Resources
This page provides structured weekly learning resources for the Microbiome Analysis micro-credential. Enrolled participants receive access to lecture slides, practical materials, quizzes, feedback forms, suggested readings and workshop datasets.
Software & Platforms
- QIIME2
- DADA2
- R and RStudio
- ggplot2
- Phyloseq
- Kraken2
- HUMAnN3
Learning Activities
- Lecture slides
- Hands-on practical materials
- Workshop datasets
- Weekly quizzes
- Feedback activities
- Discussion and Q&A
Week 1 Resources
Learning objectives
- Understand core microbiome concepts and terminology
- Explain why microbiomes are important in biological research
- Distinguish amplicon and shotgun metagenomics approaches
- Interpret the overall microbiome workflow from sample to sequencing data
Suggested Reading
- QIIME2 Documentation: Introduction to microbiome analysis
- Nature Reviews Microbiology article on microbial ecology or microbiome research
- Selected microbiome case study relevant to agriculture, health or environmental science
Week 2 Resources
Learning objectives
- Understand microbiome file formats and metadata requirements
- Compare 16S/ITS and shotgun metagenomics workflows
- Explain the roles of QIIME2, DADA2, Kraken2, Phyloseq and HUMAnN3
- Select an appropriate workflow for a microbiome research question
Suggested Reading
- QIIME2 documentation on importing sequence data and metadata
- DADA2 workflow tutorial or overview paper
- Review article comparing amplicon sequencing and shotgun metagenomics
Week 3 Resources
Learning objectives
- Interpret FASTQ quality scores and quality profiles
- Prepare metadata for microbiome analysis
- Import sequencing data into QIIME2
- Make reproducible trimming and filtering decisions
Suggested Reading
- QIIME2 documentation on sequence quality control
- FASTQ quality score guide or sequencing QC tutorial
- Best-practice guide on metadata preparation for microbiome studies
Week 4 Resources
Learning objectives
- Perform DADA2 denoising and ASV generation
- Interpret feature tables and representative sequences
- Assign taxonomy using reference databases
- Generate and interpret taxonomic composition summaries
Suggested Reading
- DADA2 paper or denoising workflow tutorial
- QIIME2 documentation on feature tables and taxonomy classification
- SILVA database overview or taxonomy reference documentation
Week 5 Resources
Learning objectives
- Interpret alpha diversity and beta diversity analyses
- Generate and interpret ordination plots
- Apply statistical testing to microbiome community data
- Understand differential abundance analysis outputs
Suggested Reading
- QIIME2 documentation on diversity analysis
- Introductory guide to alpha and beta diversity in microbiome studies
- Tutorial or review article on differential abundance analysis for microbiome data
Week 6 Resources
Learning objectives
- Create publication-quality microbiome visualisations
- Interpret microbiome results in a biological context
- Draft microbiome Methods and Results text
- Assemble analytical outputs into a coherent scientific narrative
Suggested Reading
- ggplot2 visualisation resources for biological data
- Example microbiome manuscript with clear Methods and Results reporting
- Guidance on reproducible research and scientific figure preparation
Access Model
This GitHub repository serves as the student-facing landing page for the Microbiome Analysis micro-credential. Restricted participant resources are managed separately through restricted Google Drive and Google Forms permissions.
Public-facing information is available through this website, while teaching files, workshop datasets, quizzes and feedback forms are shared only with enrolled participants.