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According to an initial keyword search, we selected the 17 most popular microbial ecology-related journals, as these were more likely to have sequence-specific data deposition instructions or requirements. We surveyed all the articles published in these journals between January 2015 and March 2019 (n = 26,927 articles, Supplementary Table S1), as concerns over data deposition practices began to grow in 201514 and were soon followed by stricter standards for data availability12. A custom-built pattern-based text extraction algorithm followed by manual curation, we selected those studies which performed 16S rRNA gene amplicon sequencing and listed INSDC-compliant accession numbers (n = 2015, Supplementary Table S1; 145,203 samples).
To confirm that our parsing algorithm did not miss accession numbers in articles containing 16S rRNA gene amplicon sequencing, we randomly selected 150 articles which mentioned 16S rRNA, but for which no accession numbers were detected, for manual inspection. Of these, one contained a misspelled accession number, two had archived their sequences in unconventional repositories (Google Drive and GEO, a gene expression database, Supplementary Data 2), and 19 were identified as having performed 16S rRNA gene amplicon sequencing, but had not included any reference to the data. We found no cases in which accession numbers or sequence data were stored in supplementary materials. From this group, we estimate that 18% of the studies in our database (n = 469) performed 16S rRNA gene amplicon sequencing but did not provide access to the data (Fig. 1a). Four studies mentioned deposition data in dbGaP18, and we could verify the existence of three of these studies. We found that an additional 6.5% of the studies had deposited their data in the Qiita19, MG-RAST20, and figshare databases (n = 14, n = 134, and n = 24 studies, respectively). Of the estimated 2,656 studies employing 16S rRNA gene amplicon sequencing, 75.9% deposited their data to an INSDC database in the period studied (Fig. 1a).
Fig. 1: Popular locations for data storage.

Data for all studies which contained 16S rRNA amplicon sequencing (a), and the V3–V4 subset (b); n = 2656 and n = 635 studies, respectively. For the entirety of the study, studies which contained amplicon sequences but did not deposit them were inferred by manually checking 150 randomly-selected articles which did not contain INSDC accession numbers or refer to alternative databases, indicated in lighter yellow. For the V3–V4 subset, studies which contained the keywords “16S rRNA”, “515”, and “806” were selected. Studies for which INSDC-compliant accession numbers were reported but which did not exist on any INSDC database are shown in lighter blue.

Full size image

To obtain more precise estimates of the percentage of articles which deposited their data in each database, we focused on the subset of 635 studies which sequenced the V3–V4 region of the 16S rRNA gene between base pairs 515 and 806 (heretofore V3–V4 subset), a target region which has gained popularity since its development and use by the Earth Microbiome Project21,22. Of these, 74.5% (n = 474) studies listed INSDC-compliant accession numbers within the article, but of these, accession numbers from 5% of the studies (n = 33) were not findable on any INSDC database. Additionally, 19% (n = 121) did not provide an identifiable link to the data, and 6.8% of the studies deposited their data in the Qiita, MG-RAST, and figshare databases (n = 9, n = 24, n = 7, respectively, Fig. 1b). Two studies provided SRA submission IDs rather than accession numbers, and were also inaccessible.
The increasing popularity of microbial community sequencing was evident in our data. Over the period studied, the number of studies in the V3–V4 subset rose from 56 in 2015 to 214 in 2018 (Supplementary Fig. 1a). The proportion of publications which claimed to deposit data to INSDC databases increased slightly over time, from 33/56 in 2015 to 172/214 in 2018 (χ2 = 6.6, p = 0.01, Supplementary Fig. 1b), suggesting an increasing tendency towards deposition in INSDC databases. Deposition to alternative databases decreased (χ2 = 14.04, p  More