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

From BugSigDB
Needs review
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Alvarez-Silva C, Kashani A, Hansen TH, Pinna NK, Anjana RM, Dutta A, Saxena S, Støy J, Kampmann U, Nielsen T, Jørgensen T, Gnanaprakash V, Gnanavadivel R, Sukumaran A, Rani CSS, Færch K, Radha V, Balasubramanyam M, Nair GB, Das B, Vestergaard H, Hansen T, Mande SS, Mohan V, Arumugam M, Pedersen O
Journal
Genome medicine
Year
2021
Keywords:
Danes, Gut microbiota, Indians, Metformin, Populations, Trans-ethnic, Type 2 diabetes
BACKGROUND: Type 2 diabetes (T2D), a multifactorial disease influenced by host genetics and environmental factors, is the most common endocrine disease. Several studies have shown that the gut microbiota as a close-up environmental mediator influences host physiology including metabolism. The aim of the present study is to examine the compositional and functional potential of the gut microbiota across individuals from Denmark and South India with a focus on T2D. Many earlier studies have investigated the microbiome aspects of T2D, and it has also been anticipated that such microbial associations would be dependent on diet and ethnic origin. However, there has been no large scale trans-ethnic microbiome study earlier in this direction aimed at evaluating any "universal" microbiome signature of T2D. METHODS: 16S ribosomal RNA gene amplicon sequencing was performed on stool samples from 279 Danish and 294 Indian study participants. Any differences between the gut microbiota of both populations were explored using diversity measures and negative binomial Wald tests. Study samples were stratified to discover global and country-specific microbial signatures for T2D and treatment with the anti-hyperglycemic drug, metformin. To identify taxonomical and functional signatures of the gut microbiota for T2D and metformin treatment, we used alpha and beta diversity measures and differential abundances analysis, comparing metformin-naive T2D patients, metformin-treated T2D patients, and normoglycemic individuals. RESULTS: Overall, the gut microbial communities of Danes and Indians are compositionally very different. By analyzing the combined study materials, we identify microbial taxonomic and functional signatures for T2D and metformin treatment. T2D patients have an increased relative abundance of two operational taxonomic units (OTUs) from the Lachnospiraceae family, and a decreased abundance of Subdoligranulum and Butyricicoccus. Studying each population per se, we identified T2D-related microbial changes at the taxonomic level within the Danish population only. Alpha diversity indices show that there is no significant difference between normoglycemic individuals and metformin-naive T2D patients, whereas microbial richness is significantly decreased in metformin-treated T2D patients compared to metformin-naive T2D patients and normoglycemic individuals. Enrichment of two OTUs from Bacteroides and depletion of Faecalibacterium constitute a trans-ethnic signature of metformin treatment. CONCLUSIONS: We demonstrate major compositional differences of the gut microbiota between Danish and South Indian individuals, some of which may relate to differences in ethnicity, lifestyle, and demography. By comparing metformin-naive T2D patients and normoglycemic individuals, we identify T2D-related microbiota changes in the Danish and Indian study samples. In the present trans-ethnic study, we confirm that metformin changes the taxonomic profile and functional potential of the gut microbiota.

Experiment 1


Needs review

Curated date: 2023/11/05

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Subjects

Location of subjects
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
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
response to metformin response to metformin
Group 0 name Corresponds to the control (unexposed) group for case-control studies
metformin-naive type 2 diabetes (T2D) patients
Group 1 name Corresponds to the case (exposed) group for case-control studies
metformin-treated T2D patients
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
T2D patients treated with the anti-hyperglycemic drug, metformin
Group 0 sample size Number of subjects in the control (unexposed) group
71
Group 1 sample size Number of subjects in the case (exposed) group
86
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
None

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
Confounders controlled for: "sulfonyl urea" 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.sulfonyl urea, Confounders controlled for: "proton pump inhibitors" 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.proton pump inhibitors, Confounders controlled for: "statin" 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.statin, body mass index, age, Confounders controlled for: "gender" 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.gender

Alpha Diversity

Richness Number of species
decreased

Signature 1

Needs review

Curated date: 2023/11/06

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Source: Supplemental Table S11

Description: Differential abundant taxa between metformin-naive T2D and metformin-treated T2D in the Indian substudy

Abundance in Group 1: decreased abundance in metformin-treated T2D patients

NCBI Quality ControlLinks
Lachnoclostridium

Revision editor(s): ChiomaBlessing

Experiment 2


Needs review

Curated date: 2023/11/05

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Differences from previous experiment shown

