Quarterly User Update (October – December 2025) and review of 2025
Welcome to our final community update from 2025 – covering announcements and highlights; and celebrating accomplishments from our team, users, and collaborators.
Community Highlights
Our latest stories come from two members, Aaron Schirmer and Bridget Allen, that showcase diverse perspectives when collaborating with KBase. Aaron uses KBase to teach bioinformatics to undergraduates and to integrate computational biology skills into Course-based Undergraduate Research Experiences. Bridget began integrating a new KBase App – bamtofastq, data handling tool from bedtools – as part of her summer internship at Brookhaven National Laboratory. These and other highlights are available on the KBase News page: https://www.kbase.us/news/aaron-schirmer/ and https://www.kbase.us/news/bridget-allen/.
Long-time KBase Educators Community Member and MICROnet Steering Committee Member, Steve Biller of Wellesley College, was awarded as an Outstanding Instructor from ASM MRA! It’s been great to help make student research contributions more visible through the KBase collection. Let us know when you’re publishing with your students in Microbiology Resource Announcements so we can make sure it’s added to the collection!
If you are interested in a KBase Highlight on your work or projects, email us at engage@kbase.us.
Workshops and Training
Undergraduate faculty participate in the MICROnet workshop at ASMCUE in San Antonio, Texas.
In November, KBase traveled to San Antonio, Texas to provide in-person workshops for graduate students and faculty at Texas A&M University-San Antonio and undergraduate instructors at the American Society for Microbiology Conference for Undergraduate Educators.
This fall also brought two new webinars to support the community with updated tools. Find the recorded webinars on Metabolic Modeling with ModelSEED2 and Microbial Genomics in KBase on our YouTube Channel.
Platform Updates
The KBase platform had one new app released, NanoPlot, for long-read sequences quality assessment, alongside an update to Kaiju and a bugfix to GTDB-Tk. Details on latest releases and updates at: https://www.kbase.us/news/app-releases-and-updates-q4-2025/.
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:
- Identifying the potential for the genus Geobacillus to be a probiotic using KBase for comparative genomic analysis (Najar et al 2025);
- Using metagenomics to map microbial pathways of organic matter degrading and methane production in natural gas wells (Moore et al. 2025); and
- How the combined toxicity of nickel and copper affects key pathways of microbes in contaminated environments (Darwiche et al. 2025).
Over 2025, there were 152 publications citing the use of KBase! 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 our annual user numbers in 2025. Keep doing great science in KBase. Remember, the KBase team is here to support you!
KBase by the numbers from 2025.
