Project Goal

The Hospital Microbiome Project will characterize the taxonomic composition of surface-, air-, water-, and human-associated microbial communities in two hospitals to monitor changes in community structure following the introduction of patients and hospital staff. The specific aim is to determine the influence of population demographics, how the demographic interfaces with a space, and the building materials used to create that space, on the community succession, and rate of colonization by potential pathogens. This will be performed in a newly constructed private US hospital in Chicago, and a US Army medical center in Germany.


This proposed sampling design will test several hypotheses concerning the microbial interaction of multiple demographics with the hospital infrastructure and may lead to recommendations for best practice in reducing HAIs. Four hypotheses that will be tested are:

  1. Microbial community structure on hospital surfaces can be predicted by human demographics, physical conditions (e.g. humidity, temperature), and building materials for each location and time.
  2. A patient-room microbiota is influenced by the current patient and their duration of occupancy, and shows community succession with the introduction of a new occupant.
  3. The colonization of the surfaces and patients by potential pathogens is influenced by composition and diversity of the existing microbial community derived from previous occupants of the space.
  4. The rate of microbial succession is driven by demographic usage and building materials.

Proposed Activities

In Chicago, 12,392 samples will be collected using sterile swabs from patients, staff, rooms, common areas, water, and air filters from 52 or 365 time points prior to and following the official opening of the hospital. Absolute microbial abundance (plate counts and qPCR), building science measurements, and antibiotic resistance microarrays will be combined with relative taxonomic abundance via amplicon sequencing (16S/18S/ITS). In Germany, one military room will be targeted over 16 time points, with 100 samples collected per time for a total of 1600 samples.

Expected Products

The results will be of interest to the microbial ecology, health sciences, and building sciences communities; as such, we will publish in PLoS Pathogens, Nature Medicine, Indoor Air, and Science. Additionally, our findings will be made accessible to the general public through a website (hospitalmicrobiome.com) and social media networks. We will develop a model that leverages building conditions to predict microbial succession and the potential for HAIs. Data will be deposited in MobeDAC and will be associated with the Earth Microbiome Project. We are developing a Hospital Microbiome Consortium, which brings together leaders from diverse disciplines in two annual meeting over the course of this study to discuss this research field and potential avenues for development, funding, etc. Meetings will continue, with additional funding.

Expected Outcomes

Approximately 100,000 people die every year from HAIs. This study will be the first of its kind in examining how microbial communities develop in a hospital. In light of these facts, we expect our findings to be applied to improving patient care through better-informed approaches to predicting the role of building design and materials in controlling the spread of microorganisms within a built environment.