Analysis on the change of gut microbiota and metabolome in lung transplant patients
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
associated with the success of organ transplantation. However, the specific changes in the gut microbiota of lung transplant patients remain unclear. Hence, this study aimed to elucidate the interplay between the gut microbiota, metabolome, and lung transplantation outcomes. Using 16S metagenomics sequencing and untargeted metabolic profiling, we conducted a comprehensive analysis of gut microbial and metabolic alterations in lung transplant recipients relative to non-transplant group. Our findings revealed the predominance of Enterococcus and Streptococcus genera within the lung transplant cohort, accompanied by the significant reduction in Bacteroides, Epulopiscium, Faecalibacterium, and Prevotella abundance. In addition, a significant reduction in ATRA (all-trans retinoic acid) levels and suppression of IgA production were observed in lung transplant recipients, which were found to be closely associated with the Enterococcus genus. It was speculated that the association might have implications for the prognosis of lung transplant patients. Notably, the differences in gut microbial composition and metabolomic profiles between successful transplant recipients and those experiencing chronic rejection were not statistically significant. These novel insights shed light on the putative implications of the gut microbiota and metabolome in shaping lung transplantation outcomes, and provide a foundation for future investigations and targeted therapeutic interventions.
Experiment 1
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
- Lung transplantation lung transplant,transplant of lung,transplantation of lung,Lung transplantation,lung transplantation
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No lung transplant group (NT)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Lung transplant event-free group (EF)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- cases without any symptoms and with negative pathology were considered event-free patients after transplantation.
- 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
- 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
- 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
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Source: figure 3 A
Description: Lefse analysis to identify the microbial species that exhibited the most significant differences between NT and EF
Abundance in Group 1: increased abundance in Lung transplant event-free group (EF)
Revision editor(s): Glorious, Fiddyhamma, Folakunmi
Signature 2
Source: figure 3 A
Description: Lefse analysis to identify the microbial species that exhibited the most significant differences between NT and EF
Abundance in Group 1: decreased abundance in Lung transplant event-free group (EF)
Revision editor(s): Glorious, Fiddyhamma, Folakunmi
Experiment 2
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Lung transplant chronic rejection group (CR)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The lung transplant rejection participants were patients who survived more than 6 months after transplant and were all cases of chronic rejection.
- Group 1 sample size Number of subjects in the case (exposed) group
- 17
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Source: Figure 3B
Description: From the LEfSe analysis, CR group exhibited a higher abundance of Lacticaseibacillus, Enterococcus, Streptococcus and other significant taxas
Abundance in Group 1: increased abundance in Lung transplant chronic rejection group (CR)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacilli | ||
| Bacillus | ||
| Enterococcaceae | ||
| Enterococcus | ||
| Lacticaseibacillus | ||
| Lactobacillales | ||
| Streptococcus | ||
| Streptococcaceae | ||
| Enterobacteriaceae | ||
| Lactobacillaceae |
Revision editor(s): Glorious, Fiddyhamma
Signature 2
Source: Figure 3B
Description: Within the lung transplant cohort, a significant decrease in Bacteroides, Epulopiscium, Faecalibacterium, Prevotella and other significant taxas was observed.
Abundance in Group 1: decreased abundance in Lung transplant chronic rejection group (CR)
Revision editor(s): Glorious, Fiddyhamma
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Lung transplant event-free group (EF)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
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
Signature 1
Source: Figure 3c
Description: In analyzing the EF and CR cohorts (Fig. 3C), only Ruminococcus gnavus group was found dominant in the EF group.
Abundance in Group 1: decreased abundance in Lung transplant chronic rejection group (CR)
| NCBI | Quality Control | Links |
|---|---|---|
| Mediterraneibacter gnavus |
Revision editor(s): Fiddyhamma, Folakunmi
