Evaluation of the gastric microbiota based on body mass index using 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 Uniform resource identifier for web resources.
Authors
Lee S.H., Kim E.B., Park S.C., Nam S.J., Cho H., Jeon H.J., Lee S.P.
Journal
Frontiers in cellular and infection microbiology
Year
2025
Keywords:
16S rRNA sequencing, body mass index, gastric microbiota, metabolic dysregulation, obesity
INTRODUCTION: Obesity is a multifactorial condition influenced by various factors, including the gut microbiota. However, the relationship between the gastric microbiota and obesity remains poorly understood. This study aimed to investigate the composition of gastric microbiota, excluding Helicobacter pylori, in relation to body mass index (BMI) and metabolic indicators. METHODS: Thirty participants undergoing health checkups were classified into three groups-normal weight (BMI 18.5-22.9), overweight (BMI 23.0-24.9), and obese (BMI ≥25.0)-with ten individuals per group. Those with H. pylori infection, atrophic gastritis, or intestinal metaplasia were excluded. Gastric microbiota from four antral biopsies per subject were analyzed using 16S rRNA sequencing and functional profiling by metagenomic prediction. RESULTS AND DISCUSSION: Alpha diversity (Gini-Simpson index) was significantly lower in the combined overweight/obese group than that in the normal group (P=0.049). Beta diversity analysis revealed clear group separation (Bray-Curtis, P=0.005; unweighted UniFrac, P=0.004). Significant species differences between the groups were observed; specifically, the abundances of Muribaculum gordoncarteri, Turicibacter bilis, and Duncaniella dubosii, were significantly reduced in the overweight/obese group. Functional predictions showed differential enrichment of pathways related to fatty acid, amino acid, vitamin, and carbohydrate metabolism across BMI categories. These findings suggest that alterations in the gastric microbiota may be linked to obesity and metabolic dysregulation.
Experiment 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2025-10-19
Subjects
- Location of subjects
- South Korea
- 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
- Mucosa of stomach Magenschleimhaut,Gastric mucosa,Gastric mucous membrane,Mucosa of organ of stomach,Mucosa of organ of ventriculus,Mucosa of ventriculus,Mucous membrane of stomach,Mucous membrane of ventriculus,Organ mucosa of stomach,Organ mucosa of ventriculus,Stomach mucosa,Stomach mucosa of organ,Stomach mucous membrane,Stomach organ mucosa,Tunica mucosa (gaster),Tunica mucosa gastricae,Tunica mucosa gastris,Ventriculus mucosa,Ventriculus mucosa of organ,Ventriculus mucous membrane,Ventriculus organ mucosa,Mucosa of stomach,mucosa of stomach
- 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
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Overweight/obese
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants with a body mass index of 23.0–24.9 kg/m² for overweight and ≥25.0 kg/m² for obese
- 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
- 20
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
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
- LEfSe
- 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
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2025-10-19
Source: Figure 2C and 2D
Description: Linear discriminant analysis effect size (LEfSe) analysis for abundance between overweight/obese and normal weight groups
Abundance in Group 1: decreased abundance in Overweight/obese
Revision editor(s): EniolaAde
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2025-10-19
Source: Figure 2C and 2D
Description: Linear discriminant analysis effect size (LEfSe) analysis for abundance between overweight/obese and normal weight groups
Abundance in Group 1: increased abundance in Overweight/obese
Revision editor(s): EniolaAde
Experiment 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2025-10-19
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Overweight/obese
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Normal weight
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants with a body mass index of 18.5–22.9 kg/m²
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2025-10-19
Source: Supplementary Figure 3 and text page 4, subheading "Composition of gastric microbiota", paragraph 3
Description: Differential abundance between normal weight and overweight/obese group
Abundance in Group 1: increased abundance in Normal weight
Revision editor(s): EniolaAde
Experiment 3
Reviewed Marked as Reviewed by ChiomaBlessing on 2025-10-19
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal/Overweight
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Obese
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants with a body mass mass ≥25.0 kg/m²)
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2025-10-19
Source: Supplementary Figure 3
Description: Differential abundance between obese weight and normal/overweight group
Abundance in Group 1: increased abundance in Obese
| NCBI | Quality Control | Links |
|---|---|---|
| Negativicutes | ||
| Coriobacteriales | ||
| Segatella | ||
| Ruminococcus gauvreauii | ||
| Marinilabiliaceae | ||
| Marinilabiliales | ||
| [Clostridium] innocuum |
Revision editor(s): EniolaAde
Experiment 4
Reviewed Marked as Reviewed by ChiomaBlessing on 2025-10-19
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal/Obese
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Overweight
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants with a body mass index of 23.0–24.9 kg/m²
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2025-10-19
Source: Supplementary Figure 3
Description: Differential abundance between overweight and normal/obese group
Abundance in Group 1: increased abundance in Overweight
Revision editor(s): EniolaAde
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