Sloan Qiime/Vamps - Adams/BIMERC

Processes and sources for indoor microbial communities Rachel Adams, Tom Bruns, John Taylor, MarziaMiletto, Steve Lindow, SeemaBhangar, BillNazaroff, Allen Goldstein, Gary Andersen, Ed Ahrens

Background

Study design: samplesBioaerosols Settled dust Vacuum-pumped Size-fractionated HouseholdSurfaces surfaces + foreheadsEnvironments Classrooms Residences OutdoorsqPCR + Pyrosequencedamplicons- 16S & ITS (&18S)

#metadataBuilding & room characteristics Geographic location Function Temperature & relative humidity Construction materials Building floors Ventilation system (& exchange rate)Human behavior Occupancy Activity & its frequency

Data and metadata sharing• Genetic data – deposition in NCBI’s SRA – Raw data, no link between individual sample and its metadata• Metadata – no formal development for our binders full of metadata – General factors included in papers• IRB requirements – anonymity of human subjects: we do not know identity, gender, age – building location not exact but general area – promised an easy-to-digest explanation to the volunteers and university administration

Data analysis - founder effects• Mothur for conversion of .sff file to .sff.txt file• QIIME for pyrosequencing pipeline: barcode assignment, denoising, chimera-checking, and OTU clustering to make an OTU table• R and QIIME for community analysis• BLAST on lab server for fungal taxonomy assignment against the UNITE database, analyze output in MEGAN and FHiTINGS

• What are the main roadblocks at present to publishingyour data? Hours in the day

QIIME/VAMPS workshop• What tools would allow us to better utilize our data?  Fungal tree of life – one locus gives species identity & phylogenic relationships for the kingdom fungi  Detecting live from dead with PCR-based surveys  Long (enough) reads from Illumina to get near- species status

Sloan Qiime/Vamps - Adams/BIMERC

by adamsri on Oct 19, 2012

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