A comprehensive literature review (2014–2025) was conducted to evaluate the reproducibility of microbiome metadata in original research articles. Studies were identified via PubMed using microbiome and sequencing-related keywords. Reviews and meta-analyses were excluded. Each study's sequencing method (16S, shotgun, or both), availability of supplementary metadata (e.g., sample IDs, biological and demographic data), and data accessibility (e.g., GitHub, NCBI, SRA) were recorded.

Researchers systematically extracted and validated metadata and sequencing information using a structured checklist. Key metadata elements—such as sample IDs, age, gender, health status, and environmental context—were analyzed. Metadata reproducibility was assessed based on (1) whether metadata was provided, (2) if sample IDs matched those in SRA explorer, and (3) whether data were differentiable for downstream analysis, including machine learning use.

Validation included cross-checking accession codes and confirming consistency between metadata files and public repositories. Studies were reviewed by multiple individuals to ensure reliability and transparency. The final dataset was used to assess trends in metadata completeness, publication year, and journal impact.