Analysis of the Gut Mycobiome in Adult Patients with Type 1 and Type 2 Diabetes Using Next-Generation Sequencing (NGS) with Increased Sensitivity-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.
Authors
Salamon D, Sroka-Oleksiak A, Gurgul A, Arent Z, Szopa M, Bulanda M, Małecki MT, Gosiewski T
Journal
Nutrients
Year
2021
Keywords:
diabetes, gut mycobiome, next-generation sequencing (NGS)
The studies on microbiome in the human digestive tract indicate that fungi could also be one of the external factors affecting development of diabetes. The aim of this study was to evaluate the quantitative and qualitative mycobiome composition in the colon of the adults with type 1 (T1D), n = 26 and type 2 (T2D) diabetes, n = 24 compared to the control group, n = 26. The gut mycobiome was characterized in the stool samples using the analysis of the whole internal transcribed spacer (ITS) region of the fungal rDNA gene cluster by next-generation sequencing (NGS) with increased sensitivity. At the L2 (phylum) level, Basidiomycota fungi were predominant in all 3 study groups. Group T1D presented significantly lower number of Ascomycota compared to the T2D group, and at the L6 (genus) level, the T1D group presented significantly lower number of Saccharomyces genus compared to control and T2D groups. In the T1D group, a significant positive correlation between total cholesterol and low-density lipoprotein cholesterol (LDL-C) levels and fungi of the genus Saccharomyces, and in the T2D group, a negative correlation between the total cholesterol level and Malassezia genus was found. The obtained results seem to be a good foundation to extend the analysis of the relationship between individual genera and species of fungi and the parameters determining the metabolism of carbohydrates and lipids in the human body.
Experiment 1
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-24
Curated date: 2021/06/20
Curator: Madhubani Dey
Revision editor(s): Madhubani Dey, WikiWorks, Claregrieve1
Subjects
- Location of subjects
- Poland
- 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
- Healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Individuals diagnosed with Type 1 Diabetes Mellitus
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individuals diagnosed with Type 1 Diabetes Mellitus in 2012–2015 at the Department of Metabolic Diseases, University Hospital, Krakow, Poland
- Group 0 sample size Number of subjects in the control (unexposed) group
- 26
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 30 days
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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
- PERMANOVA
- 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
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-24
Source: Table 4
Description: Differential abundance of fungal genus in individuals diagnosed with Type 1 Diabetes compared to healthy controls
Abundance in Group 1: decreased abundance in Individuals diagnosed with Type 1 Diabetes Mellitus
| NCBI | Quality Control | Links |
|---|---|---|
| Dioszegia | ||
| Saccharomyces |
Revision editor(s): Madhubani Dey, Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-24
Source: Table 4
Description: Differential abundance of fungal genus in individuals diagnosed with Type 1 Diabetes compared to healthy controls
Abundance in Group 1: increased abundance in Individuals diagnosed with Type 1 Diabetes Mellitus
| NCBI | Quality Control | Links |
|---|---|---|
| Mortierella | ||
| Udeniomyces | ||
| Xylodon |
Revision editor(s): Madhubani Dey, Claregrieve1
Experiment 2
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-24
Curated date: 2021/06/20
Curator: Madhubani Dey
Revision editor(s): Madhubani Dey, WikiWorks, Claregrieve1
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,Type II diabetes mellitus
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Individuals diagnosed with Type 2 Diabetes Mellitus
- Group 1 sample size Number of subjects in the case (exposed) group
- 26
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-24
Source: Table 4
Description: Differential abundance of the fungal genus in individuals diagnosed with Type 2 Diabetes compared to the healthy controls
Abundance in Group 1: decreased abundance in Individuals diagnosed with Type 2 Diabetes Mellitus
| NCBI | Quality Control | Links |
|---|---|---|
| Bullera | ||
| Ganoderma | ||
| Naganishia | ||
| Saitoella | ||
| Wallemia |
Revision editor(s): Madhubani Dey, Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-24
Source: Table 4
Description: Differential abundance of the fungal genus in individuals diagnosed 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 |
|---|---|---|
| Tilletiopsis | ||
| Udeniomyces | ||
| Vishniacozyma |
Revision editor(s): Madhubani Dey, Claregrieve1
Experiment 3
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-24
Curated date: 2021/06/20
Curator: Madhubani Dey
Revision editor(s): Madhubani Dey, WikiWorks, Claregrieve1
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Diabetes mellitus Diabetes,diabetes,diabetes mellitus,diabetes mellitus (disease),Diabetes mellitus (disorder),Diabetes mellitus, NOS,Diabetes NOS,DM,DM - Diabetes mellitus,Diabetes mellitus
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Individuals diagnosed with Type 1 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 in 2012–2015 at the Department of Metabolic Diseases, University Hospital, Krakow, Poland
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-24
Source: Table 4
Description: Differential abundance in the fungal communities in Type 2 Diabetes patients compared to Type 1 Diabetes patients
Abundance in Group 1: decreased abundance in Individuals diagnosed with Type 2 Diabetes Mellitus
| NCBI | Quality Control | Links |
|---|---|---|
| Bullera | ||
| Ganoderma | ||
| Naganishia | ||
| Udeniomyces |
Revision editor(s): Madhubani Dey, Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-24
Source: Table 4 and Figure 6
Description: Differential abundance in the fungal communities in Type 2 Diabetes patients compared to Type 1 Diabetes patients
Abundance in Group 1: increased abundance in Individuals diagnosed with Type 2 Diabetes Mellitus
| NCBI | Quality Control | Links |
|---|---|---|
| Ascomycota | ||
| Saccharomyces | ||
| Tilletiopsis |
Revision editor(s): Madhubani Dey, Claregrieve1
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