Disordered microbial communities in the upper respiratory tract of cigarette smokers

Your review change was submittedDuplicate this Experiment Add a new Signature

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

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

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

Experiment 2

Your review change was submittedDuplicate this Experiment Add a new Signature

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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks, ChiomaBlessing

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: left oropharynx of nonsmokers

Group 1 name Corresponds to the case (exposed) group for case-control studies: left oropharynx of smokers

Lab analysis

Statistical Analysis

Signature 1

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 S5

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

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

NCBI	Quality Control	Links
Capnocytophaga
Fusobacterium
Neisseria
Aggregatibacter

Revision editor(s): WikiWorks

Signature 2

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 S6

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

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

NCBI	Quality Control	Links
Actinomyces
Eggerthella
Megasphaera
Veillonella
Streptobacillus

Revision editor(s): WikiWorks

Experiment 3

Your review change was submittedDuplicate this Experiment Add a new Signature

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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks, ChiomaBlessing

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Nasopharynx Nasenrachenraum,Epipharynx,Nasal part of pharynx,Pars nasalis pharyngis,Rhinopharynx,Nasopharynx,nasopharynx

Group 0 name Corresponds to the control (unexposed) group for case-control studies: right nasopharynx of nonsmokers

Group 1 name Corresponds to the case (exposed) group for case-control studies: right nasopharynx of smokers

Lab analysis

Statistical Analysis

Signature 1

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 S7

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

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

NCBI	Quality Control	Links
Actinomyces
Leuconostoc
Acinetobacter
Aquitalea
Shigella
Zoogloea

Revision editor(s): WikiWorks

Signature 2

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 S8

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

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

NCBI	Quality Control	Links
Eggerthella
Dorea
Eubacterium
Abiotrophia
Allobaculum
Anaerovorax
Coprococcus
Erysipelotrichaceae
Finegoldia
Gemella
Lachnospiraceae
Peptostreptococcaceae
Oscillospiraceae
Syntrophococcus
Anaerofilum

Revision editor(s): WikiWorks

Experiment 4

Your review change was submittedDuplicate this Experiment Add a new Signature

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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks, ChiomaBlessing

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: left nasopharynx of nonsmokers

Group 1 name Corresponds to the case (exposed) group for case-control studies: left nasopharynx of smokers

Lab analysis

Statistical Analysis

Signature 1

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 S9

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

Abundance in Group 1: increased abundance in left nasopharynx of smokers

NCBI	Quality Control	Links
Flavobacterium
Erysipelothrix
Gemella
Shigella
Sutterella

Revision editor(s): WikiWorks

Signature 2