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/Experiment 1
From BugSigDB
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
