Cigarette smoking and oral microbiota in low-income and African-American populations

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Reviewed Marked as Reviewed by Atrayees on 2023-6-1

Curated date: 2023/03/14

Curator: Nnadichioma

Revision editor(s): Nnadichioma, Fiddyhamma

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: Mouth Adult mouth,Cavital oralis,Cavitas oris,Cavum oris,Mouth cavity,Oral region,Oral vestibule,Regio oralis,Rima oris,Stoma,Stomatodaeum,Trophic apparatus,Vestibule of mouth,Vestibulum oris,Mouth,mouth

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

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Never-Smokers

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Participants with a smoking history were chosen based on four nested-control cases for incident cases of upper-aerodigestive tract cancer, type 2 diabetes, lung cancer, and colorectal cancer.

Group 0 sample size Number of subjects in the control (unexposed) group: 547

Group 1 sample size Number of subjects in the case (exposed) group: 592

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): Participants who took antibiotics within a year before sample collection.

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V4

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).: relative abundances

Statistical test: Logistic Regression

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)?: No

Matched on Factors on which subjects have been matched on in a case-control study: age, alcohol drinking, body mass index, race, sex, Matched on: "total energy intake" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.total energy intake, Matched on: "disease status at the first follow-up and sequencing batch" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.disease status at the first follow-up and sequencing batch, oral hygiene

Alpha Diversity

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample: increased

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-1

Curated date: 2023/03/14

Curator: Nnadichioma

Revision editor(s): Merit, Atrayees, Nnadichioma, Aiyshaaaa

Source: Table 2,3,and 4

Description: Higher prevalence of probiotic bacterial taxa among current-smokers than among never-smokers and former-smokers and Individual taxa showing a differential prevalence between current-smokers and never-smokers

Abundance in Group 1: increased abundance in Current-Smokers

NCBI	Quality Control	Links
Bifidobacteriaceae
Bifidobacterium
Bifidobacterium longum
Lactobacillus
Lactobacillus crispatus
Lactobacillus gasseri
Lancefieldella parvula
Limosilactobacillus fermentum
Limosilactobacillus oris
Limosilactobacillus panis
Limosilactobacillus reuteri
Actinomycetota
Actinomycetaceae
Actinomyces
Actinomyces graevenitzii
Rothia
Schaalia odontolytica
Coriobacteriaceae
Rothia mucilaginosa
Atopobium
Prevotella sp. oral taxon 313
Streptococcus sp. oral taxon 057
Megasphaera
Megasphaera micronuciformis
Actinomyces lingnae
Lactobacillaceae
Treponema denticola

Revision editor(s): Merit, Atrayees, Nnadichioma, Aiyshaaaa

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-1

Curated date: 2023/03/14

Curator: Nnadichioma

Revision editor(s): Nnadichioma, Aiyshaaaa, Atrayees

Source: Table 3 and 4

Description: Individual taxa showing a differential relative abundance between current-smokers and never-smokers and former-smokers and Individual taxa showing a differential prevalence between current-smokers and never-smokers

Abundance in Group 1: decreased abundance in Current-Smokers

NCBI	Quality Control	Links
Burkholderiaceae
Cardiobacterium
Enterococcus
Kingella
Kingella denitrificans
Lautropia
Neisseria
Neisseria oralis
Neisseriaceae
Hoylesella nanceiensis
Capnocytophaga sputigena
Lachnospiraceae
[Eubacterium] infirmum
Lachnoanaerobaculum umeaense
Pseudomonadota
Neisseria pharyngis
Neisseria subflava
Pasteurellaceae
Aggregatibacter
Haemophilus
Haemophilus parahaemolyticus
Haemophilus paraphrohaemolyticus
Flavobacteriaceae
Gemella
Streptococcus cristatus

