Systematic analysis of the association between gut flora and obesity through high-throughput sequencing and bioinformatics approaches
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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 Uniform resource identifier for web resources.
Authors
Chiu CM, Huang WC, Weng SL, Tseng HC, Liang C, Wang WC, Yang T, Yang TL, Weng CT, Chang TH, Huang HD
Journal
BioMed research international
Year
2014
Eighty-one stool samples from Taiwanese were collected for analysis of the association between the gut flora and obesity. The supervised analysis showed that the most, abundant genera of bacteria in normal samples (from people with a body mass index (BMI) ≤ 24) were Bacteroides (27.7%), Prevotella (19.4%), Escherichia (12%), Phascolarctobacterium (3.9%), and Eubacterium (3.5%). The most abundant genera of bacteria in case samples (with a BMI ≥ 27) were Bacteroides (29%), Prevotella (21%), Escherichia (7.4%), Megamonas (5.1%), and Phascolarctobacterium (3.8%). A principal coordinate analysis (PCoA) demonstrated that normal samples were clustered more compactly than case samples. An unsupervised analysis demonstrated that bacterial communities in the gut were clustered into two main groups: N-like and OB-like groups. Remarkably, most normal samples (78%) were clustered in the N-like group, and most case samples (81%) were clustered in the OB-like group (Fisher's P value = 1.61E - 07). The results showed that bacterial communities in the gut were highly associated with obesity. This is the first study in Taiwan to investigate the association between human gut flora and obesity, and the results provide new insights into the correlation of bacteria with the rising trend in obesity.
Experiment 1
Needs review
Subjects
- Location of subjects
- Taiwan
- 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
- Obesity Adiposis,Adiposity,Obese,Obese (finding),obesity,Obesity (disorder),Obesity [Ambiguous],obesity disease,obesity disorder,Obesity NOS,Obesity, unspecified,Overweight and obesity,Obesity
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal (N-like group)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Case (OB-like group)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants with a Body Mass Index ≥ 27
- Group 0 sample size Number of subjects in the control (unexposed) group
- 45
- Group 1 sample size Number of subjects in the case (exposed) group
- 36
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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
- ANOVA
- Kolmogorov-Smirnov Test
- 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
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Needs review
Source: Table 2
Description: Genera with significantly different proportions between normal and case samples.
Abundance in Group 1: increased abundance in Case (OB-like group)
| NCBI | Quality Control | Links |
|---|---|---|
| Acinetobacter | ||
| Halomonas | ||
| Lachnospira | ||
| Megamonas | ||
| Shewanella |
Revision editor(s): Shulamite, Anne-mariesharp
Signature 2
Needs review
Source: Table 2
Description: Genera with significantly different proportions between normal and case samples.
Abundance in Group 1: decreased abundance in Case (OB-like group)
| NCBI | Quality Control | Links |
|---|---|---|
| Erwinia | ||
| Morganella | ||
| Serratia | ||
| Tatumella | ||
| Collinsella | ||
| Barnesiella | ||
| Clostridium | ||
| Coprococcus | ||
| Oscillibacter | ||
| Veillonella | ||
| Citrobacter | ||
| Cronobacter | ||
| Enterobacter | ||
| Escherichia | ||
| Leclercia |
Revision editor(s): Shulamite, Anne-mariesharp
Experiment 2
Needs review
Differences from previous experiment shown
Subjects
Lab analysis
Statistical Analysis
- Statistical test
- Fisher's Exact Test
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Needs review
Source: Table 3 and S2
Description: Genera & species with a significantly different presence between normal and case samples
Abundance in Group 1: increased abundance in Case (OB-like group)
Revision editor(s): Shulamite, Anne-mariesharp
Signature 2
Needs review
Source: Table 3 and S2
Description: Genera & species with a significantly different presence between normal and case samples
Abundance in Group 1: decreased abundance in Case (OB-like group)
Revision editor(s): Shulamite, Anne-mariesharp
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