title: Chemostat culture systems support diverse bacteriophage communities from human feces.
abstract: BACKGROUND
  Most human microbiota studies focus on bacteria inhabiting body surfaces, but these surfaces also are home to large populations of viruses. Many are bacteriophages, and their role in driving bacterial diversity is difficult to decipher without the use of in vitro ecosystems that can reproduce human microbial communities.
  
  
  RESULTS
  We used chemostat culture systems known to harbor diverse fecal bacteria to decipher whether these cultures also are home to phage communities. We found that there are vast viral communities inhabiting these ecosystems, with estimated concentrations similar to those found in human feces. The viral communities are composed entirely of bacteriophages and likely contain both temperate and lytic phages based on their similarities to other known phages. We examined the cultured phage communities at five separate time points over 24 days and found that they were highly individual-specific, suggesting that much of the subject-specificity found in human viromes also is captured by this culture-based system. A high proportion of the community membership is conserved over time, but the cultured communities maintain more similarity with other intra-subject cultures than they do to human feces. In four of the five subjects, estimated viral diversity between fecal and cultured communities was highly similar.
  
  
  CONCLUSIONS
  Because the diversity of phages in these cultured fecal communities have similarities to those found in humans, we believe these communities can serve as valuable ecosystems to help uncover the role of phages in human microbial communities.
authors.affiliation: Department of Pathology, University of California, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA.
authors.forename: Tasha M
authors.initials: TM
authors.lastname: Santiago-Rodriguez
authors.affiliation: Department of Pathology, University of California, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA.
authors.forename: Melissa
authors.initials: M
authors.lastname: Ly
authors.affiliation: Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.
authors.forename: Michelle C
authors.initials: MC
authors.lastname: Daigneault
authors.affiliation: Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.
authors.forename: Ian H L
authors.initials: IH
authors.lastname: Brown
authors.affiliation: Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.
authors.forename: Julie A K
authors.initials: JA
authors.lastname: McDonald
authors.affiliation: Department of Biology, San Diego State University, San Diego, CA, USA.
authors.forename: Natasha
authors.initials: N
authors.lastname: Bonilla
authors.affiliation: Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.
authors.forename: Emma Allen
authors.initials: EA
authors.lastname: Vercoe
authors.affiliation: Department of Pathology, University of California, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA. dpride@ucsd.edu.|Department of Medicine, University of California, San Diego, CA, USA. dpride@ucsd.edu.
authors.forename: David T
authors.initials: DT
authors.lastname: Pride
mesh_terms: D001419:Bacteria / Q000821:virology; D001435:Bacteriophages / Q000145:classification* / Q000235:genetics; D044822:Biodiversity; D005243:Feces / Q000382:microbiology*; D016679:Genome, Viral; D006801:Humans; D064307:Microbiota; D016366:Open Reading Frames