Research Programs

Our research spans agricultural microbiomes, microbial genomics, vaccine development, and bioinformatics to address challenges in animal health and food safety. We develop rapid molecular detection methods, characterize pathogen biofilms under environmental stress, and apply whole-genome sequencing for epidemiological surveillance. Additionally, we use reverse vaccinology and host-pathogen interactions studies to identify promising vaccine candidates against foodborne and poultry pathogens.

Agricultural Microbiome

Overview

The microbiome plays critical roles in food safety, pathogen colonization resistance, and product quality. We apply culturomics and metagenomic approaches to characterize microbial communities in food production systems and identify beneficial microorganisms.

Research Highlights

Culturomics for Beneficial Microbe Discovery

  • Targeted cultivation and isolation of beneficial bacteria from animal gut microbiomes
  • Genomic characterization of probiotic candidate isolates
  • Evaluating colonization resistance effects against foodborne pathogens
  • Full-length 16S rRNA sequencing for species-level identification

Microbiome-Pathogen Interactions

  • Gut microbiome associations with pathogen colonization
  • Effects of dietary interventions on microbiome composition and pathogen resistance
  • Probiotic supplementation effects on food safety outcomes

Spoilage Microbiome Characterization

  • Culture-independent metagenomic analysis of spoilage bacteria
  • Microbiome dynamics during refrigerated storage
  • Identifying key spoilage organisms for targeted intervention

Key Publications

  • Wang et al. (2026) Poultry Science — Application of culturomics to explore the cultivable microbiota of broiler ceca. DOI
  • Zhang et al. (2021) Poultry Science — Cecal microbiota contribute to woody breast myopathy. DOI
  • Jia et al. (2022) Poultry Science — Woody breast myopathy-associated gut microbiome. DOI

Advanced Molecular Detection Methods

Overview

Early and accurate detection of foodborne pathogens is critical for food safety management. We develop and validate rapid molecular diagnostic tools including LAMP assays, real-time PCR, and multiplex detection methods for practical application in food safety monitoring.

Research Highlights

LAMP Assay Development

  • Developed and optimized loop-mediated isothermal amplification (LAMP) assays for Clostridium perfringens detection
  • Evaluated multiple DNA extraction methods for field compatibility
  • Validated assay performance across diverse sample matrices
  • Target: Field-deployable diagnostic systems for food safety applications

Real-Time PCR Methods

  • Developed TaqMan-based multiplex qPCR for rapid pathogen detection
  • Cytokine response profiling assays for host-pathogen interaction studies
  • Validated across tissue, environmental, and food samples

Detection Method Validation

  • Sensitivity and specificity optimization
  • Cross-reactivity assessment with related organisms
  • Performance evaluation under field conditions

Bioluminescent Pathogen Tracking

  • Construction and characterization of bioluminescent Salmonella Reading strains
  • Real-time imaging for pathogen tracking and transmission studies
  • Comparison of outbreak and non-outbreak strain characteristics

Key Publications

  • Chaudhary et al. (2025) J. Applied Poultry Research — DNA extraction method evaluation for LAMP. DOI
  • Chaudhary et al. (2024) J. Applied Poultry Research — LAMP assay optimization for C. perfringens. DOI
  • Isah et al. (2024) Microbiology Spectrum — Construction and characterization of bioluminescent Salmonella Reading outbreak and non-outbreak strains. DOI

Media Coverage

Vaccine Development & Host-Pathogen Interactions

Overview

Vaccines offer a sustainable approach to reducing foodborne pathogen contamination at the source. We apply reverse vaccinology, computational immunoinformatics, and molecular characterization to identify novel vaccine candidates against key foodborne pathogens.

Research Highlights

Reverse Vaccinology Approaches

  • Pangenome analysis to identify conserved, surface-exposed vaccine targets
  • In silico prediction of immunogenic antigens
  • Identified pagP as a potential universal vaccine candidate against pathogenic E. coli
  • Host-pathogen interaction analysis using cell culture infection models

Campylobacter jejuni Vaccine Candidates

  • In silico prediction and expression analysis of vaccine candidate genes
  • BtuB-based immune intervention strategies
  • Developing challenge models for vaccine efficacy assessment

Host Immune Response Characterization

  • Cytokine response profiling during infection
  • Macrophage infection models for pathogen-host interaction studies
  • Immune pathway analysis for vaccine target validation

Key Publications

  • Jia et al. (2025) J. Applied Microbiology — Reverse vaccinology identifies pagP vaccine candidate. DOI
  • Poudel et al. (2024) World Poultry Science Journal — C. jejuni vaccine development review. DOI
  • Poudel et al. (2023) Poultry Science — Vaccine candidate gene expression analysis. DOI
  • Ye et al. (2025) Poultry Science — Cytokine response dynamics during APEC infection. DOI

Media Coverage

Whole-Genome Sequencing & Bioinformatics

Overview

Whole-genome sequencing (WGS) has revolutionized foodborne pathogen surveillance and epidemiology. We develop and apply high-throughput sequencing pipelines and bioinformatics workflows for pathogen characterization, outbreak investigation, and antimicrobial resistance profiling.

Research Highlights

Oxford Nanopore Sequencing Pipelines

  • Developed high-throughput Nanopore-based MLST (multilocus sequence typing) pipeline for large-scale pathogen studies
  • Characterized >500 E. coli isolates using custom bioinformatics workflows
  • Implemented O-serogroup typing from long-read sequencing data
  • Real-time sequencing protocols for rapid pathogen identification

Genomic Epidemiology

  • Complete genome sequencing of outbreak and non-outbreak Salmonella Reading strains
  • Pangenome analysis revealing evolutionary clusters and transmission patterns
  • Virulence gene and antimicrobial resistance profiling from WGS data
  • Integration of genomic data with epidemiological metadata

Bioinformatics Pipeline Development

  • Custom pipelines for serotyping, MLST, and virulence profiling
  • Large dataset management for multi-hundred isolate studies
  • Automated analysis workflows for routine surveillance applications
  • High-performance computing (HPC) implementation for scalable analysis

Key Publications

  • Jia et al. (2024) Poultry Science — High-throughput Nanopore MLST pipeline. DOI
  • Jia et al. (2024) Microbiology Resource Announcements — Complete genome sequences of pathogenic E. coli. DOI
  • Li et al. (2020) J. Global Antimicrobial Resistance — Complete genome sequence of multidrug-resistant avian pathogenic E. coli strain APEC-O2-MS1170. DOI
  • Isah et al. (2024) Microbiology Spectrum — Genomic characterization of Salmonella Reading. DOI
  • Poudel et al. (2022) Microbiology Resource Announcements — Complete C. jejuni genome sequences. DOI

Foodborne and Poultry Pathogen Epidemiology

Overview

Understanding the epidemiology of foodborne and poultry pathogens—including prevalence, antimicrobial resistance patterns, and transmission dynamics—is essential for developing effective control strategies. We conduct surveillance studies and molecular epidemiology research on key foodborne and poultry pathogens.

Research Highlights

Campylobacter jejuni Surveillance

  • Characterized C. jejuni prevalence and antimicrobial resistance in production systems
  • Identified multi-drug resistance patterns and associated genetic determinants
  • MLST-based epidemiological tracking
  • Virulence gene profiling across diverse isolate collections

Salmonella Transmission Dynamics

  • Constructed bioluminescent Salmonella Reading strains for real-time tracking
  • Evaluated vertical transmission potential in poultry production
  • Characterized outbreak vs. non-outbreak strain genomic differences

Antimicrobial Resistance Profiling

  • Phenotypic susceptibility testing combined with WGS-based resistance prediction
  • Identification of resistance genes and mobile genetic elements
  • Trends in antimicrobial resistance over time and production systems

Key Publications

  • Poudel et al. (2024) Poultry Science — C. jejuni prevalence and AMR in NAE broilers. DOI
  • Poudel et al. (2022) Microbiology Spectrum — AMR molecular characterization. DOI
  • Li et al. (2021) Poultry Science — Effects of in ovo probiotic administration on the incidence of avian pathogenic E. coli in broilers and evaluation of virulence and antimicrobial resistance properties. DOI
  • Isah et al. (2024) Poultry Science — Salmonella Reading vertical transmission. DOI

Media Coverage

Foodborne Pathogen Biofilms

Overview

Biofilm formation by foodborne pathogens poses significant challenges for food safety, enabling bacteria to persist on processing surfaces and resist sanitation procedures. We investigate biofilm formation mechanisms, environmental stress responses, and intervention strategies for Salmonella, Campylobacter jejuni, and pathogenic E. coli.

Research Highlights

Campylobacter jejuni Biofilm Formation

  • Demonstrated that elevated temperatures facilitate C. jejuni biofilm formation under both aerobic and microaerobic conditions
  • Characterized aerotolerance mechanisms linking survival to food safety risks
  • Studied biofilm formation as a survival strategy in processing plant environments

Salmonella Biofilm Development

  • Investigated biofilm formation on food processing surfaces under fluidic shear stress
  • Characterized expression of biofilm-associated genes under environmental stress
  • Evaluated different surface materials for Salmonella biofilm resistance
  • Constructed bioluminescent Salmonella strains for real-time biofilm imaging

Environmental Stress Responses

  • Gene expression profiling of stress-related genes during biofilm formation
  • Temperature, oxygen tension, and surface contact effects on biofilm development
  • Developing science-based intervention strategies

Key Publications

  • Pokhrel et al. (2024) Poultry Science — Temperature effects on C. jejuni biofilm formation. DOI
  • Thames et al. (2026) J. Applied Microbiology — Environmental stress modulates expression of biofilm-related genes in Salmonella. DOI

Expertise & Capabilities

Area Skills & Methods
Genomics & Sequencing Sanger, Oxford Nanopore, Illumina
Bioinformatics Pipeline development, MLST/serotyping, microbiome, WGS analysis
Molecular Detection LAMP assay development, qPCR/RT-qPCR, multiplex PCR, primer design
Microbiology Pathogen isolation/characterization, biofilm assays, antimicrobial susceptibility testing, culturomics
Animal Models Poultry challenge studies, vaccine efficacy trials, pathogen colonization models, tissue sample collection and analysis
Data Science Python, R, statistical analysis, database management, HPC computing

Funding Sources

Our research has been supported by:

  • USDA Agricultural Research Service (ARS)
  • USDA National Institute of Food and Agriculture (NIFA)
  • U.S. Poultry & Egg Association
  • State agricultural experiment stations (MAFES)
  • Industry partners

Collaborative Network

We actively collaborate with government agencies, academic institutions, and industry partners:

  • USDA Agricultural Research Service — Ongoing collaborative projects
  • Multi-State Research Group NE-2442 — Senior Executive (2025–present)
  • University partners — Auburn, Arkansas, Oklahoma State, Tennessee, NC State
  • Industry stakeholders — Technology transfer and applied research

Interested in collaborating? Contact us to discuss potential projects.

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