approaches used by national regulatory authorities to assess the effects of veterinary-drug residues on the intestinal microflora in the human colon. His guidance in evaluating methods and in the preparation of technical documents used for assessing the potential risk of veterinary antimicrobial residues to the human intestinal microflora has been instrumental in facilitating the regulatory-review process.

Professional Societies/National and International Groups

American Academy of Microbiology
Elected Member
1985 – Present

American Association for the Advancement of Science
1980 – Present

American Chemical Society
1980 – Present

American Society for Microbiology
1972 – Present

Joint Food and Agriculture Organization of the United Nations (FAO)/World Health Organization (WHO) Expert Committee on Food Additives (JECFA)
Expert Adviser
1994 ─ Present

Joint FAO/WHO Expert Committee on Pesticide Residues (JMPR)
Expert Adviser
2016 – Present

Society for Industrial Microbiology
1980 – Present

Selected Publications

Structure and Inhibitor Specificity of L,D-Transpeptidase (LdtMt2) from Mycobacterium tuberculosis and Antibiotic Resistance: Calcium Binding Promotes Dimer Formation.
Gokulan K., Khare S., Cerniglia C., Foley S., and Varughese K.
AAPS J. 2018, 20(2):44.

Smokeless Tobacco Impacts Oral Microbiota in a Syrian Golden Hamster Cheek Pouch Carcinogenesis Model.
Jin J., Guo L., VonTungeln L., Vanlandingham M., Cerniglia C., and Chen H.
Anaerobe. 2018, pii: S1075-9964(18)30095-7.

Microbiological Survey of Commercial Tattoo and Permanent Makeup Inks Available in the United States.
Nho S., Kim S., Kweon O., Howard P., Moon M., Sadrieh N., and Cerniglia C.
J Appl Microbiol. 2018, 124(5):1294-1302.

An in vitro Study to Assess the Impact of Tetracycline on the Human Intestinal Microbiome.
Jung J., Ahn Y., Khare S., Gokulan K., Piñeiro S., and Cerniglia C.
Anaerobe. 2018, 49:85-94.

Improved High-Quality Draft Genome Sequence and Annotation of Burkholderia contaminans LMG 23361T.
Jung J., Ahn Y., Kweon O., LiPuma J., Hussong D., Marasa B., and Cerniglia C.
Genome Announc. 2017, 5(16). pii: e00245-17.

Characterizing Chronic and Acute Health Risks of Residues of Veterinary Drugs in Food: Latest Methodological Developments By the Joint FAO/WHO Expert Committee on Food Additives.
Boobis A., Cerniglia C., Chicoine A., Fattori V., Lipp M., Reuss R., Verger P., and Tritscher A.
Crit Rev Toxicol. 2017, 47(10):885-899

Comparative Functional Pan-genome Analyses to Build Connections Between Genomic Dynamics and Phenotypic Evolution in Polycyclic Aromatic Hydrocarbon Metabolism in the Genus Mycobacterium.
Kweon O., Kim S., Blom J., Kim S., Kim B., Baek D., Park S., Sutherland J., and Cerniglia C.
BMC Evol Biol. 2015, 15:21.

Investigating the Susceptibility of Mice to a Bacterial Challenge After Intravenous Exposure to Durable Nanoparticles.
Khan S., Zhang Q., Marasa B., Sung K., Cerniglia C., Ingle T., Jones M., Paredes A., Tobin G., Bancos S., Weaver J., Goering P., Howard P., Patri A., and Tyner K.
Nanomedicine (Lond). 2017, 12(17):2097-2111.

Mutation Network-based Understanding of Pleiotropic and Epistatic Mutational Behavior of Enterococcus faecalis FMN-dependent Azoreductase.
Sun J., Kweon O., Jin J., He GX., Li X., Cerniglia C., and Chen H.
Biochem Biophys Rep. 2017, 12:240-244.

Evaluation of Metabolism of Azo Dyes and Their Effects on Staphylococcus aureus Metabolome.
Sun J., Jin J., Beger R., Cerniglia C., and Chen H.
J Ind Microbiol Biotechnol. 2017, 44(10):1471-1481.

