Disordered microbial communities in the upper respiratory tract of cigarette smokers/Experiment 1

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Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks, ChiomaBlessing

Subjects

Location of subjects

United States of America

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

Oropharynx Mesopharynx,Oral part of pharynx,Pars oralis pharyngis,Oropharynx,oropharynx

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

right oropharynx of nonsmokers

Group 1 name Corresponds to the case (exposed) group for case-control studies

right oropharynx of smokers

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Smokers were defined as current smoking of .2 cigarettes daily for more than 6 months, and nonsmokers were defined as less than 100 cigarettes lifetime.

Group 0 sample size Number of subjects in the control (unexposed) group

33

Group 1 sample size Number of subjects in the case (exposed) group

29

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)

3 months

Lab analysis

Sequencing type

16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene

V1-V2

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance

Roche454

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).

relative abundances

Statistical test

Mann-Whitney (Wilcoxon)

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

Signature 1

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Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks

Source: Table3 + Table S3

Description: Bacterial taxa that distinguish airway microbial communities of smokers from nonsmokers

Abundance in Group 1: increased abundance in right oropharynx of smokers

NCBI	Quality Control	Links
Capnocytophaga
Peptostreptococcus
Fusobacterium
Acidovorax
Haemophilus
Neisseria

Revision editor(s): WikiWorks

Signature 2

EditHistoryDelete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: Shaimaa Elsafoury

Revision editor(s): WikiWorks

Source: Table3 + Table S4

Description: Bacterial taxa that distinguish airway microbial communities of smokers from nonsmokers

Abundance in Group 1: decreased abundance in right oropharynx of smokers

NCBI	Quality Control	Links
Megasphaera
Veillonella
Hallella
Streptococcus
Oscillospiraceae

Revision editor(s): WikiWorks