Bacterial-Fungal Interactions SFA

Integrating fungal computational sequence data analysis capabilities






The Bacterial-Fungal Interactions Science Focus Area (SFA) driven by Patrick Chain at Los Alamos National Laboratory (LANL) aims to address some of the knowledge gaps around bacterial-fungal interactions within the soil. The researchers are using a multi-omics approach to gain a predictive understanding of the bacterial-fungal interactions. This work will shed light on how microbial interactions in soil affect ecosystem services such as plant productivity, nutrient cycling, and carbon flux.

Collaborative Development Object

Data analysis modules:

  • Bulk retrieval of fungal sequencing data, from raw data to draft contigs to finished genome
  • Determination of unique genomic signatures at each taxonomic rank for fungal genomes
  • Specific detection of microbial species based on unique fungal signatures


  • GOTTCHA2 (Genomic Origin Through Taxonomic Challenge): This App uses a novel taxonomic profiling method for metagenomes that is both gene-independent and signature-based. It significantly reduces false discovery rates (FDR). (Released) 
  • Centrifuge Taxonomic Classifier: This App enables rapid, accurate, and sensitive labeling of metagenomic reads and quantification of species. (Beta-only)
  • Kraken2 Taxonomic Classifier: This App examines the k-mers within a query sequence and maps k-mers to the lowest common ancestor (LCA) of all genomes in the reference database known to contain a given k-mer. (in Beta-only)

Additional Information

Meet the Members

SFA Manager/PI: Patrick Chain1
KBase Contact: Paramvir Dehal5,6
Lead Developers: Mark Flynn1, Po-E Li1, and Chien-Chi Lo1
Project Team: Michal Babinski1, David Bruce1, Jean Challcombe1, James Werner1, Armand Dichosa1, Migun Shakya1, Geoffrey House1, Jamey Young2, Pilar Junier3, Debora Rodrigues4
Affiliations: 1Los Alamos National Laboratory, 2Vanderbilt University, 3University of Neuchâtel, Switzerland, 4University of Houston, 5Lawrence Berkeley National Laboratory, 6KBase