Effects of Residual Levels of Tetracycline on the Barrier Functions of Human Intestinal Epithelial Cells.
Gokulan K., Cerniglia C., Thomas C., Pineiro S., and Khare S.
Food Chem Toxicol. 2017, 109(Pt 1):253-263.

Effects of Extended Storage of Chlorhexidine Gluconate and Benzalkonium Chloride Solutions on the Viability of Burkholderia cenocepacia.
Ahn Y., Kim J., Lee Y., LiPuma J., Hussong D., Marasa B., and Cerniglia C.
J Microbiol Biotechnol. 2017, 27(12):2211-2220

Effect of Smokeless Tobacco Products on Human Oral Bacteria Growth and Viability
Liu M., Jin J., Pan H., Feng J., Cerniglia C., Yang M., and Chen H.
Anaerobe. 2016, 42:152-161

Intrinsic Resistance of Burkholderia cepacia Complex to Benzalkonium Chloride.
Ahn Y., Kim J., Kweon O., Kim S., Jones R., Woodling K., Gamboa da Costa G., LiPuma J., Hussong D., Marasa B., and Cerniglia C.
MBio. 2016, 7(6). pii: e01716-16

Metabolomics Evaluation of the Impact of Smokeless Tobacco Exposure on the Oral Bacterium Capnocytophaga sputigena.
Sun J., Jin J., Beger R., Cerniglia C., Yang M., and Chen H.
Toxicol In Vitro. 2016, 36:133-41.

Size and Dose Dependent Effects of Silver Nanoparticle Exposure on Intestinal Permeability in an In Vitro Model of the Human Gut Epithelium.
Williams K., Gokulan K., Cerniglia C., and Khare S.
J Nanobiotechnology. 2016, 14(1):62.

An Update Discussion on the Current Assessment of the Safety of Veterinary Antimicrobial Drug residues in Food with Regard to Their Impact on the Human Intestinal Microbiome.
Cerniglia C., Pineiro S., and Kotarski S.
Drug Test Anal. 2016, 8(5-6):539-48.

Genomic Sequence of a Clinical Vancomycin-Resistant Reference Strain, Enterococcus faecalis ATCC 51299.
Sung K., Khan S., Marasa B., Min S., Kweon O., Nawaz M., and Cerniglia C.
Genome Announc. 2015, 3(6).

Draft Genome Sequence of a vanA-Type Vancomycin-Resistant Reference Strain, Enterococcus faecium ATCC 51559.
Sung K., Khan S., Marasa B., Min S., Kweon O., Mohamed N., and Cerniglia C.
Genome Announc. 2015, 3(5).

Draft Genome Sequence of Multidrug-Resistant Enterococcus faecium Clinical Isolate VRE3, with a Sequence Type 16 Pattern and Novel Structural Arrangement of Tn1546.
Khan S., Sung K., Marasa B., Min S., Kweon O., Nawaz M., and Cerniglia C.
Genome Announc. 2015, 3(4).

Dynamic Response of Mycobacterium vanbaalenii PYR-1 to BP Deepwater Horizon Crude Oil.
Kim S., Kweon O., Sutherland J., Kim H., Jones R., Burback B., Graves S., Psurny E., and Cerniglia C.
Appl Environ Microbiol. 2015, 81(13):4263-76.

Survival and Susceptibility of Burkholderia cepacia Complex in Chlorhexidine Gluconate and Benzalkonium Chloride.
Kim J., Ahn Y., LiPuma J., Hussong D., and Cerniglia C.
J Ind Microbiol Biotechnol. 2015, 42(6):905-13.

Differential Gene Expression in Staphylococcus aureus Exposed to Orange II and Sudan III Azo Dyes.
Pan H., Xu J., Kweon O., Zou W., Feng J., He G., Cerniglia C., and Chen H.
J Ind Microbiol Biotechnol. 2015, 42(5):745-57.

