Genome Insider

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.
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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: [email protected] 
Matt Escobar: [email protected] 

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

To engineer yeast to do more, and understand genomes in general, Jef Boeke, Weimin Zhang (NYU Langone Health) and Leslie Mitchell (Neochromosome) have worked to replace yeast’s native chromosomes with synthetic versions. This project has turned out to be an international collaboration, with some artistic endeavors along the way. Eventually, the goal is to create an entirely human-generated yeast genome.

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: Manipulating the 3D organization of the largest synthetic yeast chromosome
NYU Release: Researchers Assemble Nine Synthetic Yeast Chromosomes

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

Three stories of JGI-supported research, connected to nutrient cycles. Francis Martin and Lucas Auer discuss their work on communities of forest floor fungi. Allison Joy looks into seagrass meadows' carbon sequestration with insights from Adam Healey and Xiao Ma. And Karen Serrano and Benjamin Cole explain their research on the symbiotic relationship between mycorrhizal fungi and plant roots. 
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

Feature: Getting to the Bottom of Fungal Functions Across Earth’s Forests
Paper: Metatranscriptomics sheds light on the links between the functional traits of fungal guilds and ecological processes in forest soil ecosystems

Feature: Eelgrass proves to be much younger than we thought
Paper: Ocean current patterns drive the worldwide colonization of eelgrass (Zostera marina)
Paper: Seagrass genomes reveal ancient polyploidy and adaptations to the marine environment

Paper: Spatial co-transcriptomics reveals discrete stages of the arbuscular mycorrhizal symbiosis

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