title: Cultivation of stable, reproducible microbial communities from different fecal donors using minibioreactor arrays (MBRAs).
abstract: BACKGROUND
  Continuous-flow culture models are one tool for studying complex interactions between members of human fecal microbiotas because they allow studies to be completed during an extended period of time under conditions where pH, nutrient availability, and washout of waste products and dead cells can be controlled. Because many of the existing well-validated continuous-flow models are large and complex, we were interested in developing a simpler continuous-flow system that would allow microbial community dynamics to be examined in higher throughput while still maintaining complex microbial communities. To this end, we developed minibioreactor arrays (MBRAs), small volume bioreactors (15 ml) that allow simultaneous cultivation of up to 48 microbial communities in a single anaerobic chamber.
  
  
  RESULTS
  We used MBRA to characterize the microbial community dynamics of replicate reactors inoculated from three different human fecal donors and reactors seeded with feces pooled from these three donors. We found that MBRA could be used to efficiently cultivate complex microbial communities that were a subset of the initial fecal inoculum (15-25 % of fecal OTUs initially observed). After an initial acclimation period of approximately 1 week, communities in each reactor stabilized and exhibited day-to-day variation similar to that observed in stable mouse fecal communities. Replicate reactors were predominately populated by shared core microbial communities; variation between replicate reactors was primarily driven by shifts in abundance of shared operational taxonomic units (OTUs). Consistent with differences between fecal donors, MBRA communities present in reactors seeded with different fecal samples had distinct composition and structure.
  
  
  CONCLUSIONS
  From these analyses, we conclude that MBRAs can be used to cultivate communities that recapitulate key features of human fecal communities and are a useful tool to facilitate higher-throughput studies of the dynamics of these communities.
authors.affiliation: Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. Jennifer.Auchtung@bcm.edu.
authors.forename: Jennifer M
authors.initials: JM
authors.lastname: Auchtung
authors.affiliation: Department of Microbiology and Molecular Genetics, Michigan State University, 567 Wilson Rd, East Lansing, MI, 48823, USA. pohlcath@uoregon.edu.|Present address: Institute for Molecular Biology, University of Oregon, 249 Klamath, Eugene, OR, 97403, USA. pohlcath@uoregon.edu.
authors.forename: Catherine D
authors.initials: CD
authors.lastname: Robinson
authors.affiliation: Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. Robert.Britton@bcm.edu.
authors.forename: Robert A
authors.initials: RA
authors.lastname: Britton
mesh_terms: D000818:Animals; D044822:Biodiversity; D019149:Bioreactors; D016000:Cluster Analysis; D005243:Feces / Q000382:microbiology*; D000069196:Gastrointestinal Microbiome; D006801:Humans; D051379:Mice; D064307:Microbiota; D015203:Reproducibility of Results