Inhalable Microorganisms in Beijing’s PM_2.5 and PM₁₀ Pollutants during a Severe Smog Event

Particulate matter (PM) air pollution poses a formidable public health threat to the city of Beijing. Among the various hazards of PM pollutants, microorganisms in PM_2.5 and PM₁₀ are thought to be responsible for various allergies and for the spread of respiratory diseases. While the physical and chemical properties of PM pollutants have been extensively studied, much less is known about the inhalable microorganisms. Most existing data on airborne microbial communities using 16S or 18S rRNA gene sequencing to categorize bacteria or fungi into the family or genus levels do not provide information on their allergenic and pathogenic potentials. Here we employed metagenomic methods to analyze the microbial composition of Beijing’s PM pollutants during a severe January smog event. We show that with sufficient sequencing depth, airborne microbes including bacteria, archaea, fungi, and dsDNA viruses can be identified at the species level. Our results suggested that the majority of the inhalable microorganisms were soil-associated and nonpathogenic to human. Nevertheless, the sequences of several respiratory microbial allergens and pathogens were identified and their relative abundance appeared to have increased with increased concentrations of PM pollution. Our findings may serve as an important reference for environmental scientists, health workers, and city planners

Metagenomic Human Repiratory Air in a Hospital Environment

<div><p>Hospital-acquired infection (HAI) or nosocomial infection is an issue that frequent hospital environment. We believe conventional regulated Petri dish method is insufficient to evaluate HAI. To address this problem, metagenomic sequencing was applied to screen airborne microbes in four rooms of Beijing Hospital. With air-in amount of sampler being setup to one person’s respiration quantity, metagenomic sequencing identified huge numbers of species in the rooms which had already qualified widely accepted petridish exposing standard, imposing urgency for new technology. Meanwhile,the comparative culture only got small portion of recovered species and remain blind for even cultivable pathogens reminded us the limitations of old technologies. To the best of our knowledge, the method demonstrated in this study could be broadly applied in hospital indoor environment for various monitoring activities as well as HAI study. It is also potential as a transmissible pathogen real-time modelling system worldwide.</p></div

Results in bacteria comparative culture of parallel hospital samples (Filter paper elution half to metagenomic sequencing and half to conventional Peri dish culture).

<p>(For those not identified to species such as Bacillus, Genus abundance instead of species abundance was used).</p><p>Results in bacteria comparative culture of parallel hospital samples (Filter paper elution half to metagenomic sequencing and half to conventional Peri dish culture).</p

Main routes of transmission for nosocomial infection.

<p>Main routes of transmission for nosocomial infection.</p

Heatmap of metagenomic recoverd species for each group of microorganisms in four rooms.

<p>For bacteria and eukaryote, top 100 abundant species for the heatmap.</p

Number of metagenomic recovered species for each group of microorganisms.

<p>a) sampling equipment, the soft tube connected to sampling head allows it to be easily fixed at any position, even could be put before the mouth. b) the sampling filter paper at Nov.6,2013. Left: blank; right: after work for 24 hours. c) Numbers of species and d) proportions of species number in each group of microbes in four rooms.</p

PCoA analysis for indoor and outdoor air.

<p>Data were normalized between 0 and 1 and compared with PM2.5 and PM10 data set[<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0139044#pone.0139044.ref047" target="_blank">47</a>]. (red: Indoor results; blue: outdoor results).</p

Species intersection of each group of microbes in four rooms.

<p>Species intersection of each group of microbes in four rooms.</p

Reported pathogens among metagenomic recovered top 100 abundant bacteria species, missed by regulated culture-based technology from parallel control.

<p>Reported pathogens among metagenomic recovered top 100 abundant bacteria species, missed by regulated culture-based technology from parallel control.</p

Rarefaction Curve for data effectiveness.

<p>Abscissa: number of reads, coordinate: number of species.</p