Effects of sex and chronic cigarette smoke exposure on the mouse cecal microbiome

Study information

Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/7

study design

laboratory experiment

Citation

PMID PubMed identifier for scientific articles.

32251484

DOI Digital object identifier for electronic documents.

10.1371/journal.pone.0230932

URI

Authors

Tam A, Filho FSL, Ra SW, Yang J, Leung JM, Churg A, Wright JL, Sin DD

Journal

PloS one

Year

2020

RATIONALE: Chronic smoke exposure is associated with weight loss in patients with Chronic Obstructive Pulmonary Disease (COPD). However, the biological contribution of chronic smoking and sex on the cecal microbiome has not been previously investigated. METHODS: Adult male, female and ovariectomized mice were exposed to air (control group) or smoke for six months using a standard nose-only smoke exposure system. DNA was extracted from the cecal content using the QIAGEN QIAamp® DNA Mini Kit. Droplet digital PCR was used to generate total 16S bacterial counts, followed by Illumina MiSeq® analysis to determine microbial community composition. The sequencing data were resolved into Amplicon Sequence Variants and analyzed with the use of QIIME2®. Alpha diversity measures (Richness, Shannon Index, Evenness and Faith's Phylogenetic Diversity) and beta diversity (based on Bray-Curtis distances) were assessed and compared according to smoke exposure and sex. RESULTS: The microbial community was different between male and female mice, while ovariectomy made the cecal microbiome similar to that of male mice. Chronic smoke exposure led to significant changes in the cecal microbial community in both male and female mice. The organism, Alistipes, was the most consistent bacteria identified at the genus level in the cecal content that was reduced with chronic cigarette exposure and its expression was positively related to the whole-body weight of these mice. CONCLUSION: Chronic smoke exposure is associated with changes in the cecal content microbiome; these changes may play a role in the weight changes that are observed in cigarette smokers.

Experiment 1

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/7

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks, Victoria

Subjects

Location of subjects: Canada

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: Caecum Blind intestine,Blindgut,Caeca,Caecum,Ceca,Cecum,Intestinum caecum,Intestinum crassum caecum,Intestinum crassum cecum,caecum

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: all other mice

Group 1 name Corresponds to the case (exposed) group for case-control studies: male mice exposed to cigarette smoke

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: male mice exposed to smoke

Group 0 sample size Number of subjects in the control (unexposed) group: 50

Group 1 sample size Number of subjects in the case (exposed) group: 8

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: 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): 0.05

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: 3.5

Alpha Diversity

Pielou Quantifies how equal the community is numerically: decreased

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

Richness Number of species: decreased

Signature 1

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Curated date: 2021/01/10

Curator: Zyaijah Bailey

Revision editor(s): Claregrieve1, WikiWorks, Merit

Source: Figure 7

Description: Differentially abundant taxa in the smoke-exposed male mice versus all other mice

Abundance in Group 1: increased abundance in male mice exposed to cigarette smoke

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Akkermansia
Akkermansiaceae
Candidatus Aenigmatarchaeota
Rhodospirillales
Verrucomicrobiia
Verrucomicrobiota

Revision editor(s): Claregrieve1, WikiWorks, Merit

Experiment 2

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Curated date: 2021/01/10

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Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies: female mice exposed to cigarette smoke

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: female mice exposed to cigarette smoke

Group 0 sample size Number of subjects in the control (unexposed) group: 48

Group 1 sample size Number of subjects in the case (exposed) group: 10

Lab analysis

Statistical Analysis

Alpha Diversity

Pielou Quantifies how equal the community is numerically: decreased

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

Richness Number of species: increased

Signature 1

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Source: Figure 7

Description: Differentially abundant taxa in the smoke-exposed female mice versus all other mice

Abundance in Group 1: increased abundance in female mice exposed to cigarette smoke

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Bacteroidaceae
Bacteroides
Muribaculaceae

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Experiment 3

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Curated date: 2021/01/10

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Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies: ovariectomized female mice exposed to cigarette smoke

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: ovariectomized female mice exposed to smoke

Lab analysis

Statistical Analysis

Alpha Diversity

Pielou Quantifies how equal the community is numerically: decreased

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

Richness Number of species: decreased

Signature 1

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/7

Curated date: 2021/01/10

Curator: Zyaijah Bailey

Revision editor(s): Claregrieve1, WikiWorks, Merit

Source: Figure 7

Description: Differentially abundant taxa in the smoke-exposed ovariectomized female mice versus all other mice

Abundance in Group 1: increased abundance in ovariectomized female mice exposed to cigarette smoke

NCBI	Quality Control	Links
Butyrivibrio
Prevotellaceae
Rikenella
Prevotella
Prevotella sp.

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Experiment 4

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Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

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

Group 1 name Corresponds to the case (exposed) group for case-control studies: mice exposed to smoke

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: male, female or ovariectomized females mice exposed to smoke