Zengye decoction induces alterations to metabolically active gut microbiota in aged constipated rats
From BugSigDB
Jump to:navigation, search
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
Liu D, Lin L, Lin Y, Zhong Y, Zhang S, Liu W, Zou B, Liao Q, Xie Z
Journal
Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie
Year
2019
Keywords:
16s rRNA, Constipation, Gut microbiome, Metabolism, Zengye decoction
Zengye decoction (ZYD), a traditional Chinese medicinal formula, has been used in the treatment of various chronic diseases, such as constipation and skin dryness syndrome. Clinically, the specific mechanisms and targets of ZYD for treating disease remain unclear. The present study was undertaken to investigate the effects of ZYD on the gut microbiota and host metabolites in aged constipated rats and the relationship between the intestinal microbiota and the host. Rats were divided randomly into three groups, the control group (n = 10), recovery group (n = 10) and ZYD group (n = 10). First, the aged constipation model was established for the ZYD group and recovery group. Then, rats in the ZYD group were treated with ZYD. Urinary and faecal samples of each animal were collected in microcentrifuge tubes. Next, 16s rRNA gene sequencing was employed to analyse the composition of the gut microbiome in faecal samples and afterwards the metabolic function of the altered gut microbiota was predicted. Additionally, 1H NMR profiling was used to detect the alterations of host metabolites in urine and faecal samples to verify the metabolic function results obtained from sequencing. As a result, ZYD reduced the level of harmful bacteria, such as Desulfovibrio, Ruminococcus, Prevotella and Dorea, and increased the abundance of Oxalobacter, Clostridium and Roseburia. The functional prediction of changes in the gut microbiota induced by ZYD revealed that ZYD promoted energy storage, regulated amino acid metabolism, inhibited methane metabolism, strengthened the physiological function of glutathione and reduced bacterial toxin. The 1H NMR profiles revealed that ZYD regulated the carbohydrates, short chain fatty acids, amino acids and amines in the aged constipated rats. In addition, most metabolic changes observed were related to the function of intestinal microbiota. These results suggest that ZYD can regulate the intestinal microbiota of constipated rats to normal levels and change the endogenous metabolites of the host through the intestinal microbiota to achieve therapeutic effects.
Experiment 1
Reviewed Marked as Reviewed by Svetlana up on 2025-4-1
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Rattus norvegicus
- 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
- Traditional Chinese medicine type TCM type,Traditional Chinese medicine type,traditional Chinese medicine type
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Combination of Control and Recovery group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- ZYD (Zengye decoction) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Aged constipated rats treated with Zengye decoction (ZYD)
- 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
- 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
- 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
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-4-1
Source: Figure 4B
Description: Differentially abundant microbial cladogram obtained by LEfSe (B)
Abundance in Group 1: increased abundance in ZYD (Zengye decoction) group
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium | ||
| Holdemania | ||
| Mollicutes | ||
| Moraxellaceae | ||
| Mycoplasmatota | ||
| Phascolarctobacterium | ||
| Pseudomonadales | ||
| Rikenellaceae | ||
| Veillonellaceae | ||
| Enterococcaceae bacterium RF39 |
Revision editor(s): Tosin
Experiment 2
Reviewed Marked as Reviewed by Svetlana up on 2025-4-1
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Combination of Recovery group and ZYD (Zengye decoction) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Control group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Aged constipated rats in the control group
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-4-1
Source: Figure 4B
Description: Differentially abundant microbial cladogram obtained by LEfSe (B)
Abundance in Group 1: increased abundance in Control group
Revision editor(s): Tosin
Experiment 3
Reviewed Marked as Reviewed by Svetlana up on 2025-4-1
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Combination of Control group and ZYD (Zengye decoction) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Recovery group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Aged constipated rats in the recovery group
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-4-1
Source: Figure 4B
Description: Differentially abundant microbial cladogram obtained by LEfSe (B)
Abundance in Group 1: increased abundance in Recovery group
Revision editor(s): Tosin, KateRasheed
Experiment 4
Reviewed Marked as Reviewed by Svetlana up on 2025-4-1
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control group
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-4-1
Source: Figure 5
Description: Comparison of relative abundance at the phylum, family and genus levels among the three groups
Abundance in Group 1: increased abundance in Recovery group
| NCBI | Quality Control | Links |
|---|---|---|
| Christensenellaceae | ||
| Desulfovibrio | ||
| Helicobacteraceae | ||
| Lactobacillaceae | ||
| Lactobacillus | ||
| Parabacteroides | ||
| Porphyromonadaceae | ||
| Prevotella | ||
| Rikenellaceae | ||
| bacterium AF12 | ||
| Deferribacterota |
Revision editor(s): Tosin
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-4-1
Source: Figure 5
Description: Comparison of relative abundance at the phylum, family and genus levels among the three groups
Abundance in Group 1: decreased abundance in Recovery group
Revision editor(s): Tosin
Experiment 5
Reviewed Marked as Reviewed by Svetlana up on 2025-4-1
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Recovery group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- ZYD (Zengye decoction) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Aged constipated rats treated with Zengye decoction (ZYD)
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-4-1
Source: Figure 5
Description: Comparison of relative abundance at the phylum, family and genus levels among the three groups
Abundance in Group 1: increased abundance in ZYD (Zengye decoction) group
| NCBI | Quality Control | Links |
|---|---|---|
| Mycoplasmatota | ||
| Oxalobacteraceae | ||
| Veillonellaceae | ||
| Clostridiaceae | ||
| Aeromonadaceae | ||
| Oxalobacter | ||
| Oligella | ||
| Phascolarctobacterium | ||
| Clostridium |
Revision editor(s): Tosin
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-4-1
Source: Figure 5
Description: Comparison of relative abundance at the phylum, family and genus levels among the three groups
Abundance in Group 1: decreased abundance in ZYD (Zengye decoction) group
| NCBI | Quality Control | Links |
|---|---|---|
| Helicobacteraceae | ||
| Lactobacillaceae | ||
| Lactobacillus | ||
| Parabacteroides | ||
| Porphyromonadaceae | ||
| Rikenellaceae | ||
| bacterium AF12 | ||
| Deferribacterota |
Revision editor(s): Tosin
Retrieved from "https://bugsigdb.org/w/index.php?title=30551387&oldid=192574"