Revision editor(s): Nnadichioma, Aiyshaaaa, Atrayees

Experiment 2

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Atrayees on 2023-6-1

Curated date: 2023/03/14

Curator: Nnadichioma

Revision editor(s): Nnadichioma, Fiddyhamma

Differences from previous experiment shown

Subjects

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

Group 1 sample size Number of subjects in the case (exposed) group: 477

Lab analysis

Statistical Analysis

Alpha Diversity

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample: increased

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-1

Curated date: 2023/03/28

Curator: Nnadichioma

Revision editor(s): Merit, Atrayees, Nnadichioma, Aiyshaaaa

Source: Table 2,3,and 4

Description: Higher prevalence of probiotic bacterial taxa among current-smokers than among never-smokers and former-smokers and Individual taxa showing a differential relative abundance between current-smokers and never-smokers

Abundance in Group 1: increased abundance in Former-Smokers

NCBI	Quality Control	Links
Bifidobacterium
Bifidobacterium longum
Lactobacillus crispatus
Lactobacillus gasseri
Limosilactobacillus fermentum
Limosilactobacillus oris
Limosilactobacillus panis
Limosilactobacillus reuteri
Streptococcus sp. oral taxon 057
Actinomycetaceae
Actinomycetota
Rothia
Rothia mucilaginosa
Haemophilus parahaemolyticus
Streptococcus cristatus
Actinomyces lingnae
Bifidobacteriaceae

Revision editor(s): Merit, Atrayees, Nnadichioma, Aiyshaaaa

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-1

Curated date: 2023/03/28

Curator: Nnadichioma

Revision editor(s): Nnadichioma, Aiyshaaaa, Atrayees

Source: Table 2, 3 and 4

Description: Individual taxa showing a differential relative abundance between current-smokers and never-smokers

Abundance in Group 1: decreased abundance in Former-Smokers

NCBI	Quality Control	Links
Capnocytophaga sputigena
Cardiobacterium
Enterococcus
Kingella denitrificans
Lachnoanaerobaculum umeaense
Lachnospiraceae
Lautropia
Neisseria oralis
Streptococcus sp. oral taxon 070
Treponema denticola
[Eubacterium] infirmum
Burkholderiaceae
Kingella
Prevotella
Lactobacillaceae
Actinomyces graevenitzii
Coriobacteriaceae
Atopobium
Lancefieldella parvula
Haemophilus
Aggregatibacter
Pseudomonadota
Neisseria
Neisseriaceae
Neisseria pharyngis
Neisseria subflava
Pasteurellaceae
Haemophilus paraphrohaemolyticus
Gemella
Streptococcus cristatus

Revision editor(s): Nnadichioma, Aiyshaaaa, Atrayees

Experiment 3

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Atrayees on 2023-6-1

Curated date: 2023/03/28

Curator: Nnadichioma

Revision editor(s): Nnadichioma, Fiddyhamma

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Former-Smokers

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

Group 0 sample size Number of subjects in the control (unexposed) group: 477

Group 1 sample size Number of subjects in the case (exposed) group: 592

Lab analysis

Statistical Analysis

Alpha Diversity

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample: increased

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-1

Curated date: 2023/03/28

Curator: Nnadichioma

Revision editor(s): Nnadichioma, Aiyshaaaa, Atrayees

Source: Table 2, 3, and 4

Description: Higher prevalence of probiotic bacterial taxa among current-smokers than among never-smokers and former-smokers and Individual taxa showing a differential relative abundance between current-smokers and never-smokers

Abundance in Group 1: increased abundance in Current-Smokers

NCBI	Quality Control	Links
Actinomyces
Actinomyces graevenitzii
Actinomyces lingnae
Actinomycetota
Atopobium
Bifidobacterium longum
Lactobacillus crispatus
Lactobacillus gasseri
Lancefieldella parvula
Limosilactobacillus fermentum
Limosilactobacillus oris
Limosilactobacillus panis
Limosilactobacillus reuteri
Megasphaera micronuciformis
Prevotella sp. oral taxon 313
Rothia mucilaginosa
Streptococcus sp. oral taxon 057
Streptococcus sp. oral taxon 070
Treponema denticola
Lactobacillaceae
Bifidobacterium
Rothia
Megasphaera
Lactobacillus

Revision editor(s): Nnadichioma, Aiyshaaaa, Atrayees

Signature 2