Effects of Subchronic Exposure of Silver Nanoparticles on Intestinal Microbiota and Gut-Associated Immune Responses in the Ileum of Sprague-Dawley Rats.
Williams K., Milner J., Boudreau M., Gokulan K., Cerniglia C., and Khare S.
Nanotoxicology. 2015, 9(3):279-89.

Approaches to Studying and Manipulating the Enteric Microbiome to Improve Autism Symptoms.
Frye R., Slattery J., MacFabe D., Allen-Vercoe E., Parker W., Rodakis J., Adams J., Krajmalnik-Brown R., Bolte E., Kahler S., Jennings J., James J., Cerniglia C., and Midtvedt T.
Microb Ecol Health Dis. 2015, 26:26878.

Phenotype-Based Identification of Key Enzymes for Polycyclic Aromatic Hydrocarbon (PAH) Metabolism from Mycobacteria Using Transposon Mutagenesis and a PAH Spray Plate.
Kim S., Kweon O., and Cerniglia C.
Hydrocarbon and Lipid Microbiology Protocols. 2015, 161–175.

Comparative Functional Pan-genome Analyses to Build Connections Between Genomic Dynamics and Phenotypic Evolution in Polycyclic Aromatic Hydrocarbon Metabolism in the Genus Mycobacterium.
Kweon O., Kim S., Blom J., Kim S., Kim B., Baek D., Park S., Sutherland J., and Cerniglia C.
BMC Evol Biol. 2015, 15:21.

Molecular Characterization of Fluoroquinolone Resistance of Methicillin –Resistant Clinical Staphylococcus aureus Isolates from Rawalpindi, Pakistan.disclaimer icon
Marasa S., Iram S., Kidon S., Kweon O., Cerniglia C., and Khan S.
Medical Research Archives. 2015, 2(2):1-14.

Pleiotropic and Epistatic Behavior of a Ring-Hydroxylating Oxygenase System in the Polycyclic Aromatic Hydrocarbon Metabolic Network from Mycobacterium Vanbaalenii PYR-1.
Kweon O., Kim S., Kim D., Kim J., Kim H., Ahn Y., Sutherland J., and Cerniglia C.
J Bacteriol. 2014, 196(19):3503-15.

A Metallo-β-Lactamase is Responsible for the Degradation of Ceftiofur by the Bovine Intestinal Bacterium Bacillus cereus P41.
Erickson B., Elkins C., Mullis L., Heinze T., Wagner R., and Cerniglia C.
Vet Microbiol. 2014, 172(3-4):499-504.

Evaluation of Liquid and Solid Culture Media for the Recovery and Enrichment of Burkholderia cenocepacia from Distilled Water.
Ahn Y., Kim J., Ahn H., Lee Y., LiPuma J., Hussong D., and Cerniglia C.
J Ind Microbiol Biotechnol. 2014, 41(7):1109-18.

Workshop Report: the 2012 Antimicrobial Agents in Veterinary Medicine: Exploring the Consequences of Antimicrobial Drug Use: A 3-D Approach.
Martinez M., Blondeau J., Cerniglia C., Fink-Gremmels J., Guenther S., Hunter R., Li X., Papich M., Silley P., Soback S., Toutain P., and Zhang Q.
J Vet Pharmacol Ther. 2014, 37(1):e1-e16.

Division Scientists

Contact information for all lab members:
(870) 543-7121

Youngbeom Ahn
Staff Fellow

Marli Azevedo
Senior Staff Fellow

Huizhong Chen

Bruce Erickson
Senior Staff Fellow

Steven Foley

Kuppan Gokulan
Staff Fellow

Mark Hart

Jinshan Jin
Staff Fellow

Shemedia Johnson

Bijay Khajanchi
Staff Fellow

Ashraf Khan

Saeed Khan

Sangeeta Khare

Seong-Jae Kim
Staff Fellow

Ohgew Kweon
Staff Fellow

Lisa Mullis

Mohamed Nawaz

Fatemeh Rafii

Kidon Sung
Staff Fellow  

Robert Wagner

Contact Information
Carl Cerniglia
(870) 543-7121
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