Modeling microbial metabolism on indoor surfaces

We have recently been awarded a new research program by the Alfred P Sloan Foundation to further develop out understanding of how bacterial, archaeal, viral and fungal communities interact on indoor surfaces. This research will be led by Jack Gilbert (University of Chicago), in collaboration with Chris Henry (UChicago), Brent Stephens (Illinois Institute of Technology), Paul Thomas (Northwestern University) and Scott Kelley (San Diego State University). This 3 year initiative will build on existing work that has explored how the microbiome of people and animals in the built environment shapes the successional ecology of the surface microbiome.

The aim of this study is to construct mechanistic metabolic ecosystem models of the bacteria and viruses that survive, colonize and grow on different BE materials under different environmental conditions. What do we mean by this? It is extremely likely that the majority of bacteria that arrive onto surfaces such as a floor or kitchen counter top, die very quickly. However, the extent of this mortality also depends on surface properties and physical conditions such as temperature and humidity. Previous work by our group has demonstrated that most bacterial populations on restroom floors are likely to be inactive (Gibbons et al., 2014). However, in this same study, despite no change in the source of microorganisms, the community inhabiting this surface type underwent directed, repeatable succession, usually reaching a stable state within 8 hours. This succession to a stable state is suggestive of an active assemblage of microorganisms that are interacting with each other, and the physicochemical environment they inhabit. Any ability to modulate or control this ecosystem, so as to reach a desired ecological outcome, must be predicated on our ability to understand how these communities undergo succession, and to quantitate how their biochemical interaction with the ecosystem supports this succession.

We propose to fundamentally characterize the microbial ecology of BE surfaces; to study what selection pressures shape their community structure, evolution, and metabolism; and to identify whether there are environment-specific signatures of ecological stability. We will explicitly define the causal influence of surface materials, microbial source and the environmental variables that are classically mediated during controlled building operation.

Quantifying the microbial metabolic dynamics of BE surfaces will lead to more sophisticated, parameterized and considered architectural and interior design. This translational impact will be mediated through our industrial (Skidmore Owings and Merrill (SOM)) and academic (BioBE ( and Flexlab ( partners. SOM is a major international architectural and design firm, with whom we are exploring novel techniques to use bio-inspired design to build healthier indoor environments. BioBE and Flexlab have sophisticated indoor environmental testbeds that can be leveraged to explore the influence of design choices on built environment microbiota. Improving the diversity and stability of microbial ecology associated with indoor environments requires significant changes in the design and operation of buildings, and characterizing these operating guidelines represents a future goal, which will be precipitated by the proposed research.

This research program will continue for the next 3 years and will lead to the development of sophisticated flux balance models of the microbial community interaction structure on surfaces in built environments.

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Jack Gilbert

Microbial ecologist at Argonne-UChicago-MBL