Environmental Microbiota

Microbes are the most diverse and abundant entities on Earth, and they are critical to ecological and biogeochemical processes such as decomposition, plant growth, and nutrient cycling. They also have the potential to contribute to restoration and environmental amelioration efforts, which we have explored, for example, in studies of pre-agricultural soils (Fierer et al., 2013) and oil spills (Mason et al., 2014). Microbial communities are also ubiquitous and persistent in the indoor environments we inhabit, yet we understand very little about how they influence our resident microbiota. We hope to better describe how microbes affect the world we live in through a number of projects.

The Earth Microbiome Project (http://www.earthmicrobiome.org/) is a massively multi-disciplinary and highly collaborative effort to analyze microbial communities across the globe and to organize the data by categorizing the Earth into habitats. Patterns within and across habitats will provide us with a deeper understanding of the global diversity of microbes and its determinants. We have already seen evidence for a persistent and ubiquitous pool of microbes in the world’s oceans, and that the fluctuations in relative abundances in this pool lead to the differences we observe between marine microbial communities (Gibbons et al., 2013). We plan to analyze 200,000 samples using metagenomics, metatranscriptomics and amplicon sequencing and to produce a global Gene Atlas describing protein space, environmental metabolic models for each biome, novel microbial genomes, and a data-analysis portal for visualization of all information.

It is estimated that Americans spend approximately 92% of their time indoors, yet we know little of the diversity of microbes that exist in this built environment which includes our homes, workplaces, and hospitals. The Sloan House Project (contact: Antonio Gonzalez) examines the bacterial communities present in household dust and stool samples of infants to understand the influence of the indoor microbial community on the gut microbiome and ultimately on health. We are also exploring what factors most strongly influence a household’s resident microbiome. The Hospital Microbiome Project explores how reservoirs for fungal, bacterial, and viral pathogens are established and maintained in the hospital environment, which is largely unknown. Hospital-acquired or nosocomial infections affect over 1 million people in the United States alone each year. Using a recently built hospital at the University of Chicago to address these questions, this project is exploring these questions as well as factors which may influence the acquisition and persistence of nosocomial infections (Smith et al., 2013).