Exploring the gut microbiota in patients with pre-diabetes and treatment naïve diabetes type 2 - a pilot study
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Gravdal K, Kirste KH, Grzelak K, Kirubakaran GT, Leissner P, Saliou A, Casèn C
Journal
BMC endocrine disorders
Year
2023
Keywords:
16S rRNA bacterial gene, Bacterial profiling, Microbiota signatures, Prediabetes, Type 2 diabetes
BACKGROUND: Compared to their healthy counterparts, patients with type 2 diabetes (T2D) can exhibit an altered gut microbiota composition, correlated with detrimental outcomes, including reduced insulin sensitivity, dyslipidemia, and increased markers of inflammation. However, a typical T2D microbiota profile is not established. The aim of this pilot study was to explore the gut microbiota and bacteria associated with prediabetes (pre-T2D) patients, and treatment naïve T2D patients, compared to healthy subjects. METHODS: Fecal samples were collected from patients and healthy subjects (from Norway). The bacterial genomic DNA was extracted, and the microbiota analyzed utilizing the bacterial 16S rRNA gene. To secure a broad coverage of potential T2D associated bacteria, two technologies were used: The GA-map® 131-plex, utilizing 131 DNA probes complementary to pre-selected bacterial targets (covering the 16S regions V3-V9), and the LUMI-Seq™ platform, a full-length 16S sequencing technology (V1-V9). Variations in the gut microbiota between groups were explored using multivariate methods, differential bacterial abundance was estimated, and microbiota signatures discriminating the groups were assessed using classification models. RESULTS: In total, 24 pre-T2D patients, 18 T2D patients, and 52 healthy subjects were recruited. From the LUMI-Seq™ analysis, 10 and 9 bacterial taxa were differentially abundant between pre-T2D and healthy, and T2D and healthy, respectively. From the GA-map® 131-plex analysis, 10 bacterial markers were differentially abundant when comparing pre-T2D and healthy. Several of the bacteria were short-chain fatty acid (SCFA) producers or typical opportunistic bacteria. Bacteria with similar function or associated properties also contributed to the separation of pre-T2D and T2D from healthy as found by classification models. However, limited overlap was found for specific bacterial genera and species. CONCLUSIONS: This pilot study revealed that differences in the abundance of SCFA producing bacteria, and an increase in typical opportunistic bacteria, may contribute to the variations in the microbiota separating the pre-T2D and T2D patients from healthy subjects. However, further efforts in investigating the relationship between gut microbiota, diabetes, and associated factors such as BMI, are needed for developing specific diabetes microbiota signatures.
Experiment 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-1-24
Curated date: 2023/10/05
Curator:
Revision editor(s):
Subjects
- Location of subjects
- Norway
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls - based on GA- map
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Pre-Type 2 Diabetes
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Pre-Type 2 Diabetes patients are Individuals that have blood glucose levels higher than normal but below the threshold for T2D, are often overweight, and have an elevated risk of T2D and cardiovascular disease.
- 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
- 22
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 4 weeks
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V9
- 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)
- 0.01
- 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, body mass index, sex, Confounders controlled for: "f-cal" 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.f-cal
Signature 1
Needs review
Source: Table 2
Description: Differentially abundant bacteria – pre-T2D vs. healthy, GA-map® 131-plex
Abundance in Group 1: increased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Dorea | ||
| Pseudomonadota | ||
| Enterobacterales | ||
| Escherichia/Shigella sp. |
Revision editor(s): Kadeniyi, Peace Sandy, WikiWorks
Signature 2
Needs review
Source: Table 2
Description: Differentially abundant bacteria – pre-T2D vs. healthy, GA-map® 131-plex
Abundance in Group 1: decreased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Roseburia | ||
| Roseburia intestinalis | ||
| Faecalibacterium prausnitzii | ||
| Dialister invisus | ||
| Veillonella | ||
| Sutterella wadsworthensis |
Revision editor(s): Kadeniyi, Peace Sandy, WikiWorks
Experiment 2
Reviewed Marked as Reviewed by Peace Sandy on 2024-1-24
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy Controls - based on LUMI -Seq data
- Group 0 sample size Number of subjects in the control (unexposed) group
- 48
Lab analysis
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V9
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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, sex, Confounders controlled for: "F-cal" 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.F-cal
Signature 1
Needs review
Source: Table 3
Description: Diferentially abundant bacteria — pre-T2D and T2D vs. healthy, LUMI-Seq™
Abundance in Group 1: increased abundance in Pre-Type 2 Diabetes
| NCBI | Quality Control | Links |
|---|---|---|
| Bacilli | ||
| Lactobacillales | ||
| Streptococcaceae | ||
| Streptococcus | ||
| Eisenbergiella | ||
| Eisenbergiella massiliensis | ||
| Neglectibacter | ||
| Neglectibacter timonensis |
Revision editor(s): Kadeniyi, Peace Sandy, WikiWorks
Signature 2
Needs review
Source: Table 3
Description: Diferentially abundant bacteria — pre-T2D and T2D vs. healthy, LUMI-Seq™
Abundance in Group 1: decreased abundance in Pre-Type 2 Diabetes
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillibacter valericigenes | ||
| Phocaeicola coprocola |
Revision editor(s): Kadeniyi, Peace Sandy, WikiWorks
Experiment 3
Reviewed Marked as Reviewed by Peace Sandy on 2024-1-24
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Type 2 Diabetes - T2D
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Type 2 diabetes (T2D)
- Group 1 sample size Number of subjects in the case (exposed) group
- 16
Lab analysis
Statistical Analysis
Signature 1
Needs review
Source: Table 3
Description: Diferentially abundant bacteria — pre-T2D and T2D vs. healthy, LUMI-Seq™
Abundance in Group 1: increased abundance in Type 2 Diabetes - T2D
| NCBI | Quality Control | Links |
|---|---|---|
| Dorea | ||
| Enterobacterales | ||
| Dorea formicigenerans | ||
| Dorea longicatena | ||
| Erysipelotrichia | ||
| Erysipelotrichaceae | ||
| Turicibacter | ||
| Turicibacter sanguinis |
Revision editor(s): Kadeniyi, Peace Sandy, WikiWorks
Signature 2
Needs review
Source: Table 3
Description: Diferentially abundant bacteria — pre-T2D and T2D vs. healthy, LUMI-Seq™
Abundance in Group 1: decreased abundance in Type 2 Diabetes - T2D
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerotignum |
Revision editor(s): Kadeniyi, Peace Sandy, WikiWorks
Experiment 4
Reviewed Marked as Reviewed by Peace Sandy on 2024-1-24
Curated date: 2024/01/24
Curator:
Revision editor(s):
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Pre- Type 2 Diabetes individuals
- 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
- Patients with Type 2 Diabetes
- Group 0 sample size Number of subjects in the control (unexposed) group
- 22
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, sex, Confounders controlled for: "f-cal" 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.f-cal
Signature 1
Needs review
Source: Table 3
Description: Diferentially abundant bacteria — pre-T2D and T2D vs. healthy, LUMI-Seq™
Abundance in Group 1: increased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Dorea | ||
| Dorea formicigenerans | ||
| Dorea longicatena | ||
| Erysipelotrichaceae | ||
| Erysipelotrichia | ||
| Turicibacter | ||
| Turicibacter sanguinis |
Revision editor(s): Peace Sandy, WikiWorks
Signature 2
Needs review
Source: Table 3
Description: Diferentially abundant bacteria — pre-T2D and T2D vs. healthy, LUMI-Seq™
Abundance in Group 1: decreased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Bacilli | ||
| Eisenbergiella | ||
| Eisenbergiella massiliensis | ||
| Lactobacillales | ||
| Neglectibacter | ||
| Neglectibacter timonensis | ||
| Streptococcaceae | ||
| Streptococcus |
Revision editor(s): Peace Sandy, WikiWorks
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