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VAMS LABS™ · reference methods

Reference methods you can inspect and cite.

A methods library for microbiome projects — described at a level intended to support reproducibility, method review and research collaboration. Availability is confirmed during scoping.

Request Method Scoping See Sequencing Services
16S rRNA ampliconITS (fungal)Shotgun metagenomicsMetatranscriptomicsBioinformatics pipelinesResearch-use framing

Methods library

Methods, outputs and limits

Methods, outputs and limits
Method What it measures Typical output Key limit Status
16S rRNA amplicon Bacterial community composition via a marker gene. ASV/feature tables, taxonomy, diversity. Limited species/strain resolution; no activity. Available
ITS (fungal) Fungal community composition. Fungal taxonomy/diversity. Availability confirmed during scoping. Requires scoping
Shotgun metagenomics Whole-community DNA — taxonomy + functional potential. Taxonomic + functional-potential tables. Potential ≠ activity; no diagnosis. Available
Metatranscriptomics Community RNA — expression context. Expression-context summaries. RNA quality dependent; not guaranteed. Requires scoping
qPCR / targeted add-ons Targeted abundance of specific markers. Targeted quantification. Not asserted until verified. Not publicly claimed
Bioinformatics pipelines QC, taxonomy, diversity, differential abundance, functional annotation. Reproducible pipeline documentation. Scope depends on method and data quality. Available

Glossary

Key microbiome terms

ASV Amplicon Sequence Variant — an exact sequence used as a high-resolution feature unit.
OTU Operational Taxonomic Unit — clustered sequences; historically used before ASVs.
Taxonomy Assignment of features to microbial groups against a reference database.
Alpha diversity Diversity within a single sample (richness/evenness).
Beta diversity Differences in community composition between samples.
Differential abundance Features that differ between groups, with statistical caveats.
Functional potential Genomic capacity inferred from DNA — capability, not activity.
Expression context Activity signals inferred from RNA where quality supports it.
Reference database The curated catalogue features are matched against.
Confidence / QC Quality cues shown so results are read with appropriate certainty.

FAQ

Method questions

Which method fits my project?

It depends on your question, sample type and design. We compare method fit during scoping rather than defaulting to the most complex option.

Can you annotate function?

Functional-potential annotation is available for shotgun metagenomics where appropriate; expression context requires metatranscriptomics and sufficient RNA quality — confirmed during scoping.

Are these clinically validated?

These are method/workflow-level reference methods for research-use and educational outputs, not clinical diagnostics, unless a separately approved pathway exists.

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Methods and services

Sequencing services → Technology platforms → Quality & validation → Sample workflow → Research collaboration →

Choose the right method for your project

We compare method fit during scoping — sample type, question and design — rather than defaulting to the most complex option.

Request Method Scoping See Sequencing Services

Methods library

Methods you can inspect, compared honestly.

The reference library documents what each method reads and what it cannot resolve — the comparison is a map of fit, not a ranking.

One sample · three different questions

16S Foundation™

Question it answers

What is present, and how is the community structured?

Reads out

  • Marker-gene composition
  • Diversity measures
  • Ecological context

Cannot resolve

  • Species-level identity within closely related groups, such as Lactobacillus
  • Functional genes, which sit outside the marker region

WGS Advanced™

Question it answers

Which species are present, and what could the community do?

Reads out

  • Species-level structure
  • Gene content across genomes
  • Functional potential

Cannot resolve

  • Whether any annotated gene is actually being expressed
  • Organisms falling below the depth reached in a run

MetaT Functional™

Question it answers

What was being expressed when the sample was taken?

Reads out

  • Expression context at the sampled timepoint

Cannot resolve

  • Conditions before or after that timepoint
  • Genes present but not being transcribed at that moment

Not a ladder — no method supersedes another.

The three methods answer different questions and are not ranked against one another. Each has boundaries; the appropriate method depends on the question being asked. Order of presentation carries no meaning.