title: A viability-linked metagenomic analysis of cleanroom environments: eukarya, prokaryotes, and viruses.
abstract: BACKGROUND
  Recent studies posit a reciprocal dependency between the microbiomes associated with humans and indoor environments. However, none of these metagenome surveys has considered the viability of constituent microorganisms when inferring impact on human health.
  
  
  RESULTS
  Reported here are the results of a viability-linked metagenomics assay, which (1) unveil a remarkably complex community profile for bacteria, fungi, and viruses and (2) bolster the detection of underrepresented taxa by eliminating biases resulting from extraneous DNA. This approach enabled, for the first time ever, the elucidation of viral genomes from a cleanroom environment. Upon comparing the viable biomes and distribution of phylotypes within a cleanroom and adjoining (uncontrolled) gowning enclosure, the rigorous cleaning and stringent control countermeasures of the former were observed to select for a greater presence of anaerobes and spore-forming microflora. Sequence abundance and correlation analyses suggest that the viable indoor microbiome is influenced by both the human microbiome and the surrounding ecosystem(s).
  
  
  CONCLUSIONS
  The findings of this investigation constitute the literature's first ever account of the indoor metagenome derived from DNA originating solely from the potential viable microbial population. Results presented in this study should prove valuable to the conceptualization and experimental design of future studies on indoor microbiomes aimed at inferring impact on human health.
authors.affiliation: Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria. thomas.weinmaier@univie.ac.at.
authors.forename: Thomas
authors.initials: T
authors.lastname: Weinmaier
authors.affiliation: Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA. alexander.j.probst@gmail.com.
authors.forename: Alexander J
authors.initials: AJ
authors.lastname: Probst
authors.affiliation: Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, USA. myron@precisscientific.com.|Precis Scientific, Scottsdale, AZ, USA. myron@precisscientific.com.
authors.forename: Myron T
authors.initials: MT
authors.lastname: La Duc
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, CA, USA. dgciobanu@lbl.gov.
authors.forename: Doina
authors.initials: D
authors.lastname: Ciobanu
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, CA, USA. jfcheng@lbl.gov.
authors.forename: Jan-Fang
authors.initials: JF
authors.lastname: Cheng
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, CA, USA. nnivanova@lbl.gov.
authors.forename: Natalia
authors.initials: N
authors.lastname: Ivanova
authors.affiliation: Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria. thomas.rattei@univie.ac.at.
authors.forename: Thomas
authors.initials: T
authors.lastname: Rattei
authors.affiliation: Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, USA. vaishamp@jpl.nasa.gov.
authors.forename: Parag
authors.initials: P
authors.lastname: Vaishampayan
mesh_terms: D004780:Environment, Controlled; D004783:Environmental Microbiology; D056890:Eukaryota / Q000145:classification / Q000235:genetics; D006801:Humans; D054892:Metagenome; D056186:Metagenomics / Q000379:methods; D050296:Microbial Viability / Q000235:genetics*; D064307:Microbiota; D011387:Prokaryotic Cells / Q000145:classification; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D014780:Viruses / Q000145:classification / Q000235:genetics
chemical_list: D012336:RNA, Ribosomal, 16S