Intestinal microbiome changes and mechanisms of maintenance hemodialysis patients with constipation
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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.
Authors
Zhang A, Chen S, Zhu Y, Wu M, Lu B, Zhou X, Zhu Y, Xu X, Liu H, Zhu F, Lin R
Journal
Frontiers in cellular and infection microbiology
Year
2024
Keywords:
16S rRNA, Constipation, Intestinal biomarker, Maintenance haemodialysis (MHD), gut microbiome
BACKGROUND: Constipation is a common symptom in maintenance hemodialysis patients and greatly affects the quality of survival of hemodialysis patients. Fecal microbiota transplantation and probiotics are feasible treatments for functional constipation, but there is still a gap in the research on the characteristics of gut flora in patients with maintenance hemodialysis combined with constipation. The aim of this study is to clarify the characteristics of the intestinal flora and its changes in maintenance hemodialysis patients with constipation. METHODS: Fecal samples were collected from 45 participants, containing 15 in the maintenance hemodialysis constipation group,15 in the maintenance hemodialysis non-constipation group and 15 in the healthy control group. These samples were analyzed using 16S rRNA gene sequencing. The feature of the intestinal microbiome of maintenance hemodialysis constipation group and the microbiome differences among the three groups were elucidated by species annotation analysis, α-diversity analysis, β-diversity analysis, species difference analysis, and predictive functional analysis. RESULTS: The alpha diversity analysis indicated that maintenance hemodialysis constipation group was less diverse and homogeneous than maintenance hemodialysis non-constipation group and healthy control group. At the genus level, the top ten dominant genera in maintenance hemodialysis constipation group patients were Enterococcus, Escherichia-Shigella, Bacteroides, Streptococcus, Bifidobacterium, Ruminococcus_gnavus_group, Lachnospiraceae_unclassified, Faecalibacterium, Akkermansia and UCG-002. Compared with non-constipation group, the Enterococcus, Rhizobiales_unclassified, Filomicrobium, Eggerthella, Allobaculum, Prevotella_7, Gordonibacter, Mitochondria_unclassified, Lachnoanaerobaculum were significantly higher in constipation group (p<0.05). Compared with non-constipation group, the Kineothrix, Rhodopirellula, Weissella were significantly lower in constipation group (p<0.05). The predictive functional analysis revealed that compared with non-constipation group, constipation group was significantly enriched in pathways associated with pyruate metabolism, flavonoid biosynthesis. CONCLUSIONS: This study describes for the first time the intestinal microbiome characteristics of maintenance hemodialysis patients with constipation. The results of this study suggest that there is a difference in the intestinal flora between maintenance hemodialysis patients with constipation and maintenance hemodialysis patients without constipation.
Experiment 2
Reviewed Marked as Reviewed by KateRasheed on 2025-5-1
Differences from previous experiment shown
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
- Treatment outcome measurement Treatment outcome measurement,treatment outcome measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy Control Group (HCG)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Maintenance Hemodialysis with Constipation (MHDCG)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients undergoing hemodialysis also experiencing constipation.
- 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
- 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
- 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
- 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)?
- Yes
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- decreased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- 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 KateRasheed on 2025-5-1
Source: Figure 5 and 6
Description: Comparison of species abundance at the genus level.
Abundance in Group 1: increased abundance in Maintenance Hemodialysis with Constipation (MHDCG)
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia | ||
| Altererythrobacter | ||
| Dubosiella | ||
| Eggerthella | ||
| Enterococcus | ||
| Filomicrobium | ||
| Herminiimonas | ||
| Ruegeria | ||
| Verrucomicrobiota | ||
| Prevotella_7Prevotella_7 | ||
| Clostridium sp. CAG:352 |
Revision editor(s): Shulamite
Signature 2
Reviewed Marked as Reviewed by KateRasheed on 2025-5-1
Source: Figure 5 and 6
Description: Comparison of species abundance at the genus level.
Abundance in Group 1: decreased abundance in Maintenance Hemodialysis with Constipation (MHDCG)
Revision editor(s): Shulamite
Experiment 3
Reviewed Marked as Reviewed by KateRasheed on 2025-5-1
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Maintenance Hemodialysis without Constipation (MHDNCG)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Hemodialysis patients who do not experience constipation.
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- decreased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- 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 KateRasheed on 2025-5-1
Source: Figure 5 and 6
Description: Comparison of species abundance at the genus level.
Abundance in Group 1: increased abundance in Maintenance Hemodialysis without Constipation (MHDNCG)
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia | ||
| Clostridium sp. CAG:352 | ||
| Neisseria | ||
| unclassified Lachnospiraceae | ||
| Verrucomicrobiota |
Revision editor(s): Shulamite
Signature 2
Reviewed Marked as Reviewed by KateRasheed on 2025-5-1
Source: Figure 5 and 6
Description: Comparison of species abundance at the genus level.
Abundance in Group 1: decreased abundance in Maintenance Hemodialysis without Constipation (MHDNCG)
Revision editor(s): Shulamite
Experiment 4
Reviewed Marked as Reviewed by KateRasheed on 2025-5-1
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Maintenance Hemodialysis without Constipation (MHDNCG)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Maintenance Hemodialysis with Constipation (MHDCG)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients undergoing hemodialysis also experiencing constipation.
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- decreased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by KateRasheed on 2025-5-1
Source: Figure 6
Description: Comparison of species abundance at the genus level.
Abundance in Group 1: increased abundance in Maintenance Hemodialysis with Constipation (MHDCG)
| NCBI | Quality Control | Links |
|---|---|---|
| Allobaculum | ||
| Eggerthella | ||
| Enterococcus | ||
| Filomicrobium | ||
| Gordonibacter | ||
| Lachnoanaerobaculum | ||
| unclassified Hyphomicrobiales | ||
| Prevotella_7Prevotella_7 |
Revision editor(s): Shulamite
Signature 2
Reviewed Marked as Reviewed by KateRasheed on 2025-5-1
Source: Figure 6
Description: Comparison of species abundance at the genus level.
Abundance in Group 1: decreased abundance in Maintenance Hemodialysis with Constipation (MHDCG)
| NCBI | Quality Control | Links |
|---|---|---|
| Kineothrix | ||
| Rhodopirellula | ||
| Weissella |
Revision editor(s): Shulamite
Experiment 5
Reviewed Marked as Reviewed by KateRasheed on 2025-5-1
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
- Pielou Quantifies how equal the community is numerically
- decreased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by KateRasheed on 2025-5-1
Source: Figure 7
Description: LEfSe analysis. The abundance difference analysis plots for the MHDCG and MHDNCG groups at the genus level.
Abundance in Group 1: decreased abundance in Maintenance Hemodialysis with Constipation (MHDCG)
| NCBI | Quality Control | Links |
|---|---|---|
| Phocaeicola coprocola | ||
| Rhodopirellula | ||
| Veillonellaceae | ||
| Weissella | ||
| unclassified Rhodopirellula | ||
| unclassified Weissella | ||
| Veillonellales_SelenomonadalesVeillonellales_Selenomonadales |
Revision editor(s): Shulamite
Signature 2
Reviewed Marked as Reviewed by KateRasheed on 2025-5-1
Source: Figure 7
Description: LEfSe analysis. The abundance difference analysis plots for the MHDCG and MHDNCG groups at the genus level.
Abundance in Group 1: increased abundance in Maintenance Hemodialysis with Constipation (MHDCG)
Revision editor(s): Shulamite
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