Effects of smoking on the lower respiratory tract microbiome in mice

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Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI Uniform resource identifier for web resources.
Authors
Zhang R, Chen L, Cao L, Li KJ, Huang Y, Luan XQ, Li G
Journal
Respiratory research
Year
2018
BACKGROUND: Recent studies break with traditional opinion that the lower respiratory tract is sterile, and increasingly focus on the lung microbiome and disease. Smoking, as an important etiology of inflammatory lung disease, was considered as a factor influencing lung microbiome variations in our study, and we aimed to study the effect of smoking on inflammation and microbial diversity and community. METHODS: Forty male mice were selected and randomly divided into a smoking and a non-smoking group. Mice in the smoking group were exposed to smoke smog for 2 h/day for 90 days. Blood and lung tissues were obtained after the experiment, and ELISA was used to measure interleukin-6 and C reactive protein concentrations. 16S rRNA gene quantification and sequencing technology were used to compare microbial diversity and community between the two groups. SAS 9.1 and R software were used to analyze the data. RESULTS: Thirty-six mice survived, and the weight of the smoking group increased more slowly than that of the non-smoking group. Denser inflammation and congestion were observed in the lungs of the smoking mice compared with the non-smoking group Higher microbial diversity was observed in the smoking group, and Enterobacter, Acidimicrobiales_norank, and Caulobacteraceae_Unclassified genus were significantly more abundant in the non-smoking group (P < 0.001). CONCLUSIONS: Smoking altered microbial diversities and communities in the lower respiratory tract of mice. Microbial variation should be considered in future studies focusing on smoking-induced inflammatory disease.

Experiment 1


Needs review

Curated date: 2023/03/14

Curator: Sophy

Revision editor(s): Sophy

Subjects

Location of subjects
China
Host species Species from which microbiome was sampled (if applicable)
Mus musculus
Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Lung , Lower respiratory tract Pulmo,Lung,Lower respiratory system,Lower respiratory tract
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
smoking behavior smoking,smoking behavior
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Non-smoking
Group 1 name Corresponds to the case (exposed) group for case-control studies
Smoking
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Mice exposed to smoking for 2h per day for 90 days.
Group 0 sample size Number of subjects in the control (unexposed) group
20
Group 1 sample size Number of subjects in the case (exposed) group
20
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
NA

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V4-V5
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
ANOVA
LEfSe
Mann-Whitney (Wilcoxon)
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.05
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
No
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
2


Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
sex, race

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
unchanged
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
increased

Signature 1

Needs review

Curated date: 2023/03/14

Curator: Sophy

Revision editor(s): Sophy

Source: Table 2

Description: Genus differences in abundance between the smoking and non-smoking groups

Abundance in Group 1: decreased abundance in Smoking

NCBI Links
Enterobacter
Raoultella
uncultured Caulobacteraceae bacterium
uncultured Phyllobacteriaceae bacterium

Revision editor(s): Sophy