Stable Isotope Probing (SIP) is a powerful technique for studying microbial communities. These experiments can show which microbes are handling specific nutrients, or what they're doing with those nutrients, and even how quickly. But there's a catch: SIP labwork and analysis can be very demanding.

The JGI offers SIP analysis to make these experiments accessible to more researchers. Ultimately, the goal is to generate SIP data that can be useful to multiple teams and analyses.

This episode, Rex Malmstrom (JGI), and Roli Wilhelm (Purdue University), share a few different ways they're working to make this technique, SIP, more standardized -- more reproducible, more reusable, and more insightful, for the future of studying microbial communities.

Links from this episode:

• Submit your own proposal to work with the JGI
• Find all episode transcripts on our website

• JGI’s Micro-Scale Applications Group
• MISIP: a data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence and experiment
• HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

• Webinar: Metagenome quantitative SIP at the JGI: https://www.youtube.com/watch?v=5OgLDTw7eYA

• Genome Insider: Party in the Rhizosphere
• Genome Insider: A Powerful Technique to Study Microbes, Now Easier

• Simulating metagenomic stable isotope probing datasets with MetaSIPSim

• Microbes Persist: Systems Biology of the Soil Microbiome Science Focus Area (SFA), led by Dr. Jennifer Pett-Ridge at Lawrence Livermore National Laboratory (LLNL)
  • Our contact info:
• X: @JGI
• Email: jgi-comms at lbl dot gov

In this episode, undergraduates adopt genomes that the JGI sequenced, but never published in the literature. These students analyze the genomes, write reports, and publish first-author papers, making the data available for future research.

Hear from Rekha Seshadri (JGI) and Matt Escobar (California State San Marcos) about how the Adopt-A-Genome project got started. Plus, Kalyani Maitra (California State Fresno) and two students, Angela and Mark Soghomonian share what it was like to take on one of these genomes.

Links from this episode:

• Submit your own proposal to work with the JGI
• Find all episode transcripts on our website

• For more information about Adopt-A-Genome:
  • Rekha Seshadri: rseshadri@lbl.gov
  • Matt Escobar: mescobar@csusm.edu

• Adopt-A-Genome Papers:
  • Draft genome sequence of Nitrobacter vulgaris DSM 10236T
  • Draft genome sequences of Butyrivibrio hungatei DSM 14810 (JK 615T) and Butyrivibrio fibrisolvens DSM 3071 (D1T)
  • Genome sequences of key bacterial symbionts of entomopathogenic nematodes: Xenorhabdus cabanillasii DSM17905, Xenorhabdus ehlersii DSM16337, Xenorhabdus japonica DSM16522, Xenorhabdus koppenhoeferii DSM18168, and Xenorhabdus mauleonii DSM17908

• Our contact info:
  • X: @JGI
  • Email: jgi-comms at lbl dot gov

Kasey Markel and Patrick Shih (UC Berkeley and the Joint BioEnergy Institute) are looking for new ways to engineer plants. So they’ve looked into wasps that program oak trees to grow structures called galls.

In this episode, hear from Kasey and Patrick about how this project unfolded, and how they worked with the JGI's metabolomics program to find out more about these weird little pods.

Links from this episode:

• Submit your own proposal to work with the JGI
• Join us at the 2024 JGI User Meeting

• Find all episode transcripts on our website
• Paper: Cynipid wasps systematically reprogram host metabolism and restructure cell walls in developing galls

• Our contact info:
  • Twitter: @JGI
  • Email: jgi-comms at lbl dot gov

• Sound effects credits:
  • oars.wav by hazure
  • Parma Park Bird Song with Stream.WAV by muneio