High-Level PM2.5/PM10 Exposure Is Associated With Alterations in the Human Pharyngeal Microbiota Composition

Study information

Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/29

study design

time series / longitudinal observational

Citation

PMID PubMed identifier for scientific articles.

30804895

DOI Digital object identifier for electronic documents.

10.3389/fmicb.2019.00054

URI

Authors

Qin T, Zhang F, Zhou H, Ren H, Du Y, Liang S, Wang F, Cheng L, Xie X, Jin A, Wu Y, Zhao J, Xu J

Journal

Frontiers in microbiology

Year

2019

Keywords:

PM2.5/PM10, microbiome composition, pharynx, respiratory pathogen, smoking

Previous studies showed that high concentration of particulate matter (PM) 2.5 and PM10 carried a large number of bacterial and archaeal species, including pathogens and opportunistic pathogens. In this study, pharyngeal swabs from 83 subjects working in an open air farmer's market were sampled before and after exposure to smog with PM2.5 and PM10 levels up to 200 and 300 μg/m3, respectively. Their microbiota were investigated using high-throughput sequencing targeting the V3-V4 regions of the 16S rRNA gene. The genus level phylotypes was increased from 649 to 767 in the post-smog pharyngeal microbiota, of which 142 were new and detected only in the post-smog microbiota. The 142 new genera were traced to sources such as soil, marine, feces, sewage sludge, freshwater, hot springs, and saline lakes. The abundance of the genera Streptococcus, Haemophilus, Moraxella, and Staphylococcus increased in the post-smog pharyngeal microbiota. All six alpha diversity indices and principal component analysis showed that the taxonomic composition of the post-smog pharyngeal microbiota was significantly different to that of the pre-smog pharyngeal microbiota. Redundancy analysis showed that the influences of PM2.5/PM10 exposure and smoking on the taxonomic composition of the pharyngeal microbiota were statistically significant (p < 0.001). Two days of exposure to high concentrations of PM2.5/PM10 changed the pharyngeal microbiota profiles, which may lead to an increase in respiratory diseases. Wearing masks could reduce the effect of high-level PM2.5/PM10 exposure on the pharyngeal microbiota.

Experiment 1

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/29

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks, Victoria

Subjects

Location of subjects: China

Host species Species from which microbiome was sampled. Contact us to have more species added.: Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Cavity of pharynx Cavitas pharyngealis,Cavitas pharyngis,Lumen of pharynx,Pharyngeal cavity,Cavity of pharynx,cavity of pharynx

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Air pollution air pollution,Air pollution

Group 0 name Corresponds to the control (unexposed) group for case-control studies: pre-smog swabs

Group 1 name Corresponds to the case (exposed) group for case-control studies: post-smog swabs

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Vendors in an open-air farer's market who worked in the same place and were exposed to smog over the same business hours

Group 0 sample size Number of subjects in the control (unexposed) group: 83

Group 1 sample size Number of subjects in the case (exposed) group: 83

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V3-V4

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: relative abundances

Statistical test: LEfSe

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.001

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: Yes

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 4

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Chao1 Abundance-based estimator of species richness: increased

Simpson Estimator of species richness and species evenness: more weight on species evenness: unchanged

Richness Number of species: increased

Signature 1

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/29

Curated date: 2021/01/10

Curator: Victoria Goulbourne

Revision editor(s): Claregrieve1, WikiWorks

Source: Figure S3

Description: Histogram of unique biomarker bacteria in each group as analyzed by linear discriminant analysis effect size (LefSe)

Abundance in Group 1: increased abundance in post-smog swabs

NCBI	Quality Control	Links
Veillonellaceae
Bacilli
Leptotrichia

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/29

Curated date: 2021/01/10

Curator: Victoria Goulbourne

Revision editor(s): Claregrieve1, WikiWorks

Source: Figure S3

Description: Histogram of unique biomarker bacteria in each group as analyzed by linear discriminant analysis effect size (LefSe)

Abundance in Group 1: decreased abundance in post-smog swabs

NCBI	Quality Control	Links
Betaproteobacteria
Prevotella

Revision editor(s): Claregrieve1, WikiWorks