Microbes Persist SFA
Foundation for Understanding and Prediction of Microbial and Viral Ecogenomics in Soil
The Microbes Persist: Systems Biology of the Soil Microbiome Science Focus Area (SFA), led by Dr. Jennifer Pett-Ridge at Lawrence Livermore National Laboratory (LLNL), aims to understand the critical role that microbes play in the stabilization and persistence of soil carbon. Microbes Persist does so by studying microbial biochemistry, functional potential, and physiology of the soil microbiome. This SFA is producing hundreds of stable isotope probing genome-resolved metagenomes and will be implementing new tools in KBase to tackle the bioinformatic challenges associated with the corresponding data analysis. In addition, collaborations with the Banfield group (University of California, Berkeley) addresses microbial metagenome curation efforts, and the Sullivan group (The Ohio State University) has contributed iVirus tools to KBase.
Collaborative Development Projects
Towards quantitative theory-based predictions of soil microbial fitness, interaction, and function in KBase.
Quantitative Stable Isotope Probing (qSIP)*
Building community standards for qSIP sample metadata that links directly to analysis tools/workflows, and establishing a community database resource of qSIP experiments in KBase.
In collaboration with KBase, the Genomic Standards Consortium (GSC), and the National Microbiome Data Collaborative (NMDC), SIP sample metadata standards were developed as “Minimum Information for any Stable Isotope Probing Sequence” (MISIP; doi: 10.1093/gigascience/giae071.). Available via GSC MIxS templates.
Integration of Dynamic Energy Budget (DEB) microTrait^
Connects genomes and ecophysiological traits to build trait-based models for guild profiles with DEB profiles (in Development).
Metagenomic Functionality#
- FixAME: Enables curation of assembly quality in metagenome bins. (in Development)
Viral Tools&
- Two tools from iVirus, a tool designed to explore viral ecology and bring bioinformatic analyses to the study of viral genomes.
- VirMatcher: Predicts virus-host relationships using variety of bioinformatic methods: host CRISPR-spacers, integrated prophage, host tRNA genes, and k-mer signatures calculated by WIsH. (Released)
Additional Information
Meet the Members
SFA Principal Investigator: Jennifer Pett-Ridge1
SFA Contact: Jennifer Pett-Ridge1
KBase Contacts: Elisha Wood-Charlson (elishawc-at-lbl-dot-gov)2,3
Lead Developers: Ben Bolduc4, Jeff Kimbrel1, Ulas Karaoz2, Ben Koch5, Gianna Marschmann1, Rohan Sachdeva6
Project Team Leads: Jill Banfield2,6,#, Eoin Brodie2,^, Bruce Hungate5,*, Matthew B. Sullivan4,&
Affiliations: 1Lawrence Livermore National Lab, 2Lawrence Berkeley National Lab, 3KBase, 4The Ohio State University, 5Northern Arizona University, 6University of California, Berkeley,
Resources
- LLNL Microbes Persist Soil Microbiome SFA Project Website – Exploring the role microbes play in the stabilization and persistence of soil carbon
MISIP
- GitHub Respository: GSC MISIP from MIxS v6.0.0 release and onward
- Simpson, A., Wood-Charlson, E.M., Smith, M. et al. MISIP: a data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence and experiment. GigaScience. 13 (2024). https://doi.org/10.1093/gigascience/giae071
microTrait
Viral Tools
-
- GitHub Repository: vConTACT
- GitHub Repository: VirSorter
- GitHub Repository: VirMatcher
- Viral Tools in KBase (4 November 2020) – KBase tutorial webinar
- KBase Viral Tools & Narratives Documentation
- Bolduc, B., Zablocki, O., Guo, J. et al. iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology. ISME Communications. 1, 77 (2021). https://doi.org/10.1038/s43705-021-00083-3
