WDCM and CODATA Joint Workshop ICCC13 Beijing, China ONE-GENE, ONE-ENZYME Building a foundation for microbial metagenomics analysis Kevin McCluskey 1 and Scott Baker 2 1 The Fungal Genetics Stock Center 2 Department of Energy, Pacific Northwest National Laboratory
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WDCM and CODATA Joint WorkshopICCC13 Beijing, ChinaONE-GENE, ONE-ENZYME
Building a foundation for microbial
metagenomics analysisKevin McCluskey1 and Scott Baker2
1The Fungal Genetics Stock Center2Department of Energy, Pacific Northwest National Laboratory
WDCM and CODATA Joint WorkshopICCC13 Beijing, ChinaONE-GENE, ONE-ENZYME
Outline
• Background
• Role of collections
• Whole genome survey programs
• Accessing genome databases
• Evaluating genome diversity
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WDCM and CODATA Joint WorkshopICCC13 Beijing, ChinaONE-GENE, ONE-ENZYME
What is metagenomics?
• The direct genetic analysis of communities of microbes
– Environmental
– Intestinal/Rumen
• Growth of Metagenomicspublications (from Pubmed)
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WDCM and CODATA Joint WorkshopICCC13 Beijing, ChinaONE-GENE, ONE-ENZYME
Metagenomic are proliferating
• US NCBI SRA lists over 17,000 publicmetagenome studies
• 16,466 are private
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WDCM and CODATA Joint WorkshopICCC13 Beijing, ChinaONE-GENE, ONE-ENZYME
Metagenome studies depend on robust reference materials
• 2005 Most taxa are unidentifiedor Id to Phylum
• Microbial“Dark Matter”
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WDCM and CODATA Joint WorkshopICCC13 Beijing, ChinaONE-GENE, ONE-ENZYME
Resources in collections are essential for metagenomics
77 different species representing
23 different genera
59 species with 10 or fewer isolates
> 70 strains from whole genome
sequencing programs
# strains Species
18744 Neurospora crassa
1188 Aspergillus nidulans
672 Neurospora intermedia
550 Fusarium sp.
299 Neurospora tetrasperma
274 Neurospora sitophila
253 Schizophyllum commune
241 Sordaria sp.
152 Neurospora discreta
134 Magnaporthe grisea
138 Aspergillus niger
75 Pichia pastoris
52 Neurospora sp
28 Ascobolus sp.
26 Gelasinospora sp.
53 Aspergillus fumigatus
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WDCM and CODATA Joint WorkshopICCC13 Beijing, ChinaONE-GENE, ONE-ENZYME
Increasing pressure on operations of culture collections in post-genomics era
Neurospora genome was published in 2004
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Neurospora
Aspergillus
Other
Plasmids
Plates
Numbers of items distributed by the FGSC in recent years.
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WDCM and CODATA Joint WorkshopICCC13 Beijing, ChinaONE-GENE, ONE-ENZYME
Taxonomic studies and WGS
• 1000 Fungal Genomes seeks to provide one complete genome sequence for every fungal FAMILY
• GEBA will fill gaps in bacterial and archael genome sequences
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WDCM and CODATA Joint WorkshopICCC13 Beijing, ChinaONE-GENE, ONE-ENZYME
US DOE Joint Genome Institute programs
• Most are user programs
– community sequencing program
– emerging technologies opportunity program
– technology development pilot program
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WDCM and CODATA Joint WorkshopICCC13 Beijing, ChinaONE-GENE, ONE-ENZYME
US DOE Joint Genome Institute programs
• Emphasizing relationships with living microbe collection