Community Highlight: Jennifer Goff
Jennifer Goff (JG) is a professor at SUNY College of Environmental Science and Forestry (ESF) and recently launched her lab in Fall 2023. Jennifer has a PhD in Microbial Biology from Rutgers-New Brunswick and worked as a postdoctoral researcher at the University of Georgia as a part of the ENIGMA Science Focus Area. As an environmental microbiologist, her interests are in the physiological adaptations that allow bacteria to survive in anthropogenically perturbed environments.
How do you use KBase?
(JG) I am using KBase to perform (meta)genome assemblies and analyses for environmental microorganisms to understand the adaptations that allow them to survive in high-stress environments. My graduate training was primarily in microbial physiology, so KBase provided a great environment to learn bioinformatics. Starting with KBase ultimately made it easier to learn how to run programs in command-line since it’s essentially a highly visual version of the same process.
What did you take away from participating in the Long-read Isolate Sequencing and Analysis workshop?
(JG) I attended the bioinformatics portion of the Long-read Isolate Sequencing and Analysis (LISA) workshop in December 2023. Through participating in the workshop, I learned about different pipelines available in KBase for long-read sequence assembly and analysis. Taking this information back to SUNY ESF, I led a working group of undergraduate researchers through the assembly and annotation of five bacterial genomes. Prior to this experience, I had never assembled a genome on my own. Attending the LISA workshop gave me the confidence that this was something both my students and I could do – despite not having formal training in bioinformatics.
How has working with KBase supported your research/project?
I have four papers published this year that have relied heavily on KBase for computational analyses. One was an analysis I did of mobile genetic elements (e.g., plasmids, viruses) populations in the contaminated subsurface of the Oak Ridge Reservation (ORR), published in ISME Communications. Parts of the ORR are contaminated with multiple heavy metals. I showed that mobile genetic elements from the highly contaminated regions of the site had significantly higher numbers of clusters of heavy metal resistance genes compared to mobile genetic elements from unimpacted regions of the ORR. For this analysis, I used KBase for identification and analysis of viral genomes in my dataset.
I love KBase as an accessible tool for undergraduate researchers to learn about computational biology. In another study published this year in Environmental Microbiome, Elizabeth Szink – an undergraduate researcher that I worked with at the University of Georgia, used KBase to perform a pangenome analysis of the bacteria genus Castellaniella. Castellaniella species are common in anthropogenically-impacted environments like the ORR. Another undergraduate researcher I worked with used KBase to perform phylogenetic analyses for this study. Elizabeth is co-first author on that paper alongside myself and the other student is a co-author.
Jennifer Goff co-leads an undergraduate bioinformatics working group using KBase to analyze long-read sequences alongside Julie Marcesa. (Photo courtesy of Jennifer Goff)
At ESF in Spring 2024, I ran a bioinformatics working group with five undergraduate researchers. A colleague in my department, Julie Maresca, had PacBio reads from five different isolates—four from organofluorine enrichment cultures and one from a concrete cylinder. We gave each student a genome to assemble and each week in our group meeting we went step-by-step through the assembly and annotation process, using the LISA workshop materials to guide us. We generated five complete genomes, which we recently published as two reports in Microbiology Resource Announcements (MRA), alongside their associated KBase Narratives. The undergraduate researchers authored the KBase Narratives and were all listed as co-authors on the corresponding papers.
You can find Jennifer and her students’ data publications in the Promoting Microbiome Workforce Development with KBase MRA Collection.
What role do you see KBase having in open science principles?
I love being able to directly share my analyses with the scientific community by making my Narratives publicly available. KBase makes associating these Narratives with a DOI super easy, reducing the burden on the investigator to ensure the shareability of their work.
What is one “behind the scenes” thing you want to share about your work?
I really want more people to see the power of KBase for both undergraduate and graduate education. As I mentioned earlier, I’ve published a couple papers where undergraduate students used KBase for various analyses. KBase has a lot of great documentation on how to use their resources that really support undergraduate learning. I also started using KBase’s educational resources in Spring 2024 for a graduate seminar I taught at ESF. The seminar was journal club-style where students presented on environmental science papers that relied heavily on omics-based approaches. In the final weeks of class, we worked on a modified version of one of KBase’s metagenomics tutorials. For many of the students in the course, that was their favorite part of the semester. My plan is to expand on this and incorporate even more KBase into my future courses!
Links
Learn more about Jennifer research through her webpage at: www.jenniferlgoff.com. Her colleague Julie Maresca’s webpage at SUNY ESF is available at: https://www.esf.edu/faculty/maresca/index.php .
J.L. Goff, L.M. Lui, T.N. Nielsen, F.L. Poole, H.J. Smith, K.F. Walker, T.C. Hazen, M.W. Fields, A.P. Arkin, M.W.W. Adams. “Mixed waste contamination selects for a mobile genetic element population enriched in multiple heavy metal resistance genes.” ISME Communications 4(1), ycae064 (2024). https://doi.org/10.1093/ismeco/ycae064
Narrative: https://doi.org/10.25982/160429.7/2203457
J.L. Goff, E.G. Szink, K.L. Durrence, et al. Genomic and environmental controls on Castellaniella biogeography in an anthropogenically disturbed subsurface. Environmental Microbiome. 19(26), (2024). https://doi.org/10.1186/s40793-024-00570-9
Narrative: https://doi.org/10.25982/135835.33/2203552
E.A. Kiledal, I. Moxley, O. Shevchenko, J.L. Goff, J.A. Maresca. Genome sequence of Methylobacterium fujisawaense strain C14, isolated from concrete. Microbiology Resource Announcements e00531-24 (2024). https://doi.org/10.1128/mra.00531-24
Narrative: https://kbase.us/n/169030/43/
J.L. Goff, C. Hahn, R.A. Ingrassia, C. Tiyapun, G.G. Waldschmidt, E.R. Smith, M.N. Marini, O. Shevchenko, J.A. Maresca. Genome sequences of four bacterial strains isolated from organofluorine enrichment cultures. Microbiology Resource Announcements e00532-24 (2024). https://doi.org/10.1128/mra.00532-24
Narratives:
