Influence of cigarette smoking on the human duodenal mucosa-associated microbiota

From BugSigDB
Needs review
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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Lwaldron, Atrayees

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

Curated date: 2021/01/10

Curator: Zyaijah Bailey

Revision editor(s): WikiWorks

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 ControlLinks
Rothia
Streptococcus
Veillonella

Revision editor(s): WikiWorks

Experiment 2


Needs review

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Lwaldron

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

Curated date: 2021/01/10

Curator: Zyaijah Bailey

Revision editor(s): WikiWorks

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 ControlLinks
Neisseria
Prevotella

Revision editor(s): WikiWorks