Influence of cigarette smoking on the human duodenal mucosa-associated microbiota
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Shanahan ER, Shah A, Koloski N, Walker MM, Talley NJ, Morrison M, Holtmann GJ
Journal
Microbiome
Year
2018
Keywords:
Cigarettes, Duodenum, Microbiome, Mucosa, Small intestine, Smoking
BACKGROUND: Cigarette smoking is a known risk factor in a number of gastrointestinal (GI) diseases in which the microbiota is implicated, including duodenal ulcer and Crohn's disease. Smoking has the potential to alter the microbiota; however, to date, the impact of smoking on the mucosa-associated microbiota (MAM), and particularly that of the upper GI tract, remains very poorly characterised. Thus, we investigated the impact of smoking on the upper small intestinal MAM. A total of 102 patients undergoing upper GI endoscopy for the assessment of GI symptoms, iron deficiency, or Crohn's disease, but without identifiable lesions in the duodenum, were recruited. Smoking status was determined during clinical assessment and patients classified as current (n = 21), previous smokers (n = 40), or having never smoked (n = 41). The duodenal (D2) MAM was profiled via 16S rRNA gene amplicon sequencing. RESULTS: Smoking, both current and previous, is associated with significantly reduced bacterial diversity in the upper small intestinal mucosa, as compared to patients who had never smoked. This was accompanied by higher relative abundance of Firmicutes, specifically Streptococcus and Veillonella spp. The relative abundance of the genus Rothia was also observed to be greater in current smokers; while in contrast, levels of Prevotella and Neisseria were lower. The MAM profiles and diversity of previous smokers were observed to be intermediate between current and never smokers. Smoking did not impact the total density of bacteria present on the mucosa. CONCLUSIONS: These data indicate the duodenal MAM of current smokers is characterised by reduced bacterial diversity, which is partially but not completely restored in previous smokers. While the precise mechanisms remain to be elucidated, these microbiota changes may in some part explain the adverse effects of smoking on mucosa-associated diseases of the GI tract. Smoking status requires consideration when interpreting MAM data.
Experiment 1
Reviewed Marked as Reviewed by Atrayees on 2023-7-10
Subjects
- Location of subjects
- Australia
- 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
- Small intestine Anterior intestine,Intestinum tenue,Mid intestine,Small bowel,Small intestine,small intestine
- 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
- never smoked
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- patients with FD, ID,or CD who currently smoked
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patient with FD,ID or CD with who previously or currently smokes
- Group 0 sample size Number of subjects in the control (unexposed) group
- 41
- Group 1 sample size Number of subjects in the case (exposed) group
- 61
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V6-V8
- 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).
- centered log-ratio
- Statistical test
- Kruskall-Wallis
- 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
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-7-11
Source: Figure 3& Text
Description: Linear discriminant analysis effect size (LEfSe) method to identify bacterial OTUs that are associated with smoking status.
Abundance in Group 1: increased abundance in patients with FD, ID,or CD who currently smoked
NCBI | Quality Control | Links |
---|---|---|
Rothia | ||
Streptococcus | ||
Veillonella |
Revision editor(s): WikiWorks
Experiment 2
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- patients with FD, ID,or CD who currently smokes
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-7-11
Source: Figure 3 & Text
Description: Linear discriminant analysis effect size (LEfSe) method to identify bacterial OTUs that are associated with smoking status.
Abundance in Group 1: decreased abundance in patients with FD, ID,or CD who currently smokes
NCBI | Quality Control | Links |
---|---|---|
Neisseria | ||
Prevotella |
Revision editor(s): WikiWorks
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