Microbiome Analysis Micro-credential From raw sequencing data to publishable figures

Schedule

All sessions are part of the Microbiome Analysis Micro-credential.

Assessment & Completion

Participants are expected to engage with the weekly learning activities, practical workshops and final research-focused microbiome analysis task.

  • Attend weekly sessions
  • Complete weekly quizzes and feedback activities
  • Participate in hands-on microbiome analysis exercises
  • Complete a final microbiome mini-project using a real or example dataset

Participants who meet the completion requirements receive a Certificate of Completion.

Week 1: The Microbiome & How We Study It

Week 1 Theory
  • Introduction to microbiomes and ecological relevance
  • Microbiome hypotheses and biological interpretation
  • Understand amplicon vs shotgun metagenomics approaches
  • Learn the workflow from sample → sequencing → data
  • Overview of microbiome bioinformatics workflows

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: Bioinformatics Workflows for Microbiome Analysis

Week 2 Theory
  • Understand microbiome file formats and metadata
  • Learn experimental design considerations
  • Compare 16S/ITS and shotgun metagenomics workflows
  • Introduction to QIIME2, DADA2, Kraken2, Phyloseq and HUMAnN3
  • Choose appropriate workflows for biological questions

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: Quality Control & Data Preparation

Week 3 Hands-on Workshop
  • Interpret FASTQ files and sequencing quality scores
  • Prepare metadata for microbiome analysis
  • Import sequencing data into QIIME2
  • Visualise read quality and trimming decisions
  • Document reproducible quality control workflows

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: From Reads to Taxonomy

Week 4 Hands-on Workshop
  • Perform DADA2 denoising and ASV generation
  • Understand feature tables and representative sequences
  • Assign taxonomy using SILVA databases
  • Generate taxonomic composition visualisations
  • Apply workflows to research microbiome datasets

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: Microbiome Diversity, Statistical Testing & Biological Interpretation

Week 5 Hands-on Workshop
  • Explore alpha diversity and beta diversity analysis
  • Interpret NMDS and PCoA ordination methods
  • Apply statistical testing including PERMANOVA and Kruskal–Wallis
  • Perform DESeq2 differential abundance analysis
  • Generate publication-quality microbiome figures

Suggested Reading

  • QIIME2 documentation on diversity analysis
  • Introductory guide to alpha diversity and beta diversity in microbiome studies
  • Tutorial or review article on differential abundance analysis for microbiome data

Week 6: Reproducible Reporting, Visualisation & Scientific Communication

Week 6 Hands-on Workshop
  • Create publication-ready ggplot visualisations
  • Explore microbiome networks and keystone taxa
  • Interpret microbiome findings in a biological context
  • Write microbiome Methods and Results sections
  • Assemble publication-ready figure panels

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