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 Uniform resource identifier for web resources.

Authors

Shanahan ER, Shah A, Koloski N, Walker MM, Talley NJ, Morrison M, Holtmann GJ

Journal

Microbiome

Year

2018

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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Curated date: 2021/01/10

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Subjects

Location of subjects: Australia

Host species Species from which microbiome was sampled (if applicable): 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: nicotine dependence cigarette habituation, susceptibility to,Cigarette Smoking,Dependence, Nicotine,Dependence, Tobacco,Disorder, Nicotine Use,Disorder, Tobacco Use,Disorder, Tobacco-Use,Nicotine Addiction,nicotine addiction,nicotine addiction, susceptibility to,nicotine dependence,nicotine dependence, susceptibility to,NICOTINE USE DIS,Nicotine Use Disorder,Nicotine Use Disorders,smoking,smoking habit, susceptibility to,Smoking, Cigarette,Smoking, Tobacco,Smokings, Tobacco,susceptibility to tobacco addiction,tobacco addiction, susceptibility to,Tobacco Dependence,Tobacco Dependences,Tobacco Smoking,Tobacco Smokings,TOBACCO USE DIS,Tobacco Use Disorder,tobacco use disorder,Tobacco Use Disorders,Tobacco-Use Disorder,Use Disorder, Nicotine

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

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: unchanged

Signature 1

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Curated date: 2020-07-07

Curator: Zyaijah Bailey

Revision editor(s): WikiWorks743

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	Links
Rothia
Streptococcus
Veillonella

Revision editor(s): WikiWorks743

Experiment 2

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Mark reviewed

Your review change was submittedDuplicate this Experiment Add a new Signature

Needs review

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743

Subjects

Location of subjects: Australia

Host species Species from which microbiome was sampled (if applicable): 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: nicotine dependence cigarette habituation, susceptibility to,Cigarette Smoking,Dependence, Nicotine,Dependence, Tobacco,Disorder, Nicotine Use,Disorder, Tobacco Use,Disorder, Tobacco-Use,Nicotine Addiction,nicotine addiction,nicotine addiction, susceptibility to,nicotine dependence,nicotine dependence, susceptibility to,NICOTINE USE DIS,Nicotine Use Disorder,Nicotine Use Disorders,smoking,smoking habit, susceptibility to,Smoking, Cigarette,Smoking, Tobacco,Smokings, Tobacco,susceptibility to tobacco addiction,tobacco addiction, susceptibility to,Tobacco Dependence,Tobacco Dependences,Tobacco Smoking,Tobacco Smokings,TOBACCO USE DIS,Tobacco Use Disorder,tobacco use disorder,Tobacco Use Disorders,Tobacco-Use Disorder,Use Disorder, Nicotine

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 smokes
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

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

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