Oral microbiome and obesity in a large study of low-income and African-American populations/Experiment 1

Needs review

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Atrayees, Joan Chuks, Muqtadirat

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: Obesity Adiposis,Adiposity,Obese,Obese (finding),obesity,Obesity (disorder),Obesity [Ambiguous],obesity disease,obesity disorder,Obesity NOS,Obesity, unspecified,Overweight and obesity,Obesity

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

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: participants who were selected for four nested case-control studies to investigate the oral microbiome and those diagnosed after mouth rinse sample colection with type 2 diabetes, lung cancer, upper aero-digestive tract cancer, and colorectal cancer

Group 0 sample size Number of subjects in the control (unexposed) group: 647

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 1 year

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

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

Matched on Factors on which subjects have been matched on in a case-control study: age, race, sex, smoking status

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: age, alcohol drinking, smoking behavior, race, sex, Confounders controlled for: "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, Confounders controlled for: "disease status during the follow up" 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 during the follow up, Confounders controlled for: "and study 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.and study batch, number of teeth measurement

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Simpson Estimator of species richness and species evenness: more weight on species evenness: unchanged

Needs review

Curated date: 2021/01/10

Curator: Victoria Goulbourne

Revision editor(s): WikiWorks

Source: Table 2

Description: Probiotic bacterial taxa showing a significantly higher prevelance in non-obese than obese individuals

Abundance in Group 1: increased abundance in non-obese

NCBI	Quality Control	Links
Bifidobacterium
Bifidobacterium longum subsp. longum
Bifidobacterium scardovii
Bifidobacterium subtile
Lactobacillus
Limosilactobacillus fermentum
Limosilactobacillus panis
Lactobacillus ultunensis

Revision editor(s): WikiWorks