Alteration of the gut microbiota associated with childhood obesity by 16S rRNA gene sequencing
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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
Chen X, Sun H, Jiang F, Shen Y, Li X, Hu X, Shen X, Wei P
Journal
PeerJ
Year
2020
Keywords:
16S rRNA gene sequencing, Alpha diversity, Bacterial compositions, Beta Diversity, Childhood obesity, Gut microbiota
Background: Obesity is a global epidemic in the industrialized and developing world, and many children suffer from obesity-related complications. Gut microbiota dysbiosis might have significant effect on the development of obesity. The microbiota continues to develop through childhood and thus childhood may be the prime time for microbiota interventions to realize health promotion or disease prevention. Therefore, it is crucial to understand the structure and function of pediatric gut microbiota. Methods: According to the inclusion criteria and exclusion criteria, twenty-three normal weight and twenty-eight obese children were recruited from Nanjing, China. Genomic DNA was extracted from fecal samples. The V4 region of the bacterial 16S rDNA was amplified by PCR, and sequencing was applied to analyze the gut microbiota diversity and composition using the Illumina HiSeq 2500 platform. Results: The number of operational taxonomic units (OTUs) showed a decrease in the diversity of gut microbiota with increasing body weight. The alpha diversity indices showed that the normal weight group had higher abundance and observed species than the obese group (Chao1: P < 0.001; observed species: P < 0.001; PD whole tree: P < 0.001; Shannon index: P = 0.008). Principal coordinate analysis (PCoA) and Nonmetric multidimensional scaling (NMDS) revealed significant differences in gut microbial community structure between the normal weight group and the obese group. The liner discriminant analysis (LDA) effect size (LEfSe) analysis showed that fifty-five species of bacteria were abundant in the fecal samples of the normal weight group and forty-five species of bacteria were abundant in the obese group. In regard to phyla, the gut microbiota in the obese group had lower proportions of Bacteroidetes (51.35%) compared to the normal weight group (55.48%) (P = 0.030). There was no statistical difference in Firmicutes between the two groups (P = 0.436), and the Firmicutes/Bacteroidetes between the two groups had no statistical difference (P = 0.983). At the genus level, Faecalibacterium, Phascolarctobacterium, Lachnospira, Megamonas, and Haemophilus were significantly more abundant in the obese group than in the normal weight group (P = 0.048, P = 0.018, P < 0.001, P = 0.040, and P = 0.003, respectively). The fecal microbiota of children in the obese group had lower proportions of Oscillospira and Dialister compared to the normal weight group (P = 0.002 and P = 0.002, respectively). Conclusions: Our results showed a decrease in gut microbiota abundance and diversity as the BMI increased. Variations in the bacterial community structure were associated with obesity. Gut microbiota dysbiosis might play a crucial part in the development of obesity in Chinese children.
Experiment 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/23
Subjects
- Location of subjects
- China
- 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 weight children
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- obese children
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- volunteers between the ages of 6-11 years old who were determined to be obese by BMI
- Group 0 sample size Number of subjects in the control (unexposed) group
- 23
- Group 1 sample size Number of subjects in the case (exposed) group
- 28
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 4 weeks
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
- Mann-Whitney (Wilcoxon)
- 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
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/29
Source: Figure 2, Text
Description: Relative abundance of microbial taxa in normal weight group vs obese group
Abundance in Group 1: increased abundance in obese children
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibacterium | ||
| Haemophilus | ||
| Lachnospira | ||
| Megamonas | ||
| Phascolarctobacterium |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/29
Source: Figure 2, Text
Description: Relative abundance of microbial taxa in normal weight group vs obese group
Abundance in Group 1: decreased abundance in obese children
| NCBI | Quality Control | Links |
|---|---|---|
| Dialister | ||
| Oscillospira |
Revision editor(s): Claregrieve1, WikiWorks
Experiment 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/29
Differences from previous experiment shown
Subjects
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/29
Curated date: 2021/01/10
Curator: Mst Afroza Parvin
Revision editor(s): WikiWorks, Lwaldron, Claregrieve1
Source: Figure 5
Description: Relative abundance of microbial taxa in normal weight group vs obese group
Abundance in Group 1: increased abundance in obese children
Revision editor(s): WikiWorks, Lwaldron, Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/29
Curated date: 2021/01/10
Curator: Mst Afroza Parvin
Revision editor(s): WikiWorks, Lwaldron, Claregrieve1, Merit
Source: Figure 5
Description: Relative abundance of microbial taxa in normal weight group vs obese group
Abundance in Group 1: decreased abundance in obese children
Revision editor(s): WikiWorks, Lwaldron, Claregrieve1, Merit
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