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The Ferret Upper Respiratory Microbiome


Infection susceptibility and disease severity is regulated by a complex balance between the genotype of the pathogen, the genotype of the host, and environmental factors. While many studies are being conducted to evaluate the contribution of these three factors in many infectious diseases, another variable that until recently has been overlooked is the metagenome (or microbial community including viruses, bacteria and microeukaryotes which inhabit the human body). Specifically, many viruses infect through mucosal surfaces that are colonized with normal flora. Years of co-evolution of a virus with its host and its metagenome have likely selected for viruses that are able to infect a host in the presence of the most prevalent metagenome, so the characteristics of the metagenome are likely to make an impact in infection susceptibility and disease outcome. Moreover, the host innate and adaptive immune factors elicited in response to viral infection are likely to make a big impact in the normal flora, which may increase susceptibility to pathogenic bacteria colonization. We are specifically interested in the role of the upper respiratory tract metagenome in promoting or inhibiting infection by influenza viruses, and how changes in the metagenome after viral infection may promote secondary bacterial colonization and enhance disease. However, we still lack fundamental studies that address how variable the metagenome at the Upper Respiratory Tract (URT) is among hosts, and how the metagenome responds to virus infection.

Thus, our understanding of the nature and extent of a core or at least a set of common microbial members of the URT of humans is currently limited. The ferret is the most accepted and widely used mammal model system for the study of influenza virus infection, pathogenesis and transmission. The importance of this animal model system was further emphasized during the 2009 H1N1 pandemic influenza, as this model allowed the rapid assessment of the pathogenesis and transmission of this novel virus. Additional information on the microbial diversity found in different body sites of ferrets would adequately complement the results obtained through the Human Microbiome Project (HMP), and will allow further assessment of the power and limitations of this model system. Nevertheless, at this time few mechanisms are available to facilitate investigations such as those proposed here that are likely to yield strong baseline data on this critical animal model system.

We hypothesize that, upon viral infection the normal residing microbiome of the URT will be affected by the antiviral state triggered in cells of the local URT resulting in the modulation in the diversity and/or quantity of the microbial population.

Five components of ferret URT microbiome interactions will be examined:

  1. Establishing the base line microbial communities present in the URT of ferret under a normal health state (i.e. in the absence of viral infection or other microbial infection).
  2. Determine the changes that microbial communities undergo over the course of an influenza virus infection.
  3. Identify specific microbial populations that might be favored, altered, or reduced during influenza infection.
  4. Determine whether the increase or decrease of specific microorganisms correlates with the modulation of the course of disease.  These aspects will be explored using 16S sequencing of the V1-V3 and V3-V5 hypervariable regions of the rDNA gene.
  5. We also aim to evaluate gene expression of the microbial population as this will provide a more precise indication of which bacteria and which metabolic networks are active during influenza infection by assessing the transcriptome of the metagenome of the URT of ferrets.


National Institute of Allergy and Infectious Diseases (NIAID) Genome Sequencing Centers for Infectious Diseases (GSCID)

Principal Investigator

Barbara Methé


Adolfo Garcia-Sastre and
Rafael Medina Silva
Mount Sinai School of Medicine

Elodie Ghedin
University of Pittsburgh