Analysis on the change of gut microbiota and metabolome in lung transplant patients

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Reviewed Marked as Reviewed by Svetlana up on 2024-4-5
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Bo Wu, Peng Wang, Tangjuan Zhang, Ting Qian, Xiangnan Li, Xue Pan, Zheng Ding, Zhichao Hou
Journal
American Society for Microbiology
Year
2024
Pages:
16
First page:
Keywords:
gut microbiota, metabolome, lung transplantation, transplant rejection
Previous studies have shown that the gut microbiota and its metabolites are

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


Reviewed Marked as Reviewed by Folakunmi on 2024-5-14

Curated date: 2024/03/13

Curator: Glorious

Revision editor(s): Glorious, Svetlana up

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

Reviewed Marked as Reviewed by Folakunmi on 2024-5-14

Curated date: 2024/03/13

Curator: Glorious

Revision editor(s): Glorious, Fiddyhamma, Folakunmi

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)

NCBI Quality ControlLinks
Bacilli
Bacillus
Clostridiaceae
Enterobacterales
Enterobacteriaceae
Enterococcaceae
Enterococcus
Eubacteriales
Klebsiella
Lactobacillaceae
Lactobacillales
Mediterraneibacter gnavus
Ruminococcus
Streptococcaceae
Streptococcus
Thomasclavelia
ErysipelatoclostridiaceaeErysipelatoclostridiaceae

Revision editor(s): Glorious, Fiddyhamma, Folakunmi

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2024-5-14

Curated date: 2024/03/18

Curator: Glorious

Revision editor(s): Glorious, Fiddyhamma, Folakunmi

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)

NCBI Quality ControlLinks
Agathobacter
Bacteroidaceae
Bacteroidales
Bacteroides
Bacteroidia
Bacteroidota
Candidatus Epulonipiscium
Eubacteriales
Faecalibacterium
Fusobacteriaceae
Fusobacteriales
Fusobacteriia
Fusobacteriota
Leyella stercorea
Negativicutes
Oscillospiraceae
Phocaeicola coprocola
Phocaeicola dorei
Phocaeicola plebeius
Prevotella
Prevotellaceae
prevotella 9prevotella 9

Revision editor(s): Glorious, Fiddyhamma, Folakunmi

Experiment 2


Reviewed Marked as Reviewed by Folakunmi on 2024-5-14

Curated date: 2024/03/13

Curator: Glorious

Revision editor(s): Glorious, Svetlana up

Differences from previous experiment shown

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

Reviewed Marked as Reviewed by Folakunmi on 2024-5-14

Curated date: 2024/03/13