Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India/Experiment 5

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Reviewed Marked as Reviewed by Folakunmi on 2024-1-4

Curated date: 2023/11/05

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing, Folakunmi, Fiddyhamma

Subjects

Location of subjects

Denmark

India

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

Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology

Type II diabetes mellitus adult onset diabetes,Adult-Onset Diabetes,adult-onset diabetes,Adult-Onset Diabetes Mellitus,diabetes mellitis type 2,diabetes mellitis type II,DIABETES MELLITUS TYPE 02,diabetes mellitus type 2,Diabetes Mellitus, Adult Onset,Diabetes Mellitus, Adult-Onset,Diabetes Mellitus, Ketosis Resistant,Diabetes Mellitus, Ketosis-Resistant,Diabetes Mellitus, Maturity Onset,Diabetes Mellitus, Maturity-Onset,Diabetes Mellitus, Non Insulin Dependent,Diabetes Mellitus, Non-Insulin-Dependent,Diabetes Mellitus, Noninsulin Dependent,diabetes mellitus, noninsulin-dependent,Diabetes Mellitus, Slow Onset,Diabetes Mellitus, Slow-Onset,Diabetes Mellitus, Stable,Diabetes Mellitus, Type 2,diabetes mellitus, type 2,diabetes mellitus, type 2, protection against,Diabetes Mellitus, Type II,Diabetes, Type 2,diabetes, type 2,insulin resistance, susceptibility to,Ketosis-Resistant Diabetes Mellitus,Maturity Onset Diabetes Mellitus,maturity-onset diabetes,Maturity-Onset Diabetes Mellitus,MODY,NIDDM,Non-Insulin Dependent Diabetes,non-insulin dependent diabetes,Non-Insulin Dependent Diabetes Mellitus,non-insulin dependent diabetes mellitus,non-insulin-dependent diabetes mellitus,noninsulin dependent diabetes,noninsulin-dependent diabetes mellitus,Slow-Onset Diabetes Mellitus,Stable Diabetes Mellitus,T2DM - Type 2 Diabetes mellitus,T2DM - type 2 diabetes mellitus,Type 2 Diabetes,type 2 diabetes,Type 2 Diabetes Mellitus,type 2 diabetes mellitus,Type 2 Diabetes Mellitus Non-Insulin Dependent,type 2 diabetes mellitus non-insulin dependent,Type II Diabetes,type II diabetes,type II diabetes mellitus,Type II diabetes mellitus

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

Normoglycemic (NG) controls

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

Type 2 diabetes (T2D) patients

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

Individuals diagnosed with T2D

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

275

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

298

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

4 months (Denmark participants)

Lab analysis

Sequencing type

16S

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

V1-V5

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).

raw counts

Statistical test

DESeq2

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

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment

geographic area

Alpha Diversity

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

unchanged

Signature 1

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Reviewed Marked as Reviewed by Folakunmi on 2024-1-4

Curated date: 2023/11/08

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing, Folakunmi

Source: Supplemental. Table S3A

Description: Differential abundant taxa between type 2 diabetes (T2D) VS normoglycemic controls (NG) in the combined Danish-Indian group

Abundance in Group 1: decreased abundance in Type 2 diabetes (T2D) patients

NCBI	Quality Control	Links
Anaerosporobacter
Butyricicoccus
Dialister
Faecalibacterium
Lactobacillus
Romboutsia
Roseburia
Ruminococcus sp.
Subdoligranulum
uncultured Oscillospiraceae bacterium
Christensenellaceae_R7Christensenellaceae_R7

Revision editor(s): ChiomaBlessing, Folakunmi

Signature 2

EditHistoryDelete

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Your review change was submitted

Reviewed Marked as Reviewed by Folakunmi on 2024-1-4

Curated date: 2023/11/08

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing, Folakunmi

Source: Supplemental Table S3A & B

Description: Differential abundant taxa between type 2 diabetes (T2D) VS normoglycemic controls (NG) in the combined Danish-Indian group

Abundance in Group 1: increased abundance in Type 2 diabetes (T2D) patients

NCBI	Quality Control	Links
Bacteroides
Blautia sp.
Coprococcus sp.
Dorea
Firmicutes bacterium CAG:56
Lachnoclostridium
Megasphaera
Oscillibacter

Revision editor(s): ChiomaBlessing, Folakunmi