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

Study information

Needs review

study design

prospective cohort

Citation

PMID PubMed identifier for scientific articles.

30157953

DOI Digital object identifier for electronic documents.

10.1186/s40168-018-0531-3

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

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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

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: smoking behavior smoking,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

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Your review change was submitted

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 Control	Links
Rothia
Streptococcus
Veillonella

Revision editor(s): WikiWorks

Experiment 2

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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