Module: Microbial Systematics Course

Module: Computational Microbiology in the Microbial Systematics Course

This is a practical computational module I helped develop while working as a lab assistant in the Microbial Systematics course at Institut Teknologi Sepuluh Nopember. It introduces microbial diversity, taxonomy, and classification through guided exercises in R.

Module Objectives

Students will explore microbial samples from various environments, ranging from soil and water to more specialized ecosystems,and apply computational tools in R to:

• Understand microbial taxonomy and classification
• Retrieve and align genetic sequences
• Construct and interpret phylogenetic trees

What You’ll Learn

1. Dataset Preparation
   Select diverse microbial species from various ecological niches for phylogenetic analysis.

2. Genetic Data Retrieval
   Access and retrieve DNA sequence data from GenBank for selected microbial taxa.

3. Sequence Alignment
   Perform multiple sequence alignment using bioinformatics tools to identify conserved regions and ensure accurate comparisons.

4. Phylogenetic Tree Construction
   Build evolutionary trees using methods like neighbor-joining or maximum likelihood, and learn how different approaches impact the resulting topology.

Note: This module is currently available in Bahasa Indonesia.

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Feedback

If you use the module, I’d be glad to hear what worked well and what could be clearer.