Associations between bacterial and fungal communities in the human gut microbiota and their implications for nutritional status and body weight
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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.
URI
Authors
García-Gamboa R, Díaz-Torres O, Senés-Guerrero C, Gradilla-Hernández MS, Moya A, Pérez-Brocal V, Garcia-Gonzalez A, González-Avila M
Journal
Scientific reports
Year
2024
Keywords:
Candida, Bacillota/Bacteroidota (Firmicutes/Bacteroidetes) ratio, Gut bacteriota, Gut dysbiosis, Gut mycobiota, Obesity
This study examined the interplay between bacterial and fungal communities in the human gut microbiota, impacting on nutritional status and body weight. Cohorts of 10 participants of healthy weight, 10 overweight, and 10 obese individuals, underwent comprehensive analysis, including dietary, anthropometric, and biochemical evaluations. Microbial composition was studied via gene sequencing of 16S and ITS rDNA regions, revealing bacterial (bacteriota) and fungal (mycobiota) profiles. Bacterial diversity exceeded fungal diversity. Statistically significant differences in bacterial communities were found within healthy-weight, overweight, and obese groups. The Bacillota/Bacteroidota ratio (previously known as the Firmicutes/Bacteroidetes ratio) correlated positively with body mass index. The predominant fungal phyla were Ascomycota and Basidiomycota, with the genera Nakaseomyces, Kazachstania, Kluyveromyces, and Hanseniaspora, inversely correlating with weight gain; while Saccharomyces, Debaryomyces, and Pichia correlated positively with body mass index. Overweight and obese individuals who harbored a higher abundance of Akkermansia muciniphila, demonstrated a favorable lipid and glucose profiles in contrast to those with lower abundance. The overweight group had elevated Candida, positively linked to simple carbohydrate consumption. The study underscores the role of microbial taxa in body mass index and metabolic health. An imbalanced gut bacteriota/mycobiota may contribute to obesity/metabolic disorders, highlighting the significance of investigating both communities.
Experiment 1
Subjects
- Location of subjects
- Mexico
- 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
- Overweight body mass index status overweight BMI status,Overweight body mass index status,overweight body mass index status
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy-weight group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Overweight group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individuals displaying BMIs (body mass index) between 25.0 and 29.9
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
- 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
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- 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
- Linear Discriminant Analysis
- 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Figure 3a
Description: Statistically significant bacterial genera between overweight and healthy-weight groups by Volcano plots.
Abundance in Group 1: increased abundance in Overweight group
| NCBI | Quality Control | Links |
|---|---|---|
| Eggerthella | ||
| Flavonifractor |
Revision editor(s): Tosin
Signature 2
Source: Figure 3a
Description: Statistically significant bacterial genera between overweight and healthy-weight groups by Volcano plots.
Abundance in Group 1: decreased abundance in Overweight group
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibacterium | ||
| Haemophilus | ||
| Histophilus | ||
| Holdemanella | ||
| Hydrogenoanaerobacterium | ||
| Lachnospira | ||
| Rikenella |
Revision editor(s): Tosin
Experiment 2
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Obesity Adiposis,Adiposity,Obese,Obese (finding),obesity,Obesity (disorder),Obesity [Ambiguous],obesity disease,obesity disorder,Obesity NOS,Obesity, unspecified,Overweight and obesity,Obesity
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Obese group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individuals with BMIs (body mass index) in the range of 30.0–34.9
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
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Figure 3b
Description: Statistically significant bacterial genera between the obese and healthy-weight groups by Volcano plots.
Abundance in Group 1: increased abundance in Obese group
| NCBI | Quality Control | Links |
|---|---|---|
| Allisonella | ||
| Subdoligranulum | ||
| Dielma |
Revision editor(s): Tosin
Signature 2
Source: Figure 3b
Description: Statistically significant bacterial genera between the obese and healthy-weight groups by Volcano plots.
Abundance in Group 1: decreased abundance in Obese group
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella | ||
| Blautia | ||
| Lachnospira | ||
| Rikenella | ||
| Anaerostipes | ||
| Odoribacter | ||
| Marvinbryantia | ||
| Histophilus |
Revision editor(s): Tosin
Experiment 3
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Overweight group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individuals with BMIs (body mass index) in the range of 30.0–34.9.
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
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Figure 3c
Description: Statistically significant bacterial genera between the obese and overweight groups by Volcano plots.
Abundance in Group 1: increased abundance in Obese group
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium | ||
| Romboutsia |
Revision editor(s): Tosin
Signature 2
Source: Figure 3c
Description: Statistically significant bacterial genera between the obese and overweight groups by Volcano plots.
Abundance in Group 1: decreased abundance in Obese group
| NCBI | Quality Control | Links |
|---|---|---|
| Alloprevotella | ||
| Eggerthella | ||
| Flavonifractor |
Revision editor(s): Tosin
Experiment 4
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy-weight group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individuals with BMIs (body mass index) in the range of 30.0–34.9
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
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Figure 3d
Description: Statistically significant fungal genera between the obese and healthy-weight groups by Volcano plots.
Abundance in Group 1: increased abundance in Obese group
| NCBI | Quality Control | Links |
|---|---|---|
| Aspergillus | ||
| Malassezia |
Revision editor(s): Tosin
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