MOC - Bioinformatics in Microbiology

Computational analysis of microbial sequence and omics data — from raw reads to clinical and epidemiological interpretation.

Parent: Home · Map: Encyclopedia Map
Companion: MOC - AI in Microbiology (learning models on these data)
Practical: Bioinformatics Toolkit for Microbiology · Genomics Command-Line Cheatsheet

Overview

Bioinformatics turns raw reads into actionable microbial knowledge: species ID, resistance and virulence genes, plasmids, community composition, and outbreak relatedness. Clinical microbiology increasingly depends on these pipelines downstream of Whole-Genome Sequencing and amplicon PCR.

flowchart TB
  Raw[Raw reads FASTQ] --> QC[[Read QC and Preprocessing]]
  QC --> Assembly[[Genome Assembly]]
  QC --> Map[Mapping]
  Map --> Var[[Variant Calling in Bacteria]]
  Assembly --> Annot[[Genome Annotation]]
  Annot --> AMR[[AMR Gene Databases]]
  Annot --> Vir[[Virulence Factor Databases]]
  Annot --> Pan[[Pangenome Analysis]]
  Assembly --> Typ[[MLST and cgMLST]]
  Assembly --> Plas[[Plasmid and Mobile Element Analysis]]
  Var --> Tree[[Phylogenetic Tree Building]]
  Typ --> Tree
  Tree --> Dyn[[Phylodynamics]]
  Raw --> Meta[[Metagenomics]]
  AMR --> Report[Clinical / epi report]
  Tree --> Report

1. Data and Foundations

• Sequencing Technologies — Illumina, ONT, PacBio, Sanger
• Sequencing Data Formats — FASTQ, BAM, VCF, GFF
• Read QC and Preprocessing
• Sequence Alignment and BLAST
• Microbial Genomics

2. Genome Reconstruction and Interpretation

• Genome Assembly · Long-Read and Hybrid Bacterial Assembly
• Assembly Quality Control — CheckM / QUAST gates
• Contaminant and Mixed-Culture Detection
• Genome Annotation
• Variant Calling in Bacteria
• WGS Bioinformatics Pipeline — the end-to-end route
• Clinical WGS Pipelines — validated / accredited layer (Bactopia, nf-core, …)

3. Comparative and Population Genomics

• Comparative Genomics
• ANI and Species Delineation · GTDB Taxonomy
• Pangenome Analysis — core vs accessory
• Bacterial GWAS — structure-aware association
• Plasmid and Mobile Element Analysis · Prophage Detection and Annotation
• Biological drivers: Horizontal Gene Transfer · Integrons · Transposons and Insertion Sequences · Integrative Conjugative Elements · Genomic Islands · CRISPR-Cas in Bacteria

4. Typing, Phylogeny, Epidemiology

• MLST and cgMLST
• Population Structure and Clustering — PopPUNK / cluster naming
• Recombination in Bacterial Phylogenies — Gubbins / ClonalFrameML
• Phylogenomics and Outbreak Typing
• Phylogenetic Tree Building
• Phylodynamics
• Viral Genomics and Surveillance

5. Beyond the Genome (multi-omics)

• Microbial Transcriptomics
• Proteomics and MALDI Bioinformatics
• Structural Bioinformatics

6. Culture-Independent Analysis

• Metagenomics
• 16S Amplicon Analysis
• Metagenome-Assembled Genomes
• Microbiome Statistics
• Plasmid Host Attribution with ML — when plasmids lack a cultured host

7. Clinical AMR Genomics

• AMR Gene Databases
• Virulence Factor Databases
• Genotype to Phenotype Prediction
• Ground truth: Antimicrobial Susceptibility Testing

8. Practice, Data Stewardship, Reproducibility

• Reproducible Bioinformatics Workflows
• Public Sequence Databases
• FAIR Data and Genomic Surveillance
• Bioinformatics Toolkit for Microbiology
• Genomics Command-Line Cheatsheet
• Bioinformatics and AI Glossary

