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Foundations of Microbial and Metagenomic Sequencing

Introduction to Microbial Sequencing

Sequencing Workflow and Core Terminology

Selecting a Microbial Sequencing Approach

16S and 18S rRNA Amplicon Profiling

Principles of 16S and 18S rRNA Marker-Gene Profiling

Amplicon Library Preparation and Sequencing

Amplicon Data Analysis and Interpretation

Limitations of Amplicon Profiling

Shotgun Metagenomic Sequencing

Principles of Shotgun Metagenomics

Shotgun Metagenomic Laboratory Workflow

Read-Based and Assembly-Based Analysis

Taxonomic Classification of Microbial Communities

Taxonomic Hierarchy and Reference Databases

Interpreting Taxonomic Classification Results

Quality Assurance in Taxonomic Inference

Functional Metagenomics

Introduction to Functional Metagenomics

Genes, Pathways, and Functional Annotation

Antimicrobial Resistance and Virulence-Associated Genes

Pathogen Surveillance and Public Health Applications

Microbial Sequencing in Pathogen Surveillance

Outbreak Investigation and Genomic Epidemiology

Ethical, Privacy, and Reporting Considerations

Quiz

Question 1: Amplicon Profiling

Question 2: Shotgun Metagenomics

Question 3: Taxonomic Classification

Question 4: Functional Metagenomics

Question 5: Pathogen Surveillance

Survey and Feedback

Course Feedback Survey

Welcome to the "Foundations of Microbial and Metagenomic Sequencing for Pathogen Surveillance" course. In today's rapidly evolving public health and clinical landscapes, understanding the microbial world is more critical than ever.

Welcome to the "Foundations of Microbial and Metagenomic Sequencing for Pathogen Surveillance" course. In today's rapidly evolving public health and clinical landscapes, understanding the microbial world is more critical than ever. This comprehensive course is designed to introduce you to the transformative power of microbial sequencing, enabling you to study bacteria, archaea, fungi, and viruses without the need for traditional culture methods. Whether you are a public health professional, a clinical researcher, or a laboratory scientist, this course will equip you with the foundational knowledge required to navigate the complex workflows of modern genomics. You will explore the core principles of both 16S/18S rRNA amplicon profiling and shotgun metagenomic sequencing, learning how to select the right approach for your specific research or surveillance questions. Beyond the laboratory workflow, this course delves deep into bioinformatics and data interpretation. You will learn how to navigate taxonomic hierarchies, interpret functional metagenomics data, and identify critical antimicrobial resistance (AMR) and virulence-associated genes. Finally, we will bridge the gap between laboratory science and real-world application by exploring how genomic epidemiology and pathogen surveillance are used to track outbreaks, monitor environmental threats, and inform public health decisions. Join us to master the essential tools of metagenomic sequencing and take a vital step forward in the fight against infectious diseases.

Foundations of Microbial and Metagenomic Sequencing for Pathogen Surveillance

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            <p>The rapid advancement of high-throughput sequencing technologies has fundamentally transformed the landscape of microbiology, public health, and infectious disease management. "Foundations of Microbial and Metagenomic Sequencing for Pathogen Surveillance" provides a comprehensive exploration of how these modern genomic tools are utilized to detect, characterize, and monitor microbial communities without the need for traditional cultivation methods. By examining the core principles of both targeted and untargeted sequencing approaches, this course establishes a rigorous scientific framework for understanding the complex dynamics of bacteria, archaea, fungi, and viruses across diverse environments. Participants will explore the critical role of sequencing in clinical, agricultural, and environmental settings, gaining a robust understanding of how genomic data drives evidence-based public health interventions and outbreak investigations.</p>

<p>Throughout this curriculum, learners will systematically navigate the end-to-end workflows of microbial genomics, beginning with foundational terminology, sample processing, and the strategic selection of sequencing methodologies. The coursework delves deeply into the technical and analytical distinctions between 16S and 18S rRNA amplicon profiling and shotgun metagenomic sequencing, highlighting the respective advantages, limitations, and laboratory procedures of each approach. Furthermore, the modules provide detailed instruction on taxonomic classification, functional metagenomics—including the detection of antimicrobial resistance and virulence-associated genes—and the principles of genomic epidemiology. By synthesizing laboratory techniques, bioinformatic analysis, and ethical considerations, this course equips professionals with the essential knowledge required to interpret complex genomic data and apply it effectively within the context of global pathogen surveillance.</p>
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