We intend to leverage a unique model system developed in our laboratories to reproduce diverse ecosystems representing the human distal colon (DC) and use them to identify the role of the vast communities of viruses that inhabit the DC. Many of these viruses are bacteriophages that are postulated to play major roles in altering human bacterial communities, but until now there has been no available technology to assess their roles. Because bacteriophages kill their hosts or provide them with potentially beneficial gene functions, we hypothesize that they have a significant capacity to shape the human microbiome and potentially play a role in the maintenance of health and the development of disease. Our laboratories have pioneered technologies to characterize these viral communities, and have shown that viral communities are highly personal, persistent, host sex consistent, harbor genes involved in antibiotic resistance, and are readily transmissible between close contacts. We believe that the unique model ecosystems we have developed will allow us to reproduce the diverse and complex microbial ecology of the DC, and will play a critical role in helping to decipher the role of the viral communities that inhabit the human DC. We now know that bacteria in the gut play significant roles in human health and disease, yet the forces that shape the gut microbiome are still being uncovered. Much of the diversity in the DC can be grouped into distinct enterotypes; these groups are driven by the relative abundances of microbes such as Bacteroides in different individuals. Our model system simulates the diverse DC microbiota, and is the first model capable of recapitulating the enormous microbial diversity of the DC. The system incorporates bile salts, mucins, and starches to create an environment suitable for DC bacteria. Another major benefit of this system is its accurate reproduction of viral communities from the DC. We hypothesize that the use of this model system will allow us to directly test the impacts of virus-mediated perturbations on different enterotypes. The proposed studies will help decipher the impacts of viruses on the diversity and taxonomy of gut enterotypes, and determine whether virus-mediated perturbations result in enterotype switching.
Our aims are as follows:
Aim 1) Establish model systems representing different distal colon enterotypes, and Aim 2) Characterize the responses of cultured communities to virus-mediated perturbations. We believe that through the development of our model DC ecosystem, we can address fundamental questions about the roles of viruses in the human microbiome, including: 1) how do viral communities impact our DC microbiomes?, 2) are viruses important determinants of DC microbial ecology?, and 3) how do viruses from individuals with different enterotypes affect one another? We believe the proposed research is a critical first step in understanding how viral communities may be used to manipulate the human microbiome.

Public Health Relevance

Our research plan involves establishing model ecosystems that reproduce gut microbial ecology in humans to investigate the role of viruses as natural disturbances in the gut microbiome. We plan to use these model systems to reproduce gut enterotypes representing the microbiota of a large proportion of our population and identify whether viruses have the capacity to significantly alter these gut enterotypes. Understanding how viruses may be used to manipulate the human gut microbiome render this research relevant to public health and the proposed work may provide significant insights into how viruses may be used to promote gastrointestinal health.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Exploratory/Developmental Grants (R21)
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Clinical Research and Field Studies of Infectious Diseases Study Section (CRFS)
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Alarcon, Rodolfo M
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University of California, San Diego
Schools of Medicine
La Jolla
United States
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