9. Bridge to AI

• Feature tables → Machine Learning for AMR Prediction · Machine Learning Basics for Microbiology
• Confounders → Population Structure Confounding in Microbial ML
• Sequence → DNA and Genome Language Models · Protein Language Models · AlphaFold in Microbiology
• Agents → Agentic AI for Bioinformatics Workflows
• Hub: MOC - AI in Microbiology

Core Principles

• Reference and database versions are part of the result (Reproducible Bioinformatics Workflows)
• Genotype ≠ phenotype — correlate with Antimicrobial Susceptibility Testing when therapy depends on it
• Contamination, mixed cultures, and low coverage invalidate everything downstream (Contaminant and Mixed-Culture Detection)
• Metadata quality limits epidemiological value more often than sequence quality
• Every clinical result must be traceable from report back to raw reads
• Recombination and population structure must be modeled before outbreak or GWAS claims

Tool Reference Card

Category	Examples	Question answered
QC	FastQC, MultiQC, fastp	Are reads usable?
Species screen	Kraken2, Mash, GTDB-Tk	What organism(s)?
Assembly	SPAdes, Unicycler, Flye, Shovill	What is the genome?
Assembly QC	QUAST, CheckM, BUSCO	Is it complete/clean?
Annotation	Prokka, Bakta, PGAP	Which genes?
Variants	BWA/minimap2, bcftools, Snippy	Which SNPs?
AMR	AMRFinderPlus, ResFinder, CARD-RGI	Which resistance determinants?
Typing	mlst, chewBBACA, Kleborate	Which lineage/cluster?
Plasmids	PlasmidFinder, MOB-suite, geNomad	Mobile context?
Pangenome	Roary, Panaroo, PPanGGOLiN	Core vs accessory?
Phylogeny	MAFFT, IQ-TREE, Gubbins, BEAST	How related, and when?
Metagenomics	MetaPhlAn, metaSPAdes, MetaBAT2	What is in the community?
Amplicon	QIIME 2, DADA2	Taxa from 16S?
Visualization	iTOL, Microreact, Bandage	How do I show it?
Orchestration	Nextflow/nf-core, Snakemake, Docker	How do I rerun it exactly?

Important Papers

• Paper - AMR Database M.Centner 2026 — discordance between AMR databases and its downstream effects
• Add: MIMAG standards; nf-core; GTDB taxonomy; cgMLST scheme validations

Important Book Chapters

• Jawetz, Melnick & Adelberg’s Medical Microbiology - Chapter 1 — historical → molecular arc

Research Questions

1. How should labs report “gene present, MIC susceptible”?
2. What minimum metadata makes AMR genomic surveillance interoperable?
3. When do plasmids demand long reads for clinical conclusions?
4. Can pangenome-aware references replace single-reference SNP calling in routine surveillance?
5. What is the acceptable failure mode when a pipeline meets a novel species?

Review Article Opportunities

• Practical WGS pipeline for clinical microbiology laboratories
• Database discordance → reporting standards
• Metagenomic diagnostics: sensitivity, contamination, regulation
• From MAGs to clinical relevance: what is missing

Learning Aids

• Figure - AI and Bioinformatics in Microbiology
• Figure - WGS Bioinformatics Pipeline
• Figure - Omics Layers in Microbiology
• Figure - Sequencing Platform Comparison
• Computational Microbiology Study Path
• Learning Media Hub

Related MOCs

• MOC - AI in Microbiology
• MOC - Antimicrobial Resistance (AMR)
• MOC - Diagnostic & Lab Methods
• MOC - Bacteriology
• MOC - Public Health & Epidemiology
• MOC - Fundamentals of Microbiology

Build Status

Cluster	Status
Data foundations, assembly, annotation, variants	done
Assembly QC, long-read/hybrid, contamination gates	✅ 2026-08-02
Comparative / pangenome / plasmids / typing	done
ANI/GTDB, bacterial GWAS, recombination-aware trees, PopPUNK	✅
Clinical WGS pipelines + prophage annotation	✅
Phylogenetics and phylodynamics	done
Multi-omics (RNA, protein, structure)	done
Metagenomics, MAGs, microbiome statistics	done
Reproducibility, databases, FAIR, cheatsheet	done
Worked examples with real datasets	backlog