Researchers working in indoor microbial ecology have no easy way to share data.  Though the community is adopting state-of-the-art gene sequencing techniques, use of these new methods makes it difficult to compare newly collected data with older data collected using alternative methods.  What’s needed is an easy-to-use data platform that will facilitate data sharing by integrating sample handling, sequencing, analysis, and data release.  Funds from this grant support a project by Rob Knight of the University of Colorado and Mitch Sogin of the Marine Biological Laboratory to develop just such an integrated data platform. Over the next two years, Knight and Sogin will attempt to merge two data platforms used by microbial ecologists: QIIME (Quantitative Insights into Molecular Ecology) and VAMPS (Visualization and Analysis of Microbial Population Structures).  VAMPS is very user-friendly and nimble; QIIME is more powerful but harder to use.  The aim is to develop a new system that combines the best of both platforms, tying the user-friendly tools in VAMPS to the powerful analytical capacity of QIIME.  They will also develop a series of protocols and standards for the collection and analysis of microbial data using the new system.  The project will result in new standard operating procedures, better software tools, and improved methods for depositing and sharing data in indoor microbial ecology. The team expects the new tools and procedures to be adopted by at least 75 to 100 researchers, with at least 100 students and postdocs will be trained through annual workshops.

This grant provides renewed support to the Berkeley Indoor Microbial Ecology Consortium (BIMERC), a multidisciplinary group of mycologists, microbiologists, chemists, architects, and engineers who are working together to better understand the sources, factors, and processes involved in the assembly of microbial communities indoors. Grant funds support a number of planned scientific studies by the BIMERC team, including an investigation into which microbial volatile organic compounds are indicators of microbial population growth;, a study of how environment, building characteristics, and human behavior affect airborn microbes; a project to measure and model living particles using a laser-based ultraviolet spectrometer; and an analysis of microbial reproduction using gene transcripts. Additional funds support the purchase of a state-of-the-art mass spectrometer, a Proton Transfer Reaction-Time of Flight-Mass Spectrometer (PTR-ToF-MS), which will permit the team to conduct real-time chemical analysis.  The team will share their findings through peer-reviewed scientific publications, presentations at meetings and workshops, and through web-based blogs.

Funds from this grant support efforts by David A. Mills, Peter J. Shields Endowed Chair in the Department of Food Science, to examine the seasonal nature of the built environment microbiota in two types of food and beverage fermentation settings: dairies and wineries. The study aims to determine what microbial communities reside in these facilities during normal operation during all four seasons of the year; examine how these microbial communities migrate throughout the facilities; and make a series of building science measurements to evaluate how the built environment impacts these microbial communities. In the wine study, Mills and his team will examine how regional microbiota on Chardonnay grapes from four different regions--Napa, Sonoma, Central Coast, and Northern San Joaquin Valley--influences winery-associated microbiota and how room traffic, occupancy, air flows, and room surfaces affect microbial composition. In the dairy study, the team will examine how three different types of milk--goat, cheese, and cow--drive the dairy-associated microbiota at three artisanal cheese-making facilities. In both studies, the team will examine seasonal changes to indoor microbiota and their correlations with environmental parameters. The project will train at least one postdoctoral fellow and two undergraduates.  Findings will be shared with the scientific community through peer-reviewed publications and talks at scientific meetings and disseminated to the wine and dairy industry through trade publications.