Gut Microbiota Alterations and Their Functional Differences in Depression According to Enterotypes in Asian Individuals
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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
Park S, Li C, Wu X, Zhang T
Journal
International journal of molecular sciences
Year
2023
Keywords:
enterotype, glucose metabolism, gut microbiota, gut–brain axis, network analysis
This study aimed to investigate alterations in the gut microbiota of patients with depression compared to those in the gut microbiota of healthy individuals based on enterotypes as a classification framework. Fecal bacteria FASTA/Q samples from 333 Chinese participants, including 107 healthy individuals (Healthy group) and 226 individuals suffering from depression (DP group), were analyzed. The participants were classified into three enterotypes: Bacteroidaceae (ET-B), Lachnospiraceae (ET-L), and Prevotellaceae (ET-P). An α-diversity analysis revealed no significant differences in microbial diversity between the Healthy and DP groups across all enterotypes. However, there were substantial differences in the gut microbial composition for β-diversity, particularly within ET-L and ET-B. The DP group within ET-B exhibited a higher abundance of Proteobacteria, while a linear discriminant analysis (LDA) of the DP group showed an increased relative abundance of specific genera, such as Mediterraneibacter, Blautia, Bifidobacterium, and Clostridium. Within ET-L, Bifidobacterium, Blautia, Clostridium, Collinsella, and Corynebacterium were significantly higher in the DP group in the LDA and ANOVA-like differential expression-2 (ALDEx2) analyses. At the species level of ET-L, Blautia luti, Blautia provencensis, Blautia glucerasea, Clostridium innocuum, Clostridium porci, and Clostridium leptum were the primary bacteria in the DP group identified using the machine learning approach. A network analysis revealed a more tightly interconnected microbial community within ET-L than within ET-B. This suggests a potentially stronger functional relationship among the gut microbiota in ET-L. The metabolic pathways related to glucose metabolism, tryptophan and tyrosine metabolism, neurotransmitter metabolism, and immune-related functions showed strong negative associations with depression, particularly within ET-L. These findings provide insights into the gut-brain axis and its role in the pathogenesis of depression, thus contributing to our understanding of the underlying mechanisms in Asian individuals. Further research is warranted to explain the mechanistic links between gut microbiota and depression and to explore their potential for use in precision medicine interventions.
Experiment 1
Reviewed Marked as Reviewed by Folakunmi on 2024-3-20
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
- Depressive disorder depression,melancholia,melancholias,mental depression,syndrome, depressive,syndromes, depressive,Depressive disorder,depressive disorder
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Depressive group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients with depressive disorder in the high bacteroidaceae enterotype (ET-B). Enterotypes were identified through PCA using gut microbiota from the collected fecal FASTA/Q files.
- 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
- 84
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- None
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
- 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)?
- Yes
- 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
Reviewed Marked as Reviewed by Folakunmi on 2024-3-20
Source: Figure 2C
Description: Primary gut microbiota in Healthy and Depression groups in high bacteroidaceae enterotype (ET-B) using linear discriminant analysis (LDA) scores.
Abundance in Group 1: increased abundance in Depressive group
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudescherichia vulneris | ||
| Petroclostridium xylanilyticum | ||
| [Clostridium] innocuum |
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-3-20
Source: Figure 2C
Description: Primary gut microbiota in Healthy and Depression groups in high bacteroidaceae enterotype (ET-B) using linear discriminant analysis (LDA) scores.
Abundance in Group 1: decreased abundance in Depressive group
Revision editor(s): Idiat, Folakunmi, Aananditaa
Experiment 2
Reviewed Marked as Reviewed by Folakunmi on 2024-3-20
Differences from previous experiment shown
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients with depression in the high lachnospiraceae enterotype (ET-L). Enterotypes were identified through PCA using gut microbiota from the collected fecal FASTA/Q files.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 47
- Group 1 sample size Number of subjects in the case (exposed) group
- 127
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
Reviewed Marked as Reviewed by Folakunmi on 2024-3-20
Source: figure 3D
Description: Primary gut microbiota in Healthy and DP groups at the species level in high lachnospiraceae enterotype (ET-L) using linear discriminant analysis (LDA) scores.
Abundance in Group 1: increased abundance in Depressive group
Revision editor(s): Folakunmi
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-3-20
Source: figure 3D
Description: Primary gut microbiota in Healthy and DP groups at the species level in high lachnospiraceae enterotype (ET-L) using linear discriminant analysis (LDA) scores.
Abundance in Group 1: decreased abundance in Depressive group
Revision editor(s): Folakunmi, Aananditaa
Experiment 3
Reviewed Marked as Reviewed by Folakunmi on 2024-3-20
Differences from previous experiment shown
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients with depressive disorder in the high prevotellaceae enterotype (ET-P). Enterotypes were identified through PCA using gut microbiota from the collected fecal FASTA/Q files.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
Lab analysis
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
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
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