Rachel Adams, Tom Bruns, John Taylor, MarziaMiletto, Steve Lindow, SeemaBhangar, Bill

Nazaroff, Allen Goldstein, Gary Andersen, Ed Ahrens

Processes and sources for indoor microbial communities

Background

Study design: samplesBioaerosols

Settled dust Size-fractionatedVacuum-pumped

SurfacesHousehold surfaces + foreheads

Environments

Classrooms Residences Outdoors

qPCR + Pyrosequencedamplicons- 16S & ITS (&18S)

#metadata

Building & room characteristics

Geographic location

Function

Temperature & relative humidity

Construction materials

Building floors

Ventilation system (& exchange rate)

Human behaviorOccupancyActivity & 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 publishing your 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