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

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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