Quarterly User Update (April – June 2025)
Welcome to our community update for Q2 2025 – covering announcements and highlights; and celebrating accomplishments from our team, users, and collaborators.
American Society for Microbiology offered a training series on KBase
KBase collaborated with the American Society for Microbiology to provide hands-on, practical training for instructors and early career researchers in microbial data analysis. The series went step-by-step through the process of microbial isolate genome analysis from raw sequencing reads to assembling and annotating genomes in the Narrative. The last session in the series covered how to prepare an ASM Microbiology Resource Announcement data publication using resources from KBase (https://asm.org/webinars/from-bench-to-publication-identification-and-analy).
Microbial Isolate Genomics workflow followed during the From Bench to Publication series.
While this first series ended in May, there is an upcoming one beginning on September 2 covering community-wide metagenomic data, with live webinars and hands-on practice. Details here: https://asm.org/webinars/from-sample-to-mag-identifying-and-characterizing.
Community Highlights
Workshop participants at University of Massachusetts Amherst.
In May 20-22, the first regional MICROnet Training Workshop took place at the University of Massachusetts Amherst with 16 participants from 11 institutions across the Northeast (https://www.kbase.us/news/micronet-jun-2025/). These instructors will be part of the first regional MICROnet cohort integrating microbiome research modules into their courses during the 2025-26 academic year. Stay tuned to hear more about the outcomes and program milestones!
Two sessions at the American Society for Microbiology Microbe meeting in Los Angeles, California highlighted KBase and platform resources. KBase co-hosted a session with ASM Microbiology Resource Announcements to discuss FAIR – Findable, Accessible, Interoperable, Reusable – data principles and leveraging the landscape of persistent identifiers in a Lounge and Learn. KBase user Hannah Schweitzer presented on the Produced Water DNA Database (PW-DNA). This resource is readily available in KBase and open to all users!
For questions about using the PW-DNA database or comments and feedback, please reach out to us at engage@kbase.us.
KBase Publications
The platform and team behind KBase continues to support users to analyze their data and follow the FAIR (findable, accessible, interoperable, reusable) data principles through to publication. Studies published this quarter included:
- Environmental contexts with how denitrifying bacterial isolates can disrupt denitrification in contexts such as high nitrate sites (Carr et al. 2025);
- How diet has a greater impact in restoring dysbiosis in mice compared to microbiota transplants (Kennedy et al. 2025); and
- Making tools for multi-omic network analysis using the RWRtoolkit (random walk with restart toolkit) available on KBase (Kainer et al. 2025).
All publications using KBase are available at: https://www.kbase.us/research. If we are missing your publication citing KBase in your methods, please let us know at engage@kbase.us.
Summary
To close out our update, here is a summary documenting April through June 2025 user numbers. Keep doing great science in KBase. The KBase team is here to support you!
KBase by the numbers from the April through June 2025 Quarter Report.
