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  1. Science & Research (NCTR)



Director: Carl E. Cerniglia, Ph.D.

The Division of Microbiology's goals are to perform fundamental and applied research to address critical issues in support of the FDA mission. The Division's research projects are based on expertise of division staff and consultation with scientists from other FDA Centers, regulatory agencies, academia, and industry.

The Division staff includes research scientists, research support staff, postdoctoral fellows, undergraduate and graduate students, visiting scientists, and program support specialists. The Division staff has the facilities and equipment to help address the scientific challenges encountered by FDA and other government organizations. The Division of Microbiology scientists are actively engaged in research addressing FDA issues with special emphasis on:

Scientist working with microbiology culture
  1. Improving methods to detect, identify, and characterize foodborne pathogens.
  2. Determining antimicrobial resistance and virulence mechanisms of microbial pathogens.
  3. Using state-of-the-art molecular biological approaches to monitor interactions between the human microbiome and antimicrobial agents, nanomaterials, food contaminants, and FDA-regulated products.
  4. Conducting studies related to  women's health.
  5. Improving environmental risk assessments of priority pollutants, including polycyclic aromatic hydrocarbons and drugs, by integrating systems biology approaches.
  6. Conducting research involving nanotechnology.
  7. Evaluating smokeless-tobacco products for toxicity from a microbiology perspective.

Upcoming Plans for Research

Food Safety and Virology

  • Develop bioinformatics tools to characterize the genetics of plasmids and virulence in Salmonella.
  • Develop multilocus sequence typing methods for rapid detection of microorganisms in different foods.
  • Optimize methods to isolate bacteria, fungi, and their DNA from consumer products to determine product contamination.
  • Determine the effect of sunlight on the environmental survival of noroviruses and contamination of farm produce.
  • Determine the impact of viral genetic material on Salmonella infection using in vitro (cell-based) models and identify factors that are important to the transfer of viral genetic material among bacteria found in the gut.
  • Investigate the effect of nanoparticles on norovirus replication in a co-infection model with a foodborne pathogen.

Antimicrobials and Pharmaceutical Products

  • Study the contamination of pharmaceutical products by the Burkholderia cepacia complex to determine how this opportunistic pathogen survives in disinfectant solutions.
  • Develop multi-omics approaches to identify antimicrobial resistance markers of Staphylococcus aureus associated with antimicrobial-coated medical devices.
  • Identify and characterize antibiotic-resistant Salmonella from imported food samples and investigate the transferability of antibiotic-resistance genes to other intestinal bacteria.
  • Evaluate the impact of antimicrobial exposure on plasmid transfer for Salmonella strains exposed to different antimicrobial agents.
  • Evaluate the plasmid-associated antimicrobial resistance and virulence in Salmonella using DNA sequence data analysis and in vitro assessment.
  • Examine antimicrobial resistance and biofilm development in S. aureus contaminating indwelling medical devices that contain imbedded antibiotics.
  • Study the role of efflux pumps in antibiotic resistance, biofilm formation and colonization by E. coli associated with urinary tract infections.
  • Detect the effect of antimicrobial agents on the induction of resistance in Clostridium perfringens.

Microbes and Host Interactions

  • Undertake a risk assessment of the effect of xenobiotic compounds, through a National Toxicology Program funded project, on the microbiomes of experimental animals dosed with test study compounds. 
  • Evaluate the effect of residual levels of antimicrobial agents on the intestinal microbiota.
  • Evaluate the effect of nanoparticles and nanodrugs on the intestinal microbiota.
  • Investigate the effect of intestinal bacterial metabolism on genotoxicity of food contaminants, such as Sudan dyes.
  • Evaluate molecular assays and culture-based reference methods for the detection of toxigenic C. difficile.
  • Fecal transplant mechanisms: evaluation of differential pro-inflammatory responses of intestinal epithelial and dendritic cells to Clostridium difficile and commensal bacteria.
  • Identify microRNAs (biomarkers or disease indicators) involved in the control of genetic interactions and disease-development processes associated with anthrax.
  • Study how certain types of bacteria in the human intestinal microbiome influence intestinal epithelial cells and dendritic cells to inhibit or advance C. difficile infections, and better understand the mechanisms of fecal microbiota transplantation.

Office of Women’s Health Projects

  • Systematically examine toxin-producing strains of Staphylococcus aureus with a variety of tampons to determine the feasibility of generating a microbiological standard of testing.
  • Evaluate differences in mode of cellular toxicity to vaginal epithelial cells induced by various graphene nanoparticles as potential vaginal drug-delivery vehicles.
  • Characterize the efflux pump activities of cellular function contributing to antibiotic resistance in bacteria associated with diseases of the urinary tract.
  • Examine the safety of using nanoparticles as intravaginal drug delivery systems.

Environmental Biotechnology

  • Continue analysis of the mechanism of fluoroquinolone breakdown by drug-resistant bacteria from wastewater.
  • Continue analysis of the mechanism behind the bacterial degradation of BP crude oil by analyzing and utilizing a broad range of data sources.
  • Assess the biotransformation of plant-derived terpenoids by fungi to produce new compounds with antibacterial, antifungal, antiparasitic, antiviral, or antitumor activity.
  • Develop detection methods for Mycobacterium chelonae contamination of tattoo inks.


  • Examine the effects of silver nanoparticles in an in vitro cell-culture based model of intestinal permeability.
  • Establish a nonclinical model and perform risk assessment of FDA-regulated drug-nanocrystals.
  • Continue collaboration with the Arkansas Research Consortium in Nanotechnology to test graphene-induced toxicity associated with the gut and intestine.
  • Study the impacts of nanomaterials on enhancing the antibacterial activity of traditional antibiotics on Pseudomonas aeruginosa.
  • Evaluate human skin, intestinal and vaginal microbiota (bacteria and viruses), as well as host toxicity (using in vitro, ex vivo and in vivo models) in the presence of metal and carbon-based nanoscale materials.
  • Investigate the effects of nanoparticles used in dentistry on the oral microbiota.

Tobacco Product Research

  • Evaluate the effect of smokeless tobacco products on oral microbiota at the physiological and metabolomic levels and conduct bioinformatics data analysis to determine the effects of smokeless tobacco products and tobacco-specific nitrosamines on oral bacterial ecology of animals.
  • Optimize methods to isolate bacteria and fungi from smokeless tobacco products and identify the microbial population by molecular genetic approaches. 
  • Quantify nitrate, nitrite, nicotine, and tobacco-specific nitrosamines (TSNAs) content in smokeless tobacco products and examine the effects of smokeless tobacco products and TSNAs on oral bacterial ecology of animals.