Trans-ethnic gut microbial signatures of prediabetic subjects from India and Denmark/Experiment 4

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Reviewed Marked as Reviewed by Svetlana up on 2024-12-20

Curated date: 2024/11/05

Curator: KateRasheed

Revision editor(s): WikiWorks, KateRasheed

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 - Indian & Danish Cohorts
Group 1 name Corresponds to the case (exposed) group for case-control studies
Prediabetes (PD) - Indian & Danish Cohorts
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Prediabetes (PD) - Indian & Danish Cohorts refers patients in their early stage of prediabetes in both India and Denmark cohorts.
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
262
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
4 months

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

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-12-20

Curated date: 2024/11/05

Curator: KateRasheed

Revision editor(s): KateRasheed, WikiWorks, Tosin

Source: Additional file 9: Table S7

Description: Differentially abundant taxa between NG and PD subjects, belonging to the Indian and Danish cohorts (pooled together) identified using a negative binomial Wald test (corrected for geography specific cohort effect).

Abundance in Group 1: increased abundance in Prediabetes (PD) - Indian & Danish Cohorts

NCBI Quality ControlLinks
Adlercreutzia
Agathobacter
Agathobaculum desmolans
Alistipes inops
Alloprevotella
Anaerotruncus colihominis
Bacteroides
Bacteroides intestinalis
Blautia
Blautia faecis
Blautia massiliensis (ex Liu et al. 2021)
Blautia wexlerae
Candidatus Obscuribacterales
Collinsella
Coprococcus
Coprococcus comes
Dialister
Dorea formicigenerans
Dorea longicatena
Eisenbergiella
Enterobacter
Enterorhabdus
Faecalibacterium
Fusicatenibacter saccharivorans
Holdemanella
Intestinibacter bartlettii
Intestinimonas
Lachnoclostridium
Lachnospira
Lachnospira pectinoschiza
Lachnospiraceae
Lactobacillus
Lactobacillus delbrueckii
Ligilactobacillus ruminis
Megasphaera
Mitsuokella
Negativibacillus
Oscillibacter
Oscillospiraceae
Peptococcaceae
Rhodococcus
Roseburia
Senegalimassilia
Streptococcus
Subdoligranulum
Sutterella
Thomasclavelia
Veillonella
Veillonella atypica
Veillonella dispar
Veillonella parvula
Veillonella tobetsuensis
Vibrio cholerae
uncultured Oscillospiraceae bacterium
Ruminococcaceae_UCG-0013Ruminococcaceae_UCG-0013
Ruminiclostridium_9Ruminiclostridium_9
Bifidobacterium adolescentis/faecale/stercorisBifidobacterium adolescentis/faecale/stercoris
Ruminiclostridium_5Ruminiclostridium_5
Klebsiella aerogenes/oxytoca/pneumoniaeKlebsiella aerogenes/oxytoca/pneumoniae
Rhodococcus baikonurensis/boritolerans/degradans/erythropolis/globerulus/hoagii/opacus/qingshengii/rhodochrousRhodococcus baikonurensis/boritolerans/degradans/erythropolis/globerulus/hoagii/opacus/qingshengii/rhodochrous
Alistipes finegoldii/onderdonkiiAlistipes finegoldii/onderdonkii
Lactobacillus acidophilus/casei/crispatus/kitasatonisLactobacillus acidophilus/casei/crispatus/kitasatonis
Achromobacter insolitus/xylosoxidansAchromobacter insolitus/xylosoxidans
Prevotella_9Prevotella_9
Christensenellaceae_R-7_groupChristensenellaceae_R-7_group
Escherichia/Shigella albertii/boydii/coli/dysenteriae/fergusonii/flexneri/sonnei/vulnerisEscherichia/Shigella albertii/boydii/coli/dysenteriae/fergusonii/flexneri/sonnei/vulneris
Prevotella_2Prevotella_2
Staphylococcus epidermidis/haemolyticus/hominisStaphylococcus epidermidis/haemolyticus/hominis
Lactobacillus fermentum/mucosaeLactobacillus fermentum/mucosae
Veillonella dispar/parvulaVeillonella dispar/parvula
Enterococcus azikeevi/durans/faecalis/faecium/hirae/lactis/mundtii/raffinosus/ratti/thailandicus/villorumEnterococcus azikeevi/durans/faecalis/faecium/hirae/lactis/mundtii/raffinosus/ratti/thailandicus/villorum
Ruminococcaceae bacterium UCG-005

Revision editor(s): KateRasheed, WikiWorks, Tosin

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-12-20

Curated date: 2024/11/05

Curator: KateRasheed

Revision editor(s): KateRasheed, WikiWorks

Source: Additional file 9: Table S7

Description: Differentially abundant OTUs between NG and PD subjects, belonging to the Indian and Danish cohorts (pooled together) identified using a negative binomial Wald test (corrected for geography specific cohort effect).

Abundance in Group 1: decreased abundance in Prediabetes (PD) - Indian & Danish Cohorts

NCBI Quality ControlLinks
Ruminococcaceae_UCG-010Ruminococcaceae_UCG-010
Prevotella 9Prevotella 9
Bacteroides nordii
Oscillospiraceae
Faecalibacterium
Barnesiella intestinihominis
[Clostridium] nexile
Phascolarctobacterium faecium
Muribaculaceae
Christensenellaceae_R-7_groupChristensenellaceae_R-7_group
Flavonifractor plautii
Agathobacter
Ruminococcaceae_UCG-002Ruminococcaceae_UCG-002
Family_XIII_AD3011_groupFamily_XIII_AD3011_group

Revision editor(s): KateRasheed, WikiWorks