Subjects

Location of subjects
Denmark


Group 0 sample size Number of subjects in the control (unexposed) group
61
Group 1 sample size Number of subjects in the case (exposed) group
80
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

Statistical Analysis

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
age, body mass index, Confounders controlled for: "sulfonyl urea" 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.sulfonyl urea, Confounders controlled for: "proton pump inhibitors" 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.proton pump inhibitors, Confounders controlled for: "statin" 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.statin, Confounders controlled for: "gender" 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.gender

Alpha Diversity

Richness Number of species
decreased

Signature 1

Needs review

Curated date: 2023/11/06

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Source: Supplemental Table S10b

Description: Differential abundant taxa between metformin-naive T2D and metformin-treated T2D in the Danish substudy

Abundance in Group 1: decreased abundance in metformin-treated T2D patients

NCBI Quality ControlLinks
Escherichia/Shigella sp.

Revision editor(s): ChiomaBlessing

Experiment 3


Needs review

Curated date: 2023/11/05

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Differences from previous experiment shown

Subjects

Location of subjects
Denmark
India


Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
population population
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Indians (normoglycaemic controls and T2D patients)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Denmark (normoglycaemic controls and T2D patients)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Gut microbiota in Denmark participants
Group 0 sample size Number of subjects in the control (unexposed) group
294
Group 1 sample size Number of subjects in the case (exposed) group
279
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

Statistical Analysis

Signature 1

Needs review

Curated date: 2023/11/06

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Source: Supplemental Table S2b

Description: Differentially abundant taxa in the gut microbiome between Danes and Indians (normoglycaemic controls and T2D patients)

Abundance in Group 1: increased abundance in Denmark (normoglycaemic controls and T2D patients)

NCBI Quality ControlLinks
Adlercreutzia
Akkermansia
Alistipes
Anaerofilum
Anaerotruncus
Angelakisella
Bacteroides
Barnesiella
Bilophila
Bradyrhizobium
Butyricimonas
Christensenella
Coprobacter
Desulfovibrio
Eisenbergiella
Faecalibacterium
Flavonifractor
Holdemania
Hungatella
Lachnoclostridium
Lachnospira
Lachnospiraceae bacterium NK4A136
Merdibacter
Merdimmobilis
Negativibacillus
Odoribacter
Oscillibacter
Oscillospira
Oxalobacter
Parabacteroides
Paraprevotella
Parasutterella
Peptococcus
Phascolarctobacterium
Pseudoflavonifractor
Rhodococcus
Ruminiclostridium
Ruminiclostridium sp.
Sanguibacteroides
Subdoligranulum
Sutterella
uncultured Erysipelotrichaceae bacterium
uncultured Lachnospiraceae bacterium
uncultured Oscillospiraceae bacterium
DTU089DTU089
Ruminococcaceae_NK4A214Ruminococcaceae_NK4A214
UBA1819UBA1819
Christensenellaceae_R7Christensenellaceae_R7
GCA-900066225GCA-900066225
Ruminococcus sp.

Revision editor(s): ChiomaBlessing

Signature 2

Needs review

Curated date: 2023/11/06

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Source: Supplemental Table S2b

Description: Differentially abundant taxa in the gut microbiome between Danes and Indians (normoglycaemic controls and T2D patients)

Abundance in Group 1: decreased abundance in Denmark (normoglycaemic controls and T2D patients)

NCBI Quality ControlLinks
Achromobacter
Actinomyces
Agathobacter
Alloprevotella
Anaeroglobus
Anaerostipes
Bifidobacterium
Catenibacterium
Collinsella
Dorea
Fusicatenibacter
Granulicatella
Holdemanella
Howardella
Kerstersia
Lactobacillus
Marvinbryantia
Megasphaera
Mitsuokella
Olsenella
Oribacterium
Paraburkholderia caballeronis
Parolsenella
Romboutsia
Roseburia intestinalis
Senegalimassilia
Serratia
Solobacterium
Terrisporobacter
Weissella
uncultured Oscillospiraceae bacterium
Lachnospiraceae_FCS020_groupLachnospiraceae_FCS020_group
CHKCI002CHKCI002
Prevotella sp.
Coprococcus sp.

Revision editor(s): ChiomaBlessing

Experiment 4


Needs review

Curated date: 2023/11/05

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
metformin 1,1-Dimethylbiguanide,C4H11N5,CN(C)C(=N)NC(N)=N,InChI=1/C4H11N5/c1-9(2)4(7)8-3(5)6/h1-2H3,(H5,5,6,7,8)/f/h5,7-8H,6H2,InChIKey=XZWYZXLIPXDOLR-WXQAPKLBCT,Metformin,N,N-dimethylimidodicarbonimidic diamide,metformin
Group 0 name Corresponds to the control (unexposed) group for case-control studies
metformin-naive type 2 diabetes (T2D) patients
Group 1 name Corresponds to the case (exposed) group for case-control studies
metformin-treated T2D patients
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
T2D patients treated with the anti-hyperglycemic drug, metformin
Group 0 sample size Number of subjects in the control (unexposed) group
132
Group 1 sample size Number of subjects in the case (exposed) group
166

Lab analysis

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
Statistical test
Negative Binomial Regression
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
age, body mass index, Confounders controlled for: "sulfonyl urea" 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.sulfonyl urea, Confounders controlled for: "proton pump inhibitors" 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.proton pump inhibitors, Confounders controlled for: "statin" 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.statin, Confounders controlled for: "gender" 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.gender, Confounders controlled for: "country" 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.country

Alpha Diversity

Richness Number of species
decreased

Signature 1

Needs review

Curated date: 2023/11/06

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Source: Supplemental Table S9

Description: Differential abundant taxa between metformin-naive T2D and metformin-treated T2D in the combined Danish-Indian group

Abundance in Group 1: increased abundance in metformin-treated T2D patients

NCBI Quality ControlLinks
Faecalibacterium

Revision editor(s): ChiomaBlessing

Signature 2

Needs review

Curated date: 2023/11/06

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Source: Supplemental. TableS9

Description: Differential abundant taxa between metformin-naive T2D and metformin-treated T2D in the combined Danish-Indian group

Abundance in Group 1: decreased abundance in metformin-treated T2D patients

NCBI Quality ControlLinks
Bacteroides sp.

Revision editor(s): ChiomaBlessing

Experiment 5


Needs review

Curated date: 2023/11/05

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Differences from previous experiment shown

Subjects

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
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

Lab analysis

Statistical Analysis

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
Confounders controlled for: "country" 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.country

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2023/11/08

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

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: increased abundance in Type 2 diabetes (T2D) patients

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

Revision editor(s): ChiomaBlessing

Signature 2

Needs review

Curated date: 2023/11/08

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

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: decreased abundance in Type 2 diabetes (T2D) patients

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

Revision editor(s): ChiomaBlessing

Experiment 6


Needs review

Curated date: 2023/11/05

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Differences from previous experiment shown

Subjects

Lab analysis

Statistical Analysis

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
age, body mass index, Confounders controlled for: "country" 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.country, Confounders controlled for: "metformin" 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.metformin, Confounders controlled for: "sulfonyl urea" 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.sulfonyl urea, Confounders controlled for: "proton pump inhibitors" 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.proton pump inhibitors, Confounders controlled for: "statin" 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.statin, Confounders controlled for: "gender" 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.gender

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2023/11/08

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Source: Supplemental. Table S4A and 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 ControlLinks
Subdoligranulum
Butyricicoccus
Anaerosporobacter

Revision editor(s): ChiomaBlessing

Signature 2

Needs review

Curated date: 2023/11/08

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Source: Supplemental. Table S4A and B

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 ControlLinks
Lachnoclostridium
Firmicutes bacterium CAG:56

Revision editor(s): ChiomaBlessing

Experiment 7


Needs review

Curated date: 2023/11/05

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Differences from previous experiment shown

Subjects

Location of subjects
Denmark


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

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
raw counts
Statistical test
DESeq2
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
age, body mass index, Confounders controlled for: "metformin" 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.metformin, Confounders controlled for: "sulfonyl urea" 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.sulfonyl urea, Confounders controlled for: "proton pump inhibitors" 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.proton pump inhibitors, Confounders controlled for: "statin" 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.statin, Confounders controlled for: "gender" 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.gender

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2023/11/08

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Source: Supplemental Table S6A

Description: Differentially abundant taxa between type 2 diabetes (T2D) VS normoglycemic controls (NG) in the Danish substudy

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

NCBI Quality ControlLinks
Lachnoclostridium

Revision editor(s): ChiomaBlessing