Metagenomic Surveillance of Zoonotic Pathogens in Poultry | Research Project #95

Project Details

What You Will Do

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.

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.

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.

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.

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.

PathogenDiseasePrimary ReservoirPriority

Salmonella entericaSalmonellosis / TyphoidPoultry & EggsCritical

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. This project targets serovar-level identification where sequencing depth and sample quality permit.

Campylobacter jejuniCampylobacteriosisPoultry Gut MicrobiomeCritical

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 makes it a particularly challenging surveillance target in metagenomic pipelines.

Listeria monocytogenesListeriosisProcessed PoultryHigh

Listeria monocytogenes carries a high case fatality rate 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.

AMR Gene ReservoirsResistance TransmissionAll Poultry SamplesAdvanced

Antimicrobial Resistance (AMR) genes in poultry microbiomes represent one of the most pressing One Health challenges globally. This module uses resistome profiling tools to identify and quantify AMR gene families directly from metagenomic data — a rare and highly sought-after skill set.

Deliverable	Description	Use Case
Sample × Pathogen Matrix	Complete cross-sample detection and abundance summary for all target pathogens	✓ CV & Portfolio
Publication-Ready Figures	Heatmaps, abundance plots, taxonomic bar charts, and AMR profiles formatted for journal submission	✓ Research Paper
Validated Detection Results	Pathogen detections confirmed via two independent computational approaches	✓ Scientific Credibility
Structured Scientific Report	Publication-style report with methods, results, interpretation, and public health commentary	✓ SOP / PhD Application
Pipeline Documentation	Reproducible workflow documentation for all tools, parameters, and analytical decisions	✓ Industry / Jobs

Optional Advanced Module — Included in This Track

Antimicrobial Resistance (AMR) Surveillance

The WHO Global AMR Action Plan identifies antimicrobial resistance as one of the greatest threats to global health. This 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

Fees & Payment Plan

Flexible 3-Stage Payment — AMR + Publication Track

The total program fee is split across three milestones so each payment is tied to tangible research progress. Each successive payment is smaller than the last — you never pay the full amount at once.

Total program fee

$1,800

USD · per participant

Track

AMR + Publication

premium tier

Duration

6 months

3 payment stages

Largest single payment

$900

Stage 1 · at registration

Payment distribution

Stage 1

$900

50% · at registration

Stage 2

$500

28% · month 3

Stage 3

$400

22% · month 5

Month-by-month view

Month 1

Onboarding

$900 due

Month 2

QC + Profiling

—

Month 3

Validation

$500 due

Month 4

AMR Analysis

—

Month 5

Report Writing

$400 due

Month 6

Publication

—

Stage 1 window

Stage 2 window

Stage 3 window

Stage-by-stage breakdown — click to expand

Stage 1 — Project Initiation & Data Setup $900 50% Expand ⌄

Due at registration · Covers months 1–2

OnboardingData QCHost Read RemovalTaxonomic Profiling

Welcome kit — software setup guide, reading list, and NCBI SRA dataset access instructions
Phase 1 — Data discovery and metadata harmonisation of real poultry metagenomic datasets
Phase 2 — Quality control, adapter trimming, and host read removal pipeline
Phase 3 — Taxonomic profiling and abundance estimation across all samples initiated
Weekly 1:1 Zoom sessions with assigned mentor (8 sessions over 2 months)
Fortnightly progress report submitted to guide for feedback
Access to dedicated project WhatsApp / Telegram support group
Session recordings provided after every Zoom session

Why 50% at this stage? The first payment secures your seat and activates the complete onboarding infrastructure — dataset curation, software environment setup, mentor allocation, and the first two months of intensive guided pipeline work. It reflects the significant upfront effort invested by the BDG team before analytical outputs are produced. This payment is non-refundable once onboarding has commenced.

