Answers to Common Omics and Microbiome Questions
Direct 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.
Most bioinformatics questions have a direct answer if you know where to look. What depth do you need for metagenomics? When does long-read sequencing make sense? How do you control for host contamination? These pages give you the answer first, then the reasoning.
Bad data costs twice: once to generate, once to explain away.
How much sequencing depth do I need?
For gut community profiling, 10–15 Gb per sample is a practical starting point. For functional annotation or detection of rare taxa, 20–30 Gb. For soil and environmental samples with high community diversity, 30 Gb minimum. The right number depends on your biological question, not your budget.
When does long-read sequencing make sense?
When you need full-length 16S, complete gene annotations, or structural variants that short reads cannot resolve. Long reads cost more per base but answer fundamentally different questions. If your study requires resolved strain-level taxonomy, metagenome-assembled genomes, or functional context for mobile genetic elements, long-read is the appropriate platform.
What controls do I need for a microbiome study?
At minimum: extraction blanks, PCR negatives, and a mock community positive. For metagenomics, include a sequencing blank run alongside your samples. Controls are not optional — they are the calibration against which everything else is interpreted. Studies without appropriate controls cannot distinguish biology from contamination.
Can I re-analyse existing data?
Yes. Re-analysis of existing data is common and often reveals more than the original analysis. The first step is a data audit — assessing quality, documentation, and what analysis is still feasible given how the data was generated. Badly documented data limits what can be recovered.
Common questions
- How much sequencing depth do I need for metagenomics?
- For gut community profiling, 10–15 Gb per sample is a reasonable starting point. For functional annotation or rare taxa, 20–30 Gb. For soil and environmental samples with high diversity, 30 Gb minimum.
- When should I use long-read sequencing?
- When you need full-length 16S, complete gene annotations, or structural variants that short reads cannot resolve. Long reads cost more per base but answer fundamentally different questions.
- What controls do I need for a microbiome study?
- At minimum: extraction blanks, PCR negatives, and a mock community positive. For metagenomics, include a sequencing blank. Controls are not optional — they are the calibration against which everything else is interpreted.
- Can I re-analyse data that was already processed by someone else?
- Yes. Bringing in existing data is common. The first step is a data audit — assessing quality, documentation, and what analysis is still feasible given how the data was generated.
Related pages
Every page connects to the others. Start anywhere. Find everything.
- ConceptsThe ideas that separate good omics projects from great ones. Compositionality. Confounding. Replication. Effect size. Each concept explained once, clearly, with real consequences.
- GlossaryPlain definitions for the terms that matter in microbiome and omics work. No inflated jargon. Each term connects to where it appears in practice.
- 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.