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Study

Study Name: Fungi-associated bovine rumen microbial communities from the University of Illinois at Urbana-Champaign, USA, for metatranscriptome analysis

Projects

Biosamples

Organisms

Biosamples: 20 Seq. Projects: 20
STUDY INFORMATION
GOLD Study ID Gs0085735
Study Name Fungi-associated bovine rumen microbial communities from the University of Illinois at Urbana-Champaign, USA, for metatranscriptome analysis
Other Names 300806
NCBI Umbrella Bioproject Name
NCBI Umbrella Bioproject ID
Legacy ER Study ID 40735
Legacy GOLD ID Gm0040735
Added By Ionna Pagani on 2013-02-19
Last Modified By JGI automated process on 2014-08-11
PI Matthias Hess
Description Fungi play a significant role in the biomass-degrading phenotype of the cow rumen and fungal enzymes appear to have higher specific activities towards plant cell wall polymers than bacterial biomass-degrading enzymes. To identify and catalogue the biomass-degrading enzymes that are produced by fungi and other eukaryotes that colonize and degrade the real-world biofuel feedstock switchgrass and corn stover during rumen-incubation, we propose to generate a total of ~600 Gb of metatranscriptome data from eukaryotic rumen microbes.

In particular, we propose to generate ~200 Gb of metatranscriptome sequence from the eukaryotic community that colonizes the biofuel-feedstock switchgrass and corn stover, respectively, and ~200 Gb of metatranscriptome sequence from the eukaryotic community found in the rumen fluid (as control). We anticipate that the requested amount of metatranscriptome sequence will facilitate the assembly and identification of a significant number of lignocellulolytic enzymes from fungi and other eukaryotes that will be active specifically towards the biofuel-feedstock switchgrass and corn stover.

We also propose to generate a 1/4 of a lane of 454 pyrotag data of the eukaryotic internal transcribed spacer 1 (ITS1) region amplified from each of the three samples (performed in biological duplicates). (Alternatively to the ITS1 region the 18S rRNA gene could be targeted.) The obtained sequence data will allow us to determine the complexity and composition of the eukaryotic community in each sample and to reduce the allocated amount of sequence if the results obtained from the phylogenomic analysis suggest a low community complexity.

In summary, we propose to generate sequence data for metatranscriptomic and phylogenomic analyzes that correspond to 3 runs of Illumina?s HiSeq2000 and 1? lane of Roche?s 454 Titanium sequencing platform, respectively, as well as support and guidance with subsequent sequence assembly and data analysis.

Relevance
Study Information Link
Study Information Visibility Public
Metagenomic Study Yes
Publication
ECOSYSTEM CLASSIFICATION
Ecosystem Host-associated
Ecosystem Category Mammals
Ecosystem Type Digestive system
Ecosystem Subtype Foregut
Specific Ecosystem Rumen
STUDY COMPOSITION
Number of Biosamples 20
Number of Organisms 0
Number of Seq Projects 20
Number of Analysis Projects 138
Number of Related Studies 0

 

 

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