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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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
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
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 |
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Dioszegia | ||
Saccharomyces |
Revision editor(s): Madhubani Dey, Claregrieve1
Signature 2
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 |
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Mortierella | ||
Udeniomyces | ||
Xylodon |
Revision editor(s): Madhubani Dey, Claregrieve1
Experiment 2
Curated date: 2021/06/20
Curator: Madhubani Dey
Revision editor(s): Madhubani Dey, WikiWorks, Claregrieve1
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
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
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
Curated date: 2021/06/20
Curator: Madhubani Dey
Revision editor(s): Madhubani Dey, WikiWorks, Claregrieve1
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
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
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