After overcoming a number of unforeseen challenges during the preparation process, we are pleased to announce the release of the SILVA SSU 144 dataset. Working with a new team of curators, we have completely redesigned the curation workflow, in order to establish a more robust and sustainable process for future releases.
In order to guarantee a release this year, we have not yet applied this new curation workflow to the eukaryotic dataset. For the first version of this release, we have focused on curating the prokaryotic small-subunit (SSU) sequences only. However, all newly available eukaryotic sequences have been included in the datasets. At present, eukaryotic classification is based on the existing groups in the SILVA guide tree, with no further manual curation steps applied.
To ensure the quality and consistency of this release, we have decided not to publish an large-subunit (LSU) dataset as part of SILVA 144. Instead, our efforts were focused on completing the transition to the new curation workflow. In July, our new scientific lead and curator, Dr. Ayla Murray, joined the SILVA team and will spearhead the upcoming curation of the eukaryotic dataset. Over the coming year, the eukaryotes will be divided into subgroups (i.e., Fungi, Metazoa, etc.) to be curated and released incrementally. This approach allowed for a timely release of the prokaryotic dataset and will enable the broader use of SILVA 144 across a wider range of research communities in the coming future.
This release also contains DADA2, Kraken2, Megan and Qiime2 classifiers. The habitat-specific Qiime2 classifiers are still under construction and will be released as soon as they are ready.
We have also made changes to the SILVA versioning scheme with SILVA 144. Previously, the SILVA version numbers corresponded to the release number of an European Nucleotide Archive (ENA) release. These have now been discontinued with the ENA release 143, thus we have decided to use 144 as the next SILVA version. Henceforth, we will increase the version number by one with each full release (e.g., 145, 146 etc).
The SILVA 144 release was originally planned to be a streamlined release focused on rapidly incorporating newly available sequence data. As development progressed, however, it became clear that the substantial growth in sequence data since SILVA 138.2 required extensive updates to the existing pipeline. Addressing these challenges required targeted improvements to ensure that the pipeline remains robust, which inevitably extended the release timeline. At the same time, the SILVA team experienced a period of reduced staffing, including the unexpected departure of both curators. Despite these challenges, the project benefited greatly from the exceptional support of colleagues across the DSMZ Digital Diversity team. We are particularly grateful to Dr. Heike Freese and Dr. Markus Göker from the LPSN team, as well as Dr. Johannes Sikorski from the DSMZ Digital Diversity team, who joined the curation effort at short notice. Their expertise, commitment, and collaborative spirit were instrumental in making the SILVA 144 release possible. Their support exemplifies the strength of the scientific community and has helped lay the foundation for a more resilient curation and release workflows for future releases.
The next step for the SILVA team is to begin working on SILVA 145 in the summer of 2027, with a full release targeted by the end of that year. In the meantime, the software development team will focus on improving the scalability of the SILVA pipeline and re-developing software that is no longer fit to handle the current sequence volume. We will also be making additional metadata available for users (e.g. BioSamples). The overarching goal is to be able to offer a new, full SILVA release with new quality standards and workflows, while including all domains (Archaea, Bacteria and Eukaryota) from the beginning.
We would like to thank the SILVA community for its continued patience and support as we modernise our curation processes and work toward providing increasingly comprehensive and high-quality reference datasets. We always appreciate feedback to our help desk contact(at)arb-silva.de. Please also let us know if any issues arise related to the updated curation workflow in the new release. Feedback from users greatly improves our ability to quickly identify and address issues. We hope that SILVA 144 helps you to achieve your research goals and look forward to providing more improvements in the future.
The SILVA-Team (Jan, Ayla, Yeliz, Paul)
