Planning microbiome analysis: amplicon or shotgun?

Identify the assay

Marker-gene amplicon and shotgun sequencing observe different aspects of a community. Report sample type, extraction method, read layout and the biological question before choosing an analysis.

Bring the controls

Include available extraction blanks, negative controls, positive controls and batch metadata. Low-biomass samples require particular care: background contamination can affect the apparent community and the conclusions.

Set the comparison

Describe groups, paired or repeated samples and relevant covariates. Discuss whether the question concerns composition, diversity, a specific taxon or functional evidence. Avoid selecting tests solely because a plot looks different.

Scope outputs separately

Amplicon requests should identify primers and target region; shotgun requests should discuss host sequence handling, reference coverage and profiling versus assembly. Ask for QC, annotated outputs, methods and explicit inference limits.

Limitations

Relative sequence abundance does not directly measure absolute cell numbers. Missing controls and batch confounding cannot always be repaired later. Functional predictions require clear labeling and do not replace direct measurements.

Reference and next step

Editorial planning guide prepared by ANGSUMI; this is not a report of original research or a claim of independent scientific review.

Read the underlying method documentation or research guidance

Review the related service