Omics and Microbiome Glossary
Plain definitions for the terms that matter in microbiome and omics work. No inflated jargon. Each term connects to where it appears in practice.
Precise language matters in omics. Metagenomics is not the same as metatranscriptomics. Diversity is not the same as richness. This glossary defines the terms that come up in every project and connects them to the methods and contexts where they apply.
If your team uses the same words to mean different things, your results will too.
Metagenomics
Direct sequencing of all DNA in a sample without culturing. Gives taxonomic and functional profiles of an entire microbial community in one run. Does not distinguish between active and dormant organisms — for that, you need metatranscriptomics. Requires significantly more sequencing depth than amplicon approaches.
16S rRNA sequencing vs. shotgun metagenomics
16S rRNA sequencing targets a single conserved marker gene and gives taxonomy only — no functional information. Shotgun metagenomics sequences all DNA and gives taxonomy, gene content, and functional pathways. 16S is cheaper, more established, and appropriate for many community profiling studies. Shotgun gives more information but requires more depth, higher cost, and more complex analysis and interpretation.
Metatranscriptomics
Sequencing of RNA extracted from a microbial community, capturing active gene expression rather than just genetic potential. Tells you what the community is doing at the time of sampling, not just what it is capable of doing. Requires careful RNA extraction, depletion of ribosomal RNA, and rapid sample preservation to avoid expression artefacts.
Rarefaction and normalisation
Rarefaction subsamples reads to a common depth so that diversity metrics can be compared fairly across samples with different sequencing depths. Useful but controversial because it discards data. For differential abundance testing, use size-factor normalisation methods such as DESeq2 or TMM rather than rarefaction, which introduces unnecessary variance.
Common questions
- What is metagenomics?
- Direct sequencing of all DNA in a sample without culturing. Gives taxonomic and functional profiles of an entire microbial community in one run.
- What is the difference between 16S rRNA sequencing and shotgun metagenomics?
- 16S targets a single marker gene for taxonomy only. Shotgun sequences all DNA for taxonomy, function, and gene content. 16S is cheaper and more established. Shotgun gives more information but requires more depth and more complex analysis.
- What is rarefaction?
- Subsampling reads to a common depth so samples can be compared fairly on diversity metrics. Useful but controversial because it discards data. Use it carefully, or use alternative normalisation methods for differential abundance.
- What is metatranscriptomics?
- Sequencing of RNA extracted from a microbial community, capturing active gene expression rather than just genetic potential. Tells you what the community is doing, not just what it is capable of doing.
Related pages
Every page connects to the others. Start anywhere. Find everything.
- AnswersDirect answers to the questions microbiome projects run into most. What platform to use. How much sequencing depth is enough. When to stop troubleshooting and redesign.
- ConceptsThe ideas that separate good omics projects from great ones. Compositionality. Confounding. Replication. Effect size. Each concept explained once, clearly, with real consequences.
- FAQHow long does a project take. What do you deliver. How does collaboration work. What happens after the analysis. Answered directly.
- WorkflowsHow Microbiome Design projects work from start to finish. Scope. Design. Deliver. Interpret. Each phase has a clear input, output, and decision point.
- DocumentationReproducible analysis standards and handover documentation for every project. You keep full records of what was done, why, and how to reproduce it.
- PricingTransparent engagement models for bioinformatics analysis, project design, and scientific consulting. Start with a scoping call.
- Who We Work WithAcademic research groups, biotech and startup teams, and environmental or industrial projects working on microbial systems, biodegradation, wastewater, or circular bioeconomy challenges. UK-first, with selected Europe and US collaborations.
- ReviewsWhat research teams and biotech companies say after working with Microbiome Design. Real projects. Real outcomes.