Alterations in Intestinal Microbiota Correlate With Susceptibility to Type 1 Diabetes

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Reviewed Marked as Reviewed by Svetlana up on 2025-3-17

Curated date: 2025/02/24

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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: 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 I diabetes mellitus Autoimmune Diabete,Autoimmune Diabetes,Brittle Diabetes Mellitus,Diabete, Autoimmune,diabetes mellitis type 1,diabetes mellitis type I,DIABETES MELLITUS TYPE 01,Diabetes mellitus type 1,Diabetes mellitus type 1 (disorder),Diabetes mellitus type I,Diabetes mellitus type I [insulin dependent type] [IDDM] [juvenile type], not stated as uncontrolled, with unspecified complication,Diabetes mellitus type I [insulin dependent type] [IDDM] [juvenile type], uncontrolled, with unspecified complication,Diabetes Mellitus, Brittle,Diabetes Mellitus, Insulin Dependent,Diabetes Mellitus, Insulin-Dependent,Diabetes Mellitus, Juvenile Onset,Diabetes Mellitus, Juvenile-Onset,Diabetes Mellitus, Ketosis Prone,Diabetes Mellitus, Ketosis-Prone,Diabetes Mellitus, Sudden Onset,Diabetes Mellitus, Sudden-Onset,Diabetes Mellitus, Type 1,Diabetes Mellitus, Type I,Diabetes, Autoimmune,DMI UNSPF NT ST UNCNTRLD,DMI UNSPF UNCNTRLD,IDDM,IDDM - Insulin-dependent diabetes mellitus,immune mediated diabetes,Insulin Dependent Diabetes,insulin dependent diabetes,Insulin dependent diabetes mellitus,insulin dependent diabetes mellitus,Insulin-Dependent Diabetes Mellitus,insulin-dependent diabetes mellitus,Juvenile Diabetes,juvenile diabetes,Juvenile onset diabetes mellitus,Juvenile-Onset Diabetes Mellitus,Ketosis-Prone Diabetes Mellitus,Mellitus, Sudden-Onset Diabetes,Sudden-Onset Diabetes Mellitus,Type 1 Diabetes,type 1 diabetes,Type 1 Diabetes Mellitus,type 1 diabetes mellitus,Type I Diabetes,type I diabetes,type I diabetes mellitus,Type I diabetes mellitus

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Seropositive (Ab+) and Seronegative (Ab−)

Group 1 name Corresponds to the case (exposed) group for case-control studies: New onset type 1 diabetes (NO)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Participants with newly diagnosed type 1 diabetes (up to 6 months from disease diagnosis).

Group 0 sample size Number of subjects in the control (unexposed) group: 38

Group 1 sample size Number of subjects in the case (exposed) group: 34

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

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: Mann-Whitney (Wilcoxon)

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.1

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: age, sex, Confounders controlled for: "autoantibody presence" 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.autoantibody presence, Confounders controlled for: "Human leukocyte antigens (HLA) genotype" 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.Human leukocyte antigens (HLA) genotype

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-3-17

Curated date: 2025/02/24

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Table 2, Figure 2 and Supplementary Table 1

Description: Results from Wilcoxon rank-based tests after adjustment for covariates indicating the pairwise comparisons for the genera with a statistically significant difference across the groups.

Abundance in Group 1: decreased abundance in New onset type 1 diabetes (NO)

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Alistipes
Catenibacterium
Prevotellaceae
Succiniclasticum
Rikenellaceae RC9 gut groupRikenellaceae RC9 gut group

Revision editor(s): Aleru Divine

Experiment 2

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Reviewed Marked as Reviewed by Svetlana up on 2025-3-17

Curated date: 2025/02/24

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Autoantibody measurement Autoantibody measurement,autoantibody measurement

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

Group 1 name Corresponds to the case (exposed) group for case-control studies: Seropositive (Ab+) and Seronegative (Ab−)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Participants with and without autoantibodies.

Group 0 sample size Number of subjects in the control (unexposed) group: 16

Group 1 sample size Number of subjects in the case (exposed) group: 38

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-3-17

Curated date: 2025/02/24

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Table 2, Figure 2 and Supplementary Table 1

Description: Results from Wilcoxon rank-based tests after adjustment for covariates indicating the pairwise comparisons for the genera with a statistically significant difference across the groups.

Abundance in Group 1: increased abundance in Seropositive (Ab+) and Seronegative (Ab−)

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Catenibacterium
Prevotellaceae
Thalassospira
unclassified Bacteroidota
Rikenellaceae RC9 gut groupRikenellaceae RC9 gut group

Revision editor(s): Aleru Divine

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2025-3-17

Curated date: 2025/03/16

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Table 2, Figure 2 and Supplementary Table 1

Description: Results from Wilcoxon rank-based tests after adjustment for covariates indicating the pairwise comparisons for the genera with a statistically significant difference across the groups.

Abundance in Group 1: decreased abundance in Seropositive (Ab+) and Seronegative (Ab−)

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unclassified Bacteroidota
Lactobacillus
Staphylococcus

Revision editor(s): Aleru Divine

Experiment 3

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Reviewed Marked as Reviewed by Svetlana up on 2025-3-17

Curated date: 2025/02/24

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies: Seropositive (Ab+)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Participants with one to four autoantibodies.

Group 1 sample size Number of subjects in the case (exposed) group: 17

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-3-17

Curated date: 2025/02/24

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Table 2, Figure 2 and Supplementary Table 1

Description: Results from Wilcoxon rank-based tests after adjustment for covariates indicating the pairwise comparisons for the genera with a statistically significant difference across the groups.

Abundance in Group 1: increased abundance in Seropositive (Ab+)

NCBI	Quality Control	Links
Prevotellaceae
Rikenellaceae RC9 gut groupRikenellaceae RC9 gut group

Revision editor(s): Aleru Divine

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2025-3-17

Curated date: 2025/03/16

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Table 2, Figure 2 and Supplementary Table 1

Description: Results from Wilcoxon rank-based tests after adjustment for covariates indicating the pairwise comparisons for the genera with a statistically significant difference across the groups.

Abundance in Group 1: decreased abundance in Seropositive (Ab+)

NCBI	Quality Control	Links
Lactobacillus
Staphylococcus
unclassified Bacteroidota

Revision editor(s): Aleru Divine

Experiment 4

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Reviewed Marked as Reviewed by Svetlana up on 2025-3-17

Curated date: 2025/02/24

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: The seronegative group consists of first degree relatives (FDRs) of subjects with islet autoimmunity.

Group 1 sample size Number of subjects in the case (exposed) group: 21

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-3-17

Curated date: 2025/02/24

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Table 2, Figure 2 and Supplementary Table 1

Description: Results from Wilcoxon rank-based tests after adjustment for covariates indicating the pairwise comparisons for the genera with a statistically significant difference across the groups.

Abundance in Group 1: decreased abundance in Seronegative (Ab-)

NCBI	Quality Control	Links
Lactobacillus
Staphylococcus

Revision editor(s): Aleru Divine

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2025-3-17

Curated date: 2025/03/08

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Table 2, Figure 2 and Supplementary Table 1

Description: Results from Wilcoxon rank-based tests after adjustment for covariates indicating the pairwise comparisons for the genera with a statistically significant difference across the groups.

Abundance in Group 1: increased abundance in Seronegative (Ab-)

NCBI	Quality Control	Links
Thalassospira

Revision editor(s): Aleru Divine

Experiment 5

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2025-3-17

Curated date: 2025/02/24

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Type I diabetes mellitus Autoimmune Diabete,Autoimmune Diabetes,Brittle Diabetes Mellitus,Diabete, Autoimmune,diabetes mellitis type 1,diabetes mellitis type I,DIABETES MELLITUS TYPE 01,Diabetes mellitus type 1,Diabetes mellitus type 1 (disorder),Diabetes mellitus type I,Diabetes mellitus type I [insulin dependent type] [IDDM] [juvenile type], not stated as uncontrolled, with unspecified complication,Diabetes mellitus type I [insulin dependent type] [IDDM] [juvenile type], uncontrolled, with unspecified complication,Diabetes Mellitus, Brittle,Diabetes Mellitus, Insulin Dependent,Diabetes Mellitus, Insulin-Dependent,Diabetes Mellitus, Juvenile Onset,Diabetes Mellitus, Juvenile-Onset,Diabetes Mellitus, Ketosis Prone,Diabetes Mellitus, Ketosis-Prone,Diabetes Mellitus, Sudden Onset,Diabetes Mellitus, Sudden-Onset,Diabetes Mellitus, Type 1,Diabetes Mellitus, Type I,Diabetes, Autoimmune,DMI UNSPF NT ST UNCNTRLD,DMI UNSPF UNCNTRLD,IDDM,IDDM - Insulin-dependent diabetes mellitus,immune mediated diabetes,Insulin Dependent Diabetes,insulin dependent diabetes,Insulin dependent diabetes mellitus,insulin dependent diabetes mellitus,Insulin-Dependent Diabetes Mellitus,insulin-dependent diabetes mellitus,Juvenile Diabetes,juvenile diabetes,Juvenile onset diabetes mellitus,Juvenile-Onset Diabetes Mellitus,Ketosis-Prone Diabetes Mellitus,Mellitus, Sudden-Onset Diabetes,Sudden-Onset Diabetes Mellitus,Type 1 Diabetes,type 1 diabetes,Type 1 Diabetes Mellitus,type 1 diabetes mellitus,Type I Diabetes,type I diabetes,type I diabetes mellitus,Type I diabetes mellitus

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

Group 1 name Corresponds to the case (exposed) group for case-control studies: New onset type 1 diabetes (NO)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Participants with newly diagnosed type 1 diabetes (up to 6 months from disease diagnosis).

Group 0 sample size Number of subjects in the control (unexposed) group: 21

Group 1 sample size Number of subjects in the case (exposed) group: 34

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-3-17

Curated date: 2025/02/24

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Table 2, Figure 2 and Supplementary Table 1

Description: Results from Wilcoxon rank-based tests after adjustment for covariates indicating the pairwise comparisons for the genera with a statistically significant difference across the groups.

Abundance in Group 1: increased abundance in New onset type 1 diabetes (NO)

NCBI	Quality Control	Links
Lactobacillus
Succiniclasticum
Prevotellaceae

Revision editor(s): Aleru Divine

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2025-3-17

Curated date: 2025/03/08

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Table 2, Figure 2 and Supplementary Table 1

Description: Results from Wilcoxon rank-based tests after adjustment for covariates indicating the pairwise comparisons for the genera with a statistically significant difference across the groups.

Abundance in Group 1: decreased abundance in New onset type 1 diabetes (NO)

NCBI	Quality Control	Links
Alistipes

Revision editor(s): Aleru Divine

Experiment 6

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2025-3-17

Curated date: 2025/02/24

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

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

Group 0 sample size Number of subjects in the control (unexposed) group: 17

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-3-17

Curated date: 2025/02/24

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Table 2, Figure 2 and Supplementary Table 1

Description: Results from Wilcoxon rank-based tests after adjustment for covariates indicating the pairwise comparisons for the genera with a statistically significant difference across the groups.

Abundance in Group 1: increased abundance in New onset type 1 diabetes (NO)

NCBI	Quality Control	Links
Succiniclasticum

Revision editor(s): Aleru Divine

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2025-3-17

Curated date: 2025/03/08

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Table 2, Figure 2 and Supplementary Table 1

Description: Results from Wilcoxon rank-based tests after adjustment for covariates indicating the pairwise comparisons for the genera with a statistically significant difference across the groups.

Abundance in Group 1: decreased abundance in New onset type 1 diabetes (NO)

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Catenibacterium

Revision editor(s): Aleru Divine

Experiment 7

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2025-3-17

Curated date: 2025/02/24

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Autoantibody measurement Autoantibody measurement,autoantibody measurement

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

Group 1 name Corresponds to the case (exposed) group for case-control studies: Seropositive (Ab+)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Participants with one to four autoantibodies.

Group 0 sample size Number of subjects in the control (unexposed) group: 21

Group 1 sample size Number of subjects in the case (exposed) group: 17

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-3-17

Curated date: 2025/02/24

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Table 2, Figure 2 and Supplementary Table 1

Description: Results from Wilcoxon rank-based tests after adjustment for covariates indicating the pairwise comparisons for the genera with a statistically significant difference across the groups.

Abundance in Group 1: increased abundance in Seropositive (Ab+)

NCBI	Quality Control	Links
Catenibacterium
Prevotellaceae
Rikenellaceae RC9 gut groupRikenellaceae RC9 gut group

Revision editor(s): Aleru Divine

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2025-3-17

Curated date: 2025/03/16

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Table 2, Figure 2 and Supplementary Table 1

Description: Results from Wilcoxon rank-based tests after adjustment for covariates indicating the pairwise comparisons for the genera with a statistically significant difference across the groups.

Abundance in Group 1: decreased abundance in Seropositive (Ab+)

NCBI	Quality Control	Links
unclassified Bacteroidota

Revision editor(s): Aleru Divine

Experiment 8

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2025-3-17

Curated date: 2025/02/24

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Type I diabetes mellitus Autoimmune Diabete,Autoimmune Diabetes,Brittle Diabetes Mellitus,Diabete, Autoimmune,diabetes mellitis type 1,diabetes mellitis type I,DIABETES MELLITUS TYPE 01,Diabetes mellitus type 1,Diabetes mellitus type 1 (disorder),Diabetes mellitus type I,Diabetes mellitus type I [insulin dependent type] [IDDM] [juvenile type], not stated as uncontrolled, with unspecified complication,Diabetes mellitus type I [insulin dependent type] [IDDM] [juvenile type], uncontrolled, with unspecified complication,Diabetes Mellitus, Brittle,Diabetes Mellitus, Insulin Dependent,Diabetes Mellitus, Insulin-Dependent,Diabetes Mellitus, Juvenile Onset,Diabetes Mellitus, Juvenile-Onset,Diabetes Mellitus, Ketosis Prone,Diabetes Mellitus, Ketosis-Prone,Diabetes Mellitus, Sudden Onset,Diabetes Mellitus, Sudden-Onset,Diabetes Mellitus, Type 1,Diabetes Mellitus, Type I,Diabetes, Autoimmune,DMI UNSPF NT ST UNCNTRLD,DMI UNSPF UNCNTRLD,IDDM,IDDM - Insulin-dependent diabetes mellitus,immune mediated diabetes,Insulin Dependent Diabetes,insulin dependent diabetes,Insulin dependent diabetes mellitus,insulin dependent diabetes mellitus,Insulin-Dependent Diabetes Mellitus,insulin-dependent diabetes mellitus,Juvenile Diabetes,juvenile diabetes,Juvenile onset diabetes mellitus,Juvenile-Onset Diabetes Mellitus,Ketosis-Prone Diabetes Mellitus,Mellitus, Sudden-Onset Diabetes,Sudden-Onset Diabetes Mellitus,Type 1 Diabetes,type 1 diabetes,Type 1 Diabetes Mellitus,type 1 diabetes mellitus,Type I Diabetes,type I diabetes,type I diabetes mellitus,Type I diabetes mellitus

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

Group 1 name Corresponds to the case (exposed) group for case-control studies: New onset type 1 diabetes (NO)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Participants with newly diagnosed type 1 diabetes (up to 6 months from disease diagnosis).

Group 0 sample size Number of subjects in the control (unexposed) group: 16

Group 1 sample size Number of subjects in the case (exposed) group: 34

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-3-17

Curated date: 2025/02/24

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Table 2, Figure 2 and Supplementary Table 1

Description: Results from Wilcoxon rank-based tests after adjustment for covariates indicating the pairwise comparisons for the genera with a statistically significant difference across the groups.

Abundance in Group 1: increased abundance in New onset type 1 diabetes (NO)

NCBI	Quality Control	Links
Thalassospira

Revision editor(s): Aleru Divine

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2025-3-17

Curated date: 2025/03/08

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Table 2, Figure 2 and Supplementary Table 1

Description: Results from Wilcoxon rank-based tests after adjustment for covariates indicating the pairwise comparisons for the genera with a statistically significant difference across the groups.

Abundance in Group 1: decreased abundance in New onset type 1 diabetes (NO)

NCBI	Quality Control	Links
Alistipes
Lactobacillus
Staphylococcus
Succiniclasticum
unclassified Bacteroidota

Revision editor(s): Aleru Divine

Experiment 9