Genomics, Synthetic Biology, and Evolution | Chapter 10 of Brock Biology of Microorganisms

Welcome to Last Minute Lecture. This post summarizes Chapter 10 of Brock Biology of Microorganisms, which focuses on how genomics and other omics technologies revolutionize our understanding of microbes. Learn how DNA sequencing, transcriptomics, proteomics, metabolomics, and systems biology give us a complete view of microbial life — from single-cell analysis to environmental communities.

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This chapter is critical for students interested in modern microbiology, bioinformatics, and synthetic biology applications in research and health.

Genomics and Genome Annotation

• Sequencing technologies: Sanger, Illumina, Nanopore
• Genome assembly builds contigs and scaffolds from reads
• Annotation predicts gene functions using tools like BLAST
• Genome size in prokaryotes ≈ gene count (~1000 ORFs/Mbp)
• Public repositories: GenBank, GOLD

Functional and Comparative Genomics

• Comparative genomics identifies gene function and evolution
• Tn-Seq: transposon mutagenesis + sequencing to find essential genes
• Transcriptomics (RNA-Seq) shows gene expression
• Microarrays detect specific RNA/DNA sequences
• Proteomics confirms which transcripts are translated into proteins

Metagenomics: Uncultured Microbes and Environmental Analysis

• Analyzes DNA from entire microbial communities
• Reveals species composition and functional potential
• Used in ecosystems like soil, ocean, and human microbiome
• Subfields: Mycobiome (fungi), Virome (viruses), Resistome (antibiotic genes)

Proteomics and the Interactome

• Analyzes the entire protein set in cells or communities
• Techniques: mass spectrometry, Western blotting
• Interactome maps protein-protein and macromolecular interactions
• Metaproteomics = proteomics applied to microbial communities

Metabolomics

• Studies all small molecules and intermediates in cells
• Techniques: NMR, NIMS, HPLC-MS
• Tracks responses to stress, disease, and environmental change
• Supports metabolic engineering and microbial ecology

Systems Biology: Integration of Omics

• Combines genomic, transcriptomic, proteomic, and metabolomic data
• Models entire cellular systems and networks
• Dual RNA-Seq tracks host and pathogen simultaneously
• Applications in disease modeling, diagnostics, and drug discovery
• iPOP (Integrated Personal Omics Profile) supports personalized medicine

Single-Cell Omics and Microbial Dark Matter

• SCG sequences DNA from uncultured single cells
• Requires FACS sorting, MDA amplification
• Crucial for studying rare microbes and uncharacterized branches of life
• Improves genome recovery from previously unknown lineages

Glossary Highlights

• Genome: full DNA content of an organism
• Transcriptome: total RNA output under specific conditions
• Proteome: full set of proteins produced
• Metabolome: all small molecules in a cell
• Interactome: network of protein–protein and macromolecular interactions
• Metagenome: DNA from an entire microbial community
• Tn-Seq: identifies essential genes using transposons
• Microarray: chip-based method for detecting gene expression
• iPOP: integrates all omics for personalized profiles
• FACS: sorts single cells via fluorescence
• MDA: amplifies DNA from single cells

Conclusion

Chapter 10 of Brock Biology of Microorganisms showcases how modern tools — from genome sequencing to single-cell analysis — have revolutionized our ability to study and engineer microbes. These powerful omics approaches allow for integrated, predictive, and transformative research across microbiology, medicine, and biotechnology.

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