Effects of smoking on the lower respiratory tract microbiome in mice

From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2023-4-23
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Zhang R, Chen L, Cao L, Li KJ, Huang Y, Luan XQ, Li G
Journal
Respiratory research
Year
2018
Keywords:
Inflammation, Lower respiratory tract, Mice, Microbiome, Smoking
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


Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-24

Curated date: 2023/03/14

Curator: Sophy

Revision editor(s): Sophy, Claregrieve1

Subjects

Location of subjects
China
Host species Species from which microbiome was sampled. Contact us to have more species added.
Mus musculus
Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Lung Pulmo,Lung,lung
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Smoking behavior smoking,Smoking behavior,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
Male Kunming 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
LEfSe
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

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-24

Curated date: 2023/03/14

Curator: Sophy

Revision editor(s): Sophy, Aiyshaaaa, Claregrieve1

Source: Figure 10

Description: Differential microbial abundance between the smoking and non-smoking mice

Abundance in Group 1: increased abundance in Smoking

NCBI Quality ControlLinks
Alloprevotella
Blastocatella
Blastocatellales
Dyadobacter
Escherichia/Shigella sp.
Ktedonobacteraceae
Ktedonobacteria
Lactococcus
Mollicutes
Mycoplasmatota
Nitrosomonadaceae
Nitrosomonadales
Oxalobacteraceae
Pedobacter
Planomicrobium
Porphyromonas
Proteus
Pullulanibacillus
Sphingobacteriaceae
Sporolactobacillaceae
Subdoligranulum
Trichococcus

Revision editor(s): Sophy, Aiyshaaaa, Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-24

Curated date: 2023/04/23

Curator: Sophy

Revision editor(s): Sophy, Claregrieve1

Source: Figure 10

Description: Differential microbial abundance between the smoking and non-smoking mice

Abundance in Group 1: decreased abundance in Smoking

NCBI Quality ControlLinks
Brachybacterium
Brevibacillus
Burkholderiaceae
Desulfuromonadales
Diaphorobacter
Enterobacter
Enterobacterales
Enterobacteriaceae
Geobacter
Kluyvera
Lactobacillaceae
Lactobacillus
Mesorhizobium
Nesterenkonia
Oceanospirillales
Phascolarctobacterium
Phyllobacteriaceae
Ralstonia
Raoultella

Revision editor(s): Sophy, Claregrieve1

Experiment 2


Reviewed Marked as Reviewed by Atrayees on 2023-6-8

Curated date: 2023/05/29

Curator: Atrayees

Revision editor(s): Atrayees

Differences from previous experiment shown

Subjects

Lab analysis

Statistical Analysis

Statistical test
Mann-Whitney (Wilcoxon)
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
Not specified
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
Not specified

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-8

Curated date: 2023/05/29

Curator: Atrayees

Revision editor(s): Atrayees, ChiomaBlessing

Source: Table 2

Description: Differentially abundant taxon in the smoking and the non-smoking groups.

Abundance in Group 1: increased abundance in Smoking

NCBI Quality ControlLinks
Acidimicrobiales
Alloprevotella
Candidatus Thermoprofundales
Dyadobacter
Jatrophihabitans
Lactococcus
Macrococcus
Marvinbryantia
Paludibacter
Pedobacter
Planomicrobium
Porphyromonas
Proteus
Pseudochrobactrum
Pullulanibacillus
Subdoligranulum
Trichococcus
unclassified Caulobacteraceae
uncultured Planctomycetaceae bacterium
Escherichia/Shigella sp.

Revision editor(s): Atrayees, ChiomaBlessing

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-8

Curated date: 2023/05/29

Curator: Atrayees

Revision editor(s): Atrayees, ChiomaBlessing, Chinelsy

Source: Table 2

Description: Differentially abundant taxon in the smoking and the non-smoking groups.

Abundance in Group 1: decreased abundance in Smoking

NCBI Quality ControlLinks
Brachybacterium
Brevibacillus
Catenisphaera
Corynebacterium
Diaphorobacter
Enterobacter
Geobacter
Jeotgalicoccus
Kluyvera
Lactobacillus
Mesorhizobium
Mucispirillum
Nesterenkonia
Pasteurella
Paucimonas
Raoultella
Variibacter
uncultured Phyllobacteriaceae bacterium

Revision editor(s): Atrayees, ChiomaBlessing, Chinelsy