Schrödinger’s microbes: Tools for distinguishing the living from the dead in microbial ecosystems

Emerson, Joanne B.; Adams, Rachel I.; Román, Clarisse M. Betancourt; Brooks, Brandon; Coil, David A.; Dahlhausen, Katherine E.; Ganz, Holly H.; Hartmann, Erica M.; Hsu, Tiffany Y.; Justice, Nicholas B.; Paulino-Lima, Ivan G.; Luongo, Julia C.; Lymperopoulou, Despoina S.; Gómez-Silván, C.; Rothschild-Mancinelli, Brooke; Balk, Melike; Huttenhower, Curtis; Nocker, Andreas; Vaishampayan, Parag; Rothschild, Lynn J.

doi:10.1186/s40168-017-0285-3

Cited by 353 publications

(287 citation statements)

References 200 publications

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“…Although no RNA seqbased assay has been clinically validated to date for use in patients, the potential clin ical impact of RNA seq analyses is high. Interrogation of RNA reads from microorganisms corresponding to active microbial gene expression might enable the dis crimination between infection versus colonization 25 and live (viable) versus dead organisms 79 . Moreover, RNA seq analyses of the human host can be used to identify novel or underappreciated host-microbial interactions directly from clinical samples, as previously shown for patients with Lyme disease 68 , dengue 80 or malaria 81 .…”

Section: Human Host Response Analysesmentioning

confidence: 99%

Clinical metagenomics

2019

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| Clinical metagenomic next-generation sequencing (mNGS), the comprehensive analysis of microbial and host genetic material (DNA and RNA) in samples from patients, is rapidly moving from research to clinical laboratories. This emerging approach is changing how physicians diagnose and treat infectious disease, with applications spanning a wide range of areas, including antimicrobial resistance, the microbiome, human host gene expression (transcriptomics) and oncology. Here, we focus on the challenges of implementing mNGS in the clinical laboratory and address potential solutions for maximizing its impact on patient care and public health.

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Section: Human Host Response Analysesmentioning

confidence: 99%

Clinical metagenomics

2019

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“…An important feature to assess in any microbial community is the determination of which species present are alive and metabolically active [235]; rDNA and rRNA extracted from the same sources resulted in significantly different overall characterization of the microbiota [32,236]. Analyzing both RNA and DNA in combination, even just rRNA and rDNA, can provide further insight than just one method alone, such as the effect of environmental conditions on which microorganisms thrive while others struggle or perish.…”

Section: Built Environment Research Now and In The Futurementioning

confidence: 99%

Building upon current knowledge and techniques of indoor microbiology to construct the next era of theory into microorganisms, health, and the built environment

Horve

Lloyd

Mhuireach

et al. 2019

J Expo Sci Environ Epidemiol

103

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In the constructed habitat in which we spend up to 90% of our time, architectural design influences occupants' behavioral patterns, interactions with objects, surfaces, rituals, the outside environment, and each other. Within this built environment, human behavior and building design contribute to the accrual and dispersal of microorganisms; it is a collection of fomites that transfer microorganisms; reservoirs that collect biomass; structures that induce human or air movement patterns; and space types that encourage proximity or isolation between humans whose personal microbial clouds disperse cells into buildings. There have been recent calls to incorporate building microbiology into occupant health and exposure research and standards, yet the built environment is largely viewed as a repository for microorganisms which are to be eliminated, instead of a habitat which is inexorably linked to the microbial influences of building inhabitants. Health sectors have re-evaluated the role of microorganisms in health, incorporating microorganisms into prevention and treatment protocols, yet no paradigm shift has occurred with respect to microbiology of the built environment, despite calls to do so. Technological and logistical constraints often preclude our ability to link health outcomes to indoor microbiology, yet sufficient study exists to inform the theory and implementation of the next era of research and intervention in the built environment. This review presents built environment characteristics in relation to human health and disease, explores some of the current experimental strategies and interventions which explore health in the built environment, and discusses an emerging model for fostering indoor microbiology rather than fearing it.

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“…These may include the use of membrane‐impermeable DNA intercalating dyes, DNases or metatranscriptomics (Emerson et al . ).…”

Section: Introductionmentioning

confidence: 97%

Characterization of the bacterial microbiome in first‐pass meconium using propidium monoazide ( PMA ) to exclude nonviable bacterial DNA

Stinson

Keelan

Payne

2019

Lett Appl Microbiol

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Numerous studies have reported bacterial DNA in first‐pass meconium samples, suggesting that the human gut microbiome is seeded prior to birth. However, these studies have not been able to discriminate between DNA from living bacterial cells, DNA from dead bacterial cells or cell‐free DNA. Here we have used propidium monoazide (PMA) together with 16S rRNA gene sequencing to determine whether there are intact bacterial cells in the fetal gut. DNA was extracted from first‐pass meconium (n = 5) and subjected to 16S rRNA gene sequencing with/without PMA treatment. All meconium samples, regardless of PMA treatment, contained detectable levels of bacterial DNA; however, treatment with PMA prior to DNA extraction decreased the DNA yield by approximately 20%. PMA‐treated meconium samples did not differ significantly from untreated samples in terms of observed number of OTUs (P = 0·945); although they did differ taxonomically, with around one quarter of OTUs identified in untreated samples only, suggesting that they have originated from cell‐free/nonviable DNA. The mean Sørensen coefficient for treated vs untreated samples was 0·527. Our findings suggest that the fetal gut is seeded with intact bacterial cells prior to birth. This is an important finding, as exposure to live bacteria during gestation might have a significant impact on the developing fetus. Significance and Impact of the Study DNA‐based microbiome studies performed using 16S rRNA gene sequencing are limited by their inability to discriminate between live bacterial cells, dead bacterial cells and cell‐free DNA. Here we use propidium monoazide (PMA) to exclude nonviable bacteria from microbiome analysis of first‐pass meconium samples and thereby reveal that the majority of the purported fetal gut microbiome is from intact bacterial cells. This work demonstrates the importance of excluding nonviable bacteria when analysing the microbial community in low‐biomass samples such as meconium.

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Schrödinger’s microbes: Tools for distinguishing the living from the dead in microbial ecosystems

Cited by 353 publications

References 200 publications

Clinical metagenomics

Clinical metagenomics

Building upon current knowledge and techniques of indoor microbiology to construct the next era of theory into microorganisms, health, and the built environment

Characterization of the bacterial microbiome in first‐pass meconium using propidium monoazide ( PMA ) to exclude nonviable bacterial DNA

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