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

From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-24
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

Curated date: 2021/06/20

Curator: Madhubani Dey

Revision editor(s): Madhubani Dey, Claregrieve1

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 ControlLinks
Dioszegia
Saccharomyces

Revision editor(s): Madhubani Dey, Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-24

Curated date: 2021/06/20

Curator: Madhubani Dey

Revision editor(s): Madhubani Dey, Claregrieve1

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 ControlLinks
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

Curated date: 2021/06/20

Curator: Madhubani Dey

Revision editor(s): Madhubani Dey, Claregrieve1

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 ControlLinks
Bullera
Ganoderma
Naganishia
Saitoella
Wallemia

Revision editor(s): Madhubani Dey, Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-24

Curated date: 2021/06/20

Curator: Madhubani Dey

Revision editor(s): Madhubani Dey, Claregrieve1

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 ControlLinks
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

Curated date: 2021/06/20

Curator: Madhubani Dey

Revision editor(s): Madhubani Dey, Claregrieve1

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 ControlLinks
Bullera
Ganoderma
Naganishia
Udeniomyces

Revision editor(s): Madhubani Dey, Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-24

Curated date: 2021/06/20

Curator: Madhubani Dey

Revision editor(s): Madhubani Dey, Claregrieve1

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 ControlLinks
Ascomycota
Saccharomyces
Tilletiopsis

Revision editor(s): Madhubani Dey, Claregrieve1