Fecal Microbiota Composition, Their Interactions, and Metagenome Function in US Adults with Type 2 Diabetes According to Enterotypes
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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.
Authors
Park S, Zhang T, Kang S
Journal
International journal of molecular sciences
Year
2023
Keywords:
fecal bacteria, metagenome analysis, pooling data, type 2 diabetes, western diet
T2DM etiology differs among Asians and Caucasians and may be associated with gut microbiota influenced by different diet patterns. However, the association between fecal bacterial composition, enterotypes, and T2DM susceptibility remained controversial. We investigated the fecal bacterial composition, co-abundance network, and metagenome function in US adults with T2DM compared to healthy adults based on enterotypes. We analyzed 1911 fecal bacterial files of 1039 T2DM and 872 healthy US adults from the Human Microbiome Projects. Operational taxonomic units were obtained after filtering and cleaning the files using Qiime2 tools. Machine learning and network analysis identified primary bacteria and their interactions influencing T2DM incidence, clustered into enterotypes, Bacteroidaceae (ET-B), Lachnospiraceae (ET-L), and Prevotellaceae (ET-P). ET-B showed higher T2DM incidence. Alpha-diversity was significantly lower in T2DM in ET-L and ET-P (p < 0.0001), but not in ET-B. Beta-diversity revealed a distinct separation between T2DM and healthy groups across all enterotypes (p < 0.0001). The XGBoost model exhibited high accuracy and sensitivity. Enterocloster bolteae, Facalicatena fissicatena, Clostridium symbiosum, and Facalibacterium prausnitizii were more abundant in the T2DM group than in the healthy group. Bacteroides koreensis, Oscillibacter ruminantium, Bacteroides uniformis, and Blautia wexlerae were lower in the T2DM than in the healthy group regardless of the enterotypes in the XGBoost model (p < 0.0001). However, the patterns of microbial interactions varied among different enterotypes affecting T2DM risk. The interaction between fecal bacteria was more tightly regulated in the ET-L than in the ET-B and ET-P groups (p < 0.001). Metagenomic analysis revealed an inverse association between bacteria abundance in T2DM, energy utility, butanoate and propanoate metabolism, and the insulin signaling pathway (p < 0.0001). In conclusion, fecal bacteria play a role in T2DM pathogenesis, particularly within different enterotypes, providing valuable insights into the link between gut microbiota and T2DM in the US population.
Experiment 1
Subjects
- Location of subjects
- United States of America
- 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 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 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls in Total participants
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Type 2 diabetes (T2DM) in Total Participants
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants were Caucasians with T2DM aged over 30 years.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 872
- Group 1 sample size Number of subjects in the case (exposed) group
- 1039
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
- Decision Trees (xgBoost Statistical test: "Decision Trees (xgBoost" is not in the list (ANCOM, ANCOM-BC, ANOSIM, ANOVA, Beta Binomial Regression, Chi-Square, Cox Proportional-Hazards Regression, Decision Trees (xgBoost, gradient boosting), Dunn's test, DESeq2, ...) of allowed values.
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.001
- 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
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Figures 2B
Description: Fecal bacteria composition in total participants.
Abundance in Group 1: increased abundance in Type 2 diabetes (T2DM) in Total Participants
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides koreensis | ||
| Bacteroides uniformis | ||
| Fusicatenibacter saccharivorans | ||
| Gemmiger formicilis | ||
| Oscillibacter ruminantium | ||
| Phocaeicola vulgatus |
Revision editor(s): Miss Lulu
Signature 2
Source: Figure 2B
Description: Fecal bacteria composition in total participants.
Abundance in Group 1: decreased abundance in Type 2 diabetes (T2DM) in Total Participants
Revision editor(s): Miss Lulu
Experiment 2
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Diabetes mellitus biomarker Diabetes mellitus biomarker,diabetes mellitus biomarker
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls in ET-B
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Type 2 diabetes (T2DM) in ET-B
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants were Caucasians with T2DM aged over 30 years. (ET-B).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 416
- Group 1 sample size Number of subjects in the case (exposed) group
- 533
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
- Richness Number of species
- unchanged
Signature 1
Source: Figure 3B
Description: Fecal bacteria composition in Enterotype Bacteroidaceae (ET-B)
Abundance in Group 1: increased abundance in Type 2 diabetes (T2DM) in ET-B
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillibacter ruminantium | ||
| Bacteroides koreensis | ||
| Agathobacter rectalis |
Revision editor(s): Miss Lulu
Signature 2
Source: Figure 3B
Description: Fecal bacteria composition in Enterotype Bacteroidaceae (ET-B)
Abundance in Group 1: decreased abundance in Type 2 diabetes (T2DM) in ET-B
Revision editor(s): Miss Lulu
Experiment 3
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls in ET-L
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Type 2 diabetes (T2DM) in ET-L
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants were Caucasians with T2DM aged over 30 years in Enterotype Lachnospiraceae (ET-L).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 329
- Group 1 sample size Number of subjects in the case (exposed) group
- 411
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- increased
Signature 1
Source: Figure 4B
Description: Fecal bacteria composition in Enterotype Lachnospiraceae (ET-L)
Abundance in Group 1: increased abundance in Type 2 diabetes (T2DM) in ET-L
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillibacter ruminantium | ||
| Blautia wexlerae | ||
| Bacteroides koreensis | ||
| Blautia faecis | ||
| Sporobacter termitidis | ||
| Akkermansia muciniphila |
Revision editor(s): Miss Lulu
Signature 2
Source: Figure 4B
Description: Fecal bacteria composition in Enterotype Lachnospiraceae (ET-L).
Abundance in Group 1: decreased abundance in Type 2 diabetes (T2DM) in ET-L
Revision editor(s): Miss Lulu
Experiment 4
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls in ET-P
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Type 2 diabetes (T2DM) in ET-P
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants were Caucasians with T2DM aged over 30 years in Enterotype Prevotellaceae (ET-P).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 127
- Group 1 sample size Number of subjects in the case (exposed) group
- 95
Lab analysis
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- MGISEQ-2000
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Source: Figure 5B
Description: Fecal bacteria composition in Enterotype Prevotellaceae (ET-P).
Abundance in Group 1: decreased abundance in Type 2 diabetes (T2DM) in ET-P
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillibacter ruminantium | ||
| Bacteroides koreensis | ||
| Dorea longicatena | ||
| Bacteroides faecis | ||
| Blautia wexlerae | ||
| Parabacteroides merdae | ||
| Kineothrix alysoides | ||
| Segatella copri |
Revision editor(s): Miss Lulu
Signature 2
Source: Figure 5B
Description: Fecal bacteria composition in Enterotype Prevotellaceae (ET-P).
Abundance in Group 1: increased abundance in Type 2 diabetes (T2DM) in ET-P
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillibacter ruminantium | ||
| Bacteroides koreensis | ||
| Dorea longicatena | ||
| Bacteroides faecis | ||
| Parabacteroides merdae |
Revision editor(s): Miss Lulu
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