Metagenomic Surveillance of Zoonotic Pathogens in Poultry | Project #93 | BDG Lifesciences (original) (raw)

BDG LifeSciences Project #93 · Coming Soon

Project #93 · Coming Soon · Registrations Opening Shortly

A flagship research initiative by BDG Lifesciences — detecting real threats in real data, building careers at the frontier of One Health surveillance and global public health.

150+

Director Publications

The Global Imperative

Why Poultry Metagenomics Is a Global Priority

Zoonotic pathogens and antimicrobial resistance are two of the WHO's top 10 global health threats. Poultry is the world's primary reservoir — and shotgun metagenomics is now the gold-standard surveillance tool. Professionals trained in this domain are among the most in-demand globally.

Global Health Threat Severity Index

WHO priority areas — relative severity score

Career Sectors Requiring Metagenomics Skills

Industry demand distribution

Sectors: Public Health 30%, Biotech/Genomics 25%, Food Safety 20%, Academia 15%, Regulatory 10%.

Project Details

What You Will Do

1

Data Discovery & Metadata Harmonisation

Identify and curate publicly available shotgun metagenomic datasets from NCBI SRA derived from real poultry (Gallus gallus domesticus) samples, complete with metadata for stratified downstream analysis.

2

Quality Control & Host Read Removal

Apply trimming, adapter removal, and host genome decontamination to ensure only high-quality, analysis-ready microbial reads proceed — a critical step for accurate pathogen detection.

3

Taxonomic Profiling & Abundance Estimation

Use industry-standard tools for taxonomic classification to detect and quantify all microbial species present, with special focus on high-priority zoonotic pathogens across all samples.

4

Pathogen Confirmation via Mapping & Assembly

Validate all detections independently using reference-based read mapping and de novo assembly — the dual-confirmation approach used in peer-reviewed international publications.

5

Risk-Oriented Reporting & Scientific Interpretation

Translate findings into a structured, publication-style report with public health interpretation, stakeholder-ready figures, and a complete sample × pathogen detection matrix.

Click any row to expand pathogen details.

Salmonella enterica Salmonellosis / Typhoid Poultry & Eggs Critical

Salmonella enterica is the world's leading cause of foodborne illness, responsible for an estimated 93.8 million human cases annually. Poultry represents the primary transmission route to humans. In metagenomics, it requires careful discrimination from closely related Enterobacteriaceae members. This project targets serovar-level identification where the sequencing depth and sample quality permit.

Campylobacter jejuni Campylobacteriosis Poultry Gut Microbiome Critical

Campylobacter jejuni is the leading bacterial cause of human gastroenteritis globally. Poultry has been identified as the primary source of human infection in multiple population-level studies. Its low infectious dose and environmental sensitivity make it a particularly challenging surveillance target in metagenomic pipelines — making its detection here a meaningful technical achievement.

Listeria monocytogenes Listeriosis Processed Poultry High

Listeria monocytogenes is a significant foodborne pathogen with high case fatality in vulnerable populations — immunocompromised individuals, the elderly, and pregnant women. Its persistence in cold-chain poultry processing environments makes it a highly relevant surveillance target, and its detection in metagenomic data requires sensitivity at low abundance levels.

AMR Gene Reservoirs Resistance Transmission All Poultry Samples Advanced Module

Antimicrobial Resistance (AMR) genes in poultry microbiomes represent one of the most pressing one-health challenges globally. Overuse of antibiotics in poultry production has accelerated the selection and horizontal transfer of resistance genes. This optional advanced module uses resistome profiling tools to identify and quantify AMR gene families directly from metagenomic data — a rare and highly sought skill set.

Optional Advanced Module

Antimicrobial Resistance (AMR) Surveillance

The WHO Global AMR Action Plan identifies antimicrobial resistance as one of the greatest threats to global health, food security, and sustainable development. This advanced optional module adds full resistome profiling to the core pipeline — identifying, classifying, and quantifying AMR gene families directly from real poultry sequencing data.

Participants completing this module gain direct, hands-on experience that is rare, highly differentiated, and increasingly required across public health, food safety, regulatory science, and international research roles.

AMR Skills Demand by Sector

What You Gain

Skills & Competencies Built

Every phase of the project builds a distinct, portfolio-ready technical competency valued by employers and graduate programmes globally.

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Shotgun Metagenomics Pipelines

End-to-end workflow from raw FASTQ to annotated pathogen profiles using real industry-standard bioinformatics tools

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Pathogen Detection & Validation

Dual-method confirmation using taxonomic profiling plus independent read mapping and de novo assembly

⬡

AMR Gene Profiling

Resistome analysis and interpretation — one of the fastest-growing domains in global public health research

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One Health Framework

Understanding animal-human-environment pathogen dynamics applied to real-world public health decision-making

⬡

Scientific Writing

Publication-style report writing with stakeholder-appropriate language, risk interpretation, and structured methodology

⬡

Data Visualisation

Producing publication-ready heatmaps, abundance charts, and AMR profiles directly from real genomic data

Who Should Join

Is This Project For You?

No prior metagenomics experience is required. All tools and methods are introduced as part of the structured project experience.

Life Science Graduates

BSc / MSc students seeking applied bioinformatics research experience for their CV or portfolio

PhD Applicants

Candidates building competitive SOP statements and research credentials for international graduate programmes

Microbiology Researchers

Lab-trained scientists transitioning into computational metagenomics and bioinformatics

Food Safety Professionals

Practitioners in food testing, veterinary public health, or regulatory science seeking to upskill in genomics

Public Health Workers

Epidemiologists and surveillance scientists wanting genomics-based pathogen detection training

Biotechnology Professionals

Industry scientists wanting hands-on NGS and metagenomic pipeline experience for career advancement

Common Questions

Frequently Asked Questions

Shotgun metagenomics sequences all DNA present in a biological sample simultaneously — no culturing required. In this project, it allows detection of every microorganism in real poultry samples, including dangerous zoonotic pathogens at very low abundances. It is far more sensitive and comprehensive than traditional plate-based microbiology, and is now the standard approach in global pathogen surveillance programmes.

This is a real research project, not a pre-packaged training course. You will work on publicly available real-world sequencing datasets and produce genuine scientific outputs — a detection matrix, publication-ready figures, and a structured scientific report — using the same pipelines applied in peer-reviewed international publications. There are no pre-computed answers.

No prior metagenomics or bioinformatics experience is required. The project is structured with guided mentorship at every phase. A basic background in life sciences is helpful, but all tools, software, and analytical methods will be introduced as part of the experience itself.

The project uses publicly available shotgun metagenomic datasets from NCBI SRA (Sequence Read Archive), derived from real poultry samples used in international research studies. There is no simulated or pre-processed data. Your analytical decisions will genuinely affect your outputs — this is authentic research.

Graduate admissions committees at leading international universities value demonstrated, applied research experience in competitive domains. This project gives you a concrete technical credential in metagenomics and One Health surveillance — with real outputs you can reference directly in your Statement of Purpose and discuss with confidence in interviews. It is the kind of experience that distinguishes applications.

The optional AMR module adds resistome profiling to your core workflow — identifying antimicrobial resistance gene families in real poultry metagenomes. AMR surveillance is one of the most critically underfunded yet fastest-growing research areas in global health. If you plan to work in public health, food safety, regulatory science, or global health organisations, this module is strongly recommended.

Formal recognition details will be confirmed when registrations open. The primary outcome is a portfolio of real scientific deliverables — figures, a detection matrix, and a structured scientific report — which can be used directly in CVs, SOP statements, and professional job applications.

Project #93 is currently being finalised to ensure the highest standards of scientific rigour, mentorship quality, and participant experience. Registrations will open shortly — seats are limited. Email [email protected] or follow BDG Lifesciences on official channels to be notified first.

Absolutely. Professionals in food safety testing, clinical microbiology, regulatory science, and veterinary public health will find this project directly relevant and career-advancing. Metagenomics is rapidly becoming the standard approach for surveillance and outbreak investigation in all these domains. This project offers a structured, mentored path to gaining hands-on experience without leaving your current role.

Unlike generic internship programmes or pre-packaged modules, Project #93 is built around a real, unsolved research question — the detection and validation of zoonotic pathogens in real poultry metagenomic data. There are no pre-computed answers. With 88+ internationally published projects and 15+ years of experience, BDG Lifesciences delivers scientific credibility backed by a proven track record.

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