A viability-linked metagenomic analysis of cleanroom environments: eukarya, prokaryotes, and viruses

Abstract

BackgroundRecent 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.ResultsReported 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).ConclusionsThe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s40168-015-0129-y) contains supplementary material, which is available to authorized users.

Urban Dust Microbiome: Impact on Later Atopy and Wheezing

“…Therefore, an unknown, not quantifiable storage effect might have biased the results of our study. Similarly, targeting DNA of microbial community members accounts for neither activity nor for viability of these microbes, although a viability assay for whole communities has been recently published (Weinmaier et al 2015). In addition, only children for whom dust samples have been available and with follow-up information at 6 or at 10 years were included.…”

Peer Review #2 of "Optimizing de novo genome assembly from PCR-amplified metagenomes (v0.1)"

“…a few nanograms), which poses a challenge for library construction [17]. Examples include low-biomass environments like ice cores or clean rooms [18,19], tough-to-sample locations like hydrothermal vents [11], and sampling procedures that target subsets of the community, e.g. virus particles or labeled metabolically active microbes [20,21].…”

Dead or Alive? Molecular life-dead distinction in human stool samples reveals significantly different composition of the microbial community

“…PMA is most typically used in standard PCR-based assays, but has also been successfully applied in combination with e.g. qPCR [15][16][17] , metagenomics 18 , fluorescence in situ hybridization (FISH) 19 , fluorescence microscopy 20 and microarrays 21 . Another application aimed at the treatment of commercial PCR reagents to mask DNA contaminations (the "kitome"; 12 .…”

“…PMA has been applied in a wide variety of environmental and clinical microbiome studies, including research on the human microbiome [7][8][9] , indoor environments and built systems 10, but has also been successfully applied in combination with e.g. qPCR [15][16][17] , metagenomics 18 , fluorescence in situ hybridization (FISH) 19 , fluorescence microscopy 20 and microarrays 21 .…”