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VAMS LABS™ · sequencing

Microbiome sequencing services — 16S amplicon and shotgun metagenomics

From 16S rRNA amplicon profiling to shotgun metagenomics, VAMS LABS™ sequencing is designed for reproducibility and matched to your research question — with method limitations shown clearly.

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16S rRNA ampliconShotgun metagenomicsMetatranscriptomics (scoped)Method-aware explanationsNo pricing logicNo diagnostic claims

Methods

Amplicon and shotgun methods, matched to the question

Three methods, three levels of detail — and three different sets of limits. The best method is matched to your question, sample type and design; more depth is not automatically more useful.

Amplicon and shotgun methods, matched to the question
Method Best for Can show Cannot show Status
16S rRNA amplicon Community-level composition and diversity across many samples. Genus-level taxonomy, diversity, community structure. Reliable species/strain resolution or functional activity. Availability confirmed per implementation
Shotgun metagenomics Deeper taxonomic resolution and functional-potential context. Species-level structure and genomic functional potential. Active expression (potential ≠ activity); clinical diagnosis. Availability confirmed per implementation
Metatranscriptomics (RNA) Expression context where sample quality and design support it. Functional expression context under supported conditions. Guaranteed results where RNA quality is insufficient. Requires scoping
ITS (fungal) Fungal/mycobiome community context, project-dependent. Fungal community composition where supported. Public availability is not guaranteed — discuss during scoping. Requires scoping
Long-read / full-length 16S Higher-resolution amplicon reads — subject to verification. Discussed during scoping; not a public offering here. Not asserted as available until verified. Not publicly claimed

Where sequencing sits

Sequencing within the broader sample journey

  1. 1

    Sample & preservation

    Sample type and preservation determine handling readiness.

  2. 2

    Extraction & library prep

    Extraction and library preparation are QC-aware and method-matched.

  3. 3

    Sequencing

    Sequencing is coordinated. Laboratory arrangements are confirmed for each implementation.

  4. 4

    Bioinformatics

    Reproducible analysis produces research-ready tables and figures.

How depth changes the output

What sequencing depth can show later

High-level microbiome profile summary for 16S
Deeper organism and pathway-potential context for shotgun
Expression-context signals for metatranscriptomics, where quality supports it
Reproducible feature tables and diversity summaries at every level

Governance

Trust comes from precise language

Clear method scope Visible confidence cues No diagnostic or treatment claims Partner-lab processing where applicable Reproducible pipeline documentation Research-use framing

FAQ

Sequencing questions

Which method should we use?

It depends on your research question, sample type and budget — not a ranking. 16S gives a broad community baseline; shotgun metagenomics adds species-level and functional-potential detail; metatranscriptomics adds expression context where quality supports it. We confirm method fit during scoping.

Can you work with our extracted DNA/RNA or FASTQ files?

Yes — this is confirmed during scoping. We can discuss projects that start from biological material, extracted nucleic acids, or existing sequencing data, subject to QC and method fit.

Do you perform the sequencing in-house?

Laboratory arrangements are confirmed for each implementation, depending on region, assay and project scope.

Are results diagnostic?

No. Outputs are research-use, educational or wellness-oriented and method-bounded unless a separately approved, formally contracted pathway exists.

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Methods and workflow

Sample workflow → Technology platforms → Quality & validation → Reference methods → Research collaboration →

Match a sequencing approach to your study

Our team can help you select depth and method for your cohort, sample type and endpoints, and explain the controls and pipeline versioning behind each.

Request Sequencing Scoping See the Sample Workflow
A gloved hand loads a spotted target plate into the open port of a mass spectrometer. Photo: James Gathany / CDC (PHIL #23172). Illustrative of laboratory practice — not a VAMS facility or team.

Instrumentation

Every method ends at a real instrument.

Behind each sequencing choice sits physical instrumentation, loaded and run by hand. Which workflow — and which laboratory performs it — is confirmed during scoping, with method limitations shown throughout.

Sequencing methods, illustrated

Three methods, three different questions.

Each method reads a different slice of the community — one marker region, whole genomes, or expression within a sampled window. None is an upgrade of another; the right method follows the research question.

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.

16S Foundation™

One region, read broadly across the community.

  • Marker region that is sequenced
  • Surrounding genome, not sequenced
  • One organism per row

Cannot resolve

  • Species-level identity within Lactobacillus and other close relatives
  • Functional genes, which sit outside the marker region

Answers composition, diversity and ecological context.

Conceptual illustration, not analytical output. Marker-gene sequencing reads one short region per organism across the community; positions and row counts are schematic.

WGS Advanced™

More of the genome, so gene content becomes visible.

  • Sequence covered across the genome
  • Annotated gene region — functional potential
  • Genome context not covered in this run

Cannot resolve

  • Whether an annotated gene is being expressed — presence is not activity
  • Organisms present below the depth reached in a given run

Answers species-level structure and functional potential.

Conceptual illustration, not analytical output. Coverage is drawn schematically; real coverage varies by organism, sample and depth.

MetaT Functional™

Expression context at the sampled timepoint — and only there.

  • Observed within the sampled window
  • Other moments — unobserved, not assumed unchanged

Cannot resolve

  • Whether the same pattern held before, or holds after, the sample
  • A stable trait of the person or the community — a timepoint is not a baseline

Answers what was being expressed when the sample was taken.

Conceptual illustration, not analytical output. Levels and lane counts are schematic; the sampled window is the only interval the method describes.