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 Objectives

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

Tools:

• GOTTCHA2 (Genomic Origin Through Taxonomic Challenge): 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: Enables rapid, accurate, and sensitive labeling of metagenomic reads and quantification of species. (Beta-only)
• Kraken2 Taxonomic Sequence Classifier: 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. (Beta-only)

Additional Information

Meet the Members

SFA Manager/PI: Patrick Chain¹
KBase Contact: Paramvir Dehal^5,6
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

Resources

• GitHub Repository
• Empowering the Development of Genomics Expertise (EDGE) Website
• Taxonomy Tools (21 April 2021) – KBase tutorial webinar
• KBase Taxonomy Tools Documentation