Foundry120 atlas

← IBD microbiome

The reduction of dextran sulfate sodium-induced colitis severity in mice exposed to cigarette smoke is accompanied by specific gene pathway and microbial shifts

Download from source ↗

Dataset overview

Participants None
Samples None
Reuse readiness 5.6/10 evidence-backed score

The reduction of DSS-induced colitis severity in mice exposed to cigarette smoke is linked to immune modulation and microbial shifts.

Lo Sasso G, Phillips BW, Sewer A, Battey JND, Kondylis A, Talikka M, Titz B, Guedj E, et al. · Scientific reports · 2020

Abstract

Exposure to cigarette smoke (CS) causes detrimental health effects, increasing the risk of cardiovascular, pulmonary diseases and carcinogenesis in exposed individuals. The impact of CS on Inflammatory Bowel Disease (IBD) has been established by a number of epidemiological and clinical studies. In fact, CS is associated with a higher risk of developing Crohn's disease (CD) while inversely correlates with the development, disease risks, and relapse rate of ulcerative colitis (UC). To investigate the effect of CS exposure on experimental colitis, we performed a comprehensive and integrated comparative analysis of colon transcriptome and microbiome in mice exposed to dextran sodium sulfate (DSS) and CS. Colon transcriptome analysis revealed that CS downregulated specific pathways in a concentration-dependent manner, affecting both the inflammatory state and composition of the gut microbiome. Metagenomics analysis demonstrated that CS can modulate DSS-induced dysbiosis of specific bacterial genera, contributing to resolve the inflammation or accelerate recovery. The risks of smoking far outweigh any possible benefit, thus smoking cessation must always be encouraged because of its significant health benefits. However, the inverse association between active smoking and the development of UC cannot be ignored and the present study lays the foundation for investigating potential molecular mechanisms responsible for the attenuation of colitis by certain compounds of tobacco when decoupled from combustion.

doi:10.1038/s41598-020-60175-3 ↗ PMID 32123204 ↗ PMC7052152 ↗

Study facts

Organism
—
Platform
—
Age group
—
Disease groups
—
Anatomical sites
—

Data availability

Specific data assets have not been resolved from the source yet — see the source repository below for the full file listing.

Strengths & limitations for reuse

Strengths

  • Raw reads are advertised
  • Feature/OTU tables are advertised
  • Taxonomic tables are advertised

Limitations

  • Not documented: participant counts are documented
Extraction evidence & provenance

Each extracted field is shown with the source excerpt and location used to resolve it.

Assay

FieldValueEvidence
assay.paired_end True
Reads flagged as “properly paired” that had a mapping quality ≥ 5 were retained.

Section Microbiome bioinformatics, offset 47000
assay.read_length 150
trimmed to a maximum length of 150 bases

Section Microbiome bioinformatics, offset 46500
assay.sequencing_type shotgun_metagenomics
Shotgun sequencing of the metagenome was used to investigate CS-related alterations in microbial community composition

Section CS affects gut microbiota composition, offset 28000

Cohort

FieldValueEvidence
cohort.disease_activity_metadata_available True
DSS-treated mice developed colitis, as evidenced by weight loss, increased colon weight/length ratio, and the disease activity index (DAI).

Section Impact of CS exposure on DSS-induced colitis, offset 6500
cohort.study_design longitudinal
Shotgun sequencing of the metagenome was used to investigate CS-related alterations in microbial community composition in a longitudinal manner.

Section CS affects gut microbiota composition, offset 28000
cohort.treatment_exposure_documented True
Three groups of mice were exposed to three different concentrations of cigarette smoke for a total of four weeks, including five days of dextran sulfate sodium treatment

Section ena_study.description, offset —

Data_Assets

FieldValueEvidence
data_assets.feature_or_otu_table True
Reads were counted per sequence, resulting in one vector of counts per sample, and counts were merged into a single matrix.

Section Microbiome bioinformatics, offset 48000
data_assets.open_access True from source
"isOpenAccess": "Y"

Section publication metadata, offset —
data_assets.raw_reads True
Sequencing reads obtained from the previous step were cleaned of adapters

Section Microbiome bioinformatics, offset 46000
data_assets.taxonomic_table True
Sequences were assigned to taxa based on the NCBI taxonomy

Section Microbiome bioinformatics, offset 48500

Specimens

FieldValueEvidence
specimens.body_site feces
bacterial species richness in the feces of DSS-treated mice

Section CS affects gut microbiota composition, offset 28000
specimens.longitudinal_sampling True
Shotgun sequencing of the metagenome was used to investigate CS-related alterations in microbial community composition in a longitudinal manner.

Section CS affects gut microbiota composition, offset 28000
specimens.sample_type stool
Analysis of the Shannon index at the genus level showed the expected reduction in bacterial species richness in the feces of DSS-treated mice

Section CS affects gut microbiota composition, offset 28000