Stage 2 — Pathogen Validation & AMR Analysis $500 28% Expand ⌄

Due at start of month 3 · Covers months 3–4

Pathogen ConfirmationRead MappingDe Novo AssemblyAMR Resistome Profiling

Phase 4 — Dual-method pathogen confirmation via reference-based read mapping (Salmonella, Campylobacter, Listeria)
De novo assembly and annotation of key metagenomic contigs
AMR resistome profiling — identification and quantification of antimicrobial resistance gene families
Draft sample × pathogen detection matrix
First set of publication-ready figures — heatmaps, taxonomic abundance plots, AMR profiles
Weekly 1:1 Zoom sessions with mentor (8 sessions over 2 months)
Mid-project scientific review and written feedback from guide

Why $500 at this stage? By month 3 you will have already seen real taxonomic profiles from real data — tangible evidence of the project progressing. This second payment, smaller than Stage 1, unlocks the advanced analytical modules that are the scientific core of this project. Paying after two months of active work means you commit only after directly experiencing the quality of mentorship.

Stage 3 — Report, Publication & Portfolio Delivery $400 22% Expand ⌄

Due at start of month 5 · Covers months 5–6

Scientific ReportPublication SubmissionCertificateLetter of Recommendation

Phase 5 — Full scientific report (methods, results, discussion, public health interpretation)
Final validated sample × pathogen detection matrix
Complete set of publication-ready figures suitable for journal submission
Manuscript preparation support and co-authored journal submission
Reproducible pipeline documentation for your professional portfolio
Official BDG Lifesciences certificate of completion
Personalised letter of recommendation from your guide
Portfolio review session — CV, SOP, and LinkedIn profile guidance

Why $400 — the smallest payment — at this stage? By this point you have four months of research behind you and can clearly see the scientific and professional value built. Keeping Stage 3 the smallest removes any hesitation at the finish line and ensures you complete the program and receive the career-defining deliverables: publication, certificate, and your letter of recommendation.

Payment summary

Stage	When to Pay	Amount (USD)	% of Total	Unlocks
Stage 1	At registration	$900	50%	Onboarding, data setup, 2 months mentorship
Stage 2	Start of month 3	$500	28%	Pathogen validation, AMR module, draft figures
Stage 3	Start of month 5	$400	22%	Report, publication, certificate, recommendation
Total	Over 6 months	$1,800	100%	Complete AMR + Publication research project

Payment terms: Stage 1 ($900) is non-refundable once onboarding has commenced, as it covers dataset preparation, software setup, and mentor allocation. Stage 2 ($500) is due at the start of month 3 for participants in good standing. Stage 3 ($400) unlocks manuscript preparation, certificate issuance, and the letter of recommendation — these deliverables are released upon confirmation of Stage 3 payment. All fees are in USD and are non-transferable. For queries, contact [email protected]

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.

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 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.

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 in interviews.

Yes — the AMR resistome profiling module is fully included in the $1,800 AMR + Publication track. It 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.

Yes. The 3-stage plan is designed for convenience and is not mandatory. If you prefer to pay the full $1,800 upfront at registration, please contact us at [email protected] and we will arrange a single-payment option for you.

Yes — both are included in the Stage 3 deliverables. Upon successful completion of all five project phases and submission of all assigned tasks, you will receive an official BDG Lifesciences certificate of completion and a personalised letter of recommendation from your guide.

Absolutely. Professionals in food safety testing, clinical microbiology, regulatory science, and veterinary public health will find this project directly relevant. Metagenomics is rapidly becoming the standard approach for surveillance and outbreak investigation in all these domains.

Unlike generic internship programmes, Project #95 is built around a real, unsolved research question — the detection and validation of zoonotic pathogens in real poultry metagenomic data. With 88+ internationally published projects and 15+ years of experience, BDG Lifesciences delivers scientific credibility backed by a proven track record.

Team for Current / Ongoing Research Projects

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ImmunoSpatial Blueprint: Mapping Tumor-Immune Interactions in Triple-Negative Breast Cancer Using Spatial Transcriptomics

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Secure Your Place in Project #95