Characteristics of the gut microbiome in patients with prediabetes and type 2 diabetes
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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.
Authors
Zhang Z, Tian T, Chen Z, Liu L, Luo T, Dai J
Journal
PeerJ
Year
2021
Keywords:
Gut microbiome, Prediabetes, Type 2 diabetes mellitus
Background: Gut microbiome has recently been identified as a new potential risk factor in addition to well-known diabetes risk factors. The aim of this study was to analyze the differences in the composition of gut microbiome in prediabetes(PreDM), type 2 diabetes mellitus (T2DM) and non-diabetic controls. Methods: A total of 180 participants were recruited for this study: 60 with T2DM, 60 with PreDM and 60 non-diabetics (control group). Fecal samples were collected from the participants and genomic DNA was extracted. The composition and diversity of gut microbiome were investigated in fecal DNA samples using Illumina sequencing of the V3∼V4 regions of 16sRNA. Results: There were significant differences in the number of bacteria among patients with PreDM and T2DM and the control group. Compared with the control group, Proteobacteria bacteria were significantly higher in the PreDM group (P = 0.006). On the genus level, Compared with the control group, the relative abundance of Prevotella and Alloprevotella was significantly higher in the T2DM group (P = 0.016, P = 0.018), and the relative abundance of Paraprevotella in T2DM and PreDM groups was lower than that in the control group (P = 0.011, P = 0.045). Compared with the PreDM group and the control group, the relative abundance of Bacteroides in the T2DM group was significantly lower (P = 0.019, P = 0.002). Conclusions: The present study found significant differences in the gut microbiome between PreDM, T2DM and non-diabetic individuals, specifically at the genus level, suggesting that early intervention in PreDM patients could have implications for gut flora transitioning to T2DM. In addition, these results may be valuable for developing strategies to control T2DM by modifying the gut microbiome.
Experiment 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/22
Curated date: 2021/07/05
Curator: Madhubani Dey
Revision editor(s): Madhubani Dey, Claregrieve1, WikiWorks, Peace Sandy
Subjects
- Location of subjects
- China
- 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
- Healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Individuals diagnosed with Type 2 Diabetes Mellitus
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individuals diagnosed with Type 2 Diabetes Mellitus; Participants with T2DM were required to meet the following inclusion criteria: (i) fasting blood glucose test (FBG) ≥7 mmol/L and/or 2-h fasting oral glucose tolerance test (OGTT) ≥11.1 mmol/L; and (ii) all cases of T2DM were newly diagnosed.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 60
- Group 1 sample size Number of subjects in the case (exposed) group
- 60
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4-V5
- 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
- Kruskall-Wallis
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/22
Source: Table 3
Description: Differential microbial abundance in individuals with type 2 diabetes compared to healthy controls
Abundance in Group 1: increased abundance in Individuals diagnosed with Type 2 Diabetes Mellitus
| NCBI | Quality Control | Links |
|---|---|---|
| Alloprevotella | ||
| Megasphaera | ||
| Negativicutes | ||
| Prevotella |
Revision editor(s): Madhubani Dey, Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/22
Source: Table 3
Description: Differential microbial abundance in individuals with type 2 diabetes compared to healthy controls
Abundance in Group 1: decreased abundance in Individuals diagnosed with Type 2 Diabetes Mellitus
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Paraprevotella |
Revision editor(s): Madhubani Dey, Claregrieve1
Experiment 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/22
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Prediabetes syndrome borderline diabetes,Prediabetes,prediabetes,prediabetes syndrome,Prediabetic State,prediabetic state,Prediabetes syndrome
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Individuals with Prediabetes (PreDM)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individuals with Prediabetes (PreDM); PreDM was defined as FBG of 6.1–7.0 mmol/L or HbA1c levels of 6.0%–6.5%.
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/22
Source: Table 3
Description: Differential microbial abundance in individuals with prediabetes compared to healthy controls
Abundance in Group 1: increased abundance in Individuals with Prediabetes (PreDM)
| NCBI | Quality Control | Links |
|---|---|---|
| Megasphaera | ||
| Pseudomonadota | ||
| Haemophilus |
Revision editor(s): Madhubani Dey, Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/22
Source: Table 3
Description: Differential microbial abundance in individuals with prediabetes compared to healthy controls
Abundance in Group 1: decreased abundance in Individuals with Prediabetes (PreDM)
| NCBI | Quality Control | Links |
|---|---|---|
| Helicobacter |
Revision editor(s): Claregrieve1
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