Impact of non-standardized reporting on reproducibility, usability, and integration in nasopharyngeal metagenomic research: a systematic review

Introduction: The nasopharyngeal microbiome plays a critical role in respiratory health and disease and is a major focus of metagenomic research. However, inconsistent reporting practices across studies limit reproducibility, dataset usability, and cross-study integration, thereby reducing the overall scientific value of publicly available nasopharyn. Methods: A systematic review was conducted to evaluate the impact of non-standardized reporting on reproducibility, usability, and integration of nasopharyngeal metagenomic datasets. A total of 988 studies were screened, and 227 manuscripts met predefined inclusion and exclusion criteria for full-text review. Methodological reproducibility, metadata completeness, and compatibility between reported laboratory methods and deposited datasets were assessed. Reproducible datasets were further analyzed to evaluate the interchangeability of nasopharyngeal aspirates and nasopharyngeal swabs. Results: Only 78 studies (34%) contained methods sections sufficient for reproducibility, and of these, 33 studies (15%) provided analytically sufficient metadata to support secondary analysis. Mismatches between reported laboratory methods and deposited datasets were identified in 4% of studies. These deficiencies were primarily attributed to incomplete methodological reporting, inaccessible or insufficient metadata, and incompatible file formats. Comparative analysis of reproducible datasets demonstrated significant differences in microbial profiles between nasopharyngeal aspirates and nasopharyngeal swabs, confirming that these specimen types are not interchangeable within a study. Discussion: The findings demonstrate that inadequate reporting standards substantially impair the reproducibility, reuse, and integration of nasopharyngeal metagenomic data. The observed methodological and metadata inconsistencies limit the reliability of downstream analyses and cross-study comparisons. Standardized reporting guidelines are urgently needed to improve transparency, ensure reproducibility, and enhance the integrative potential of nasopharyngeal microbiome research. Adoption of comprehensive and consistent reporting practices would significantly strengthen the scientific rigor and utility of metagenomic studies in this field.