Superfund Research Program
Research Support Core B: Environmental Molecular Analysis Core
Project Leader: James M. Tiedje
Grant Number: P42ES004911
Funding Period: 2006-2021
Project Summary (2013-2021)
The Core provides methodology development and microbial informatics services.
- Improves analysis methods for high-throughput gene-targeted metagenomics. Because shotgun metagenome analysis of complex microbial communities is still difficult and costly, they are extending Functional Gene Pipeline (FunGene) to support additional functional genes of interest to the projects. They are also developing improved software tools to efficiently process the higher output of new sequencing technologies now on the horizon, such as PacBio and Ion Torrent.
- Supports RNA-Seq analysis of biodegrading strains and microbial communities. Best practices for analysis of RNA-Seq data are being developed, and the application of RNA-Seq to microbial communities, meta-transcriptiomics, is even less developed. The Core is supporting both types of analysis using a combination of available tools and new tools.
- Supports metagenome analysis and develops methods for targeted metagenome analysis. By simplifying complex microbial communities, either through culture enrichment, targeted gene enrichment, or cosmid selection procedures, the cost and complexity of metagenomics can be greatly reduced. The Core is assembling a combination of available tools and novel methods and applying these to analyze metagenomes developed from biodegrading enrichment cultures and mouse gut enriched for genes and organisms of interest.
- Develops functional gene metagenome and metatranscriptome enrichment methods. They are developing a method to simultaneously pre-enrich bacterial metagenomic DNA for large numbers of genes of potential importance in biodegradation and toxin response as a novel application of the massively parallel biotinolyated RNA oligonucleotide ’bait’ and capture’ technique.
The Core is developing the probe sequences for a large number of genes of interest by extending their FunGene database. For highly diverse genes such as aryl dioxygenase genes, they are supplementing this with sequences obtained via genetargeted sequencing. They are validating the method on DNA target fragment length and percent identity to bait sequences, and then evaluating the methodology for quantitative metatranscriptome analysis.