Preliminary characterization of gut mycobiome enterotypes reveals the correlation trends between host metabolic parameter and diet: a case study in the Thai Cohort

Study information

EditHistoryDelete

Mark reviewed

Your review change was submittedAdd a new Experiment

• Quality control
  • Retracted paper
  • Contamination issues suspected
  • Batch effect issues suspected
  • Uncontrolled confounding suspected
  • Results are suspect (various reasons)
  • Apply tags

    Tags applied

Needs review

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

38461361

DOI Digital object identifier for electronic documents.

10.1038/s41598-024-56585-2

URI Uniform resource identifier for web resources.

Authors

Mok K, Poolsawat T, Somnuk S, Wanikorn B, Patumcharoenpol P, Nitisinprasert S, Vongsangnak W, Nakphaichit M

Journal

Scientific reports

Year

2024

The association between the gut mycobiome and its potential influence on host metabolism in the Thai Cohort was assessed. Two distinct predominant enterotypes, Saccharomyces (Sa) and Aspergillus/Penicillium (Ap/Pe) showed differences in gut mycobiota diversity and composition. Notably, the Sa enterotype exhibited lower evenness and richness, likely due to the prevalence of Saccharomyces, while both enterotypes displayed unique metabolic behaviors related to nutrient metabolism and body composition. Fiber consumption was positively correlated with adverse body composition and fasting glucose levels in individuals with the Sa enterotype, whereas in the Ap/Pe enterotype it was positively correlated with fat and protein intake. The metabolic functional analysis revealed the Sa enterotype associated with carbohydrate metabolism, while the Ap/Pe enterotype involved in lipid metabolism. Very interestingly, the genes involved in the pentose and glucuronate interconversion pathway, such as polygalacturonase and L-arabinose-isomerase, were enriched in the Sa enterotype signifying a metabolic capacity for complex carbohydrate degradation and utilization of less common sugars as energy sources. These findings highlight the interplay between gut mycobiome composition, dietary habits, and metabolic outcomes within the Thai cohort studies.

Experiment 1

EditHistoryDelete

Mark reviewed

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Needs review

Curated date: 2025/07/18

Curator: Ese

Revision editor(s): Ese

Subjects

Location of subjects

Thailand

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

Gut microbiome measurement Gut microbiome measurement,gut microbiome measurement

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Saccharomyces enterotype (enterotype SA)

Group 1 name Corresponds to the case (exposed) group for case-control studies

Aspergillus/Penicillium enterotype (enterotype AP/Pe)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Individuals whose gut mycobiome composition was dominated by Aspergillus and Penicillium genera, identified through hierarchical clustering of ITS2 fungal profiles.

Group 0 sample size Number of subjects in the control (unexposed) group

111

Group 1 sample size Number of subjects in the case (exposed) group

191

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)

3 months

Lab analysis

Sequencing type

ITS / ITS2

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

LEfSe

Significance threshold p-value or FDR threshold used for differential abundance testing (if any)

0.05

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool

2

Matched on Factors on which subjects have been matched on in a case-control study

age, Matched on: "BMI" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.BMI

Alpha Diversity

Pielou Quantifies how equal the community is numerically

increased

Shannon Estimator of species richness and species evenness: more weight on species richness

increased

Chao1 Abundance-based estimator of species richness

decreased

Signature 1

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2025/07/21

Curator: Ese

Revision editor(s): Ese

Source: Figure 1b

Description: Lesfe analysis showing specific taxa significantly abundant between Saccharomyces enterotype (enterotype SA) and Aspergillus/Penicillium enterotype (enterotype AP/Pe)

Abundance in Group 1: increased abundance in Aspergillus/Penicillium enterotype (enterotype AP/Pe)

NCBI	Quality Control	Links
Agaricomycetes
Aspergillus
Basidiomycota
Cystobasidiomycetes
Dothideomycetes
Eurotiomycetes
Penicillium
Sordariomycetes
Tremellomycetes
Ustilaginomycetes

Revision editor(s): Ese

Signature 2

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2025/07/22

Curator: Ese

Revision editor(s): Ese

Source: Figure 1b

Description: Lesfe analysis showing specific taxa significantly abundant between Saccharomyces enterotype (enterotype SA) and Aspergillus/Penicillium enterotype (enterotype AP/Pe)

Abundance in Group 1: decreased abundance in Aspergillus/Penicillium enterotype (enterotype AP/Pe)

NCBI	Quality Control	Links
Saccharomyces
Saccharomycetes

Revision editor(s): Ese

Experiment 2

EditHistoryDelete

Mark reviewed

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Needs review

Curated date: 2025/07/23

Curator: Ese

Revision editor(s): Ese

Differences from previous experiment shown

Subjects

Lab analysis

Statistical Analysis

Matched on Factors on which subjects have been matched on in a case-control study

age, Matched on: "bmi" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.bmi

Alpha Diversity

Pielou Quantifies how equal the community is numerically

increased

Shannon Estimator of species richness and species evenness: more weight on species richness

increased

Chao1 Abundance-based estimator of species richness

decreased

Signature 1

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2025/07/23

Curator: Ese

Revision editor(s): Ese

Source: Table S1, S2 and S3

Description: Relative abundances of gut mycobiota at the phylum, class and genus level between Saccharomyces enterotype (enterotype SA) and Aspergillus/Penicillium enterotype (enterotype AP/Pe)

Abundance in Group 1: increased abundance in Aspergillus/Penicillium enterotype (enterotype AP/Pe)

NCBI	Quality Control	Links
Acremonium
Agaricomycetes
Aspergillus
Basidiomycota
Cladosporium
Cystobasidiomycetes
Cystobasidium
Dothideomycetes
Eurotiomycetes
Hypsizygus
Malasseziomycetes
Papiliotrema
Penicillium
Phaeosphaeria
Sordariomycetes
Tremellomycetes
Ustilaginomycetes
Wallemia
Wallemiomycetes

Revision editor(s): Ese

Signature 2

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2025/07/24

Curator: Ese

Revision editor(s): Ese

Source: Table S1, S2 and S3

Description: Relative abundances of gut mycobiota at the phylum, class and genus level between enterotype SA (Saccharomyces enterotype) and enterotype AP/Pe (Aspergillus/Penicillium enterotype)

Abundance in Group 1: decreased abundance in Aspergillus/Penicillium enterotype (enterotype AP/Pe)

NCBI	Quality Control	Links
Ascomycota
Saccharomyces
Saccharomycetes

Revision editor(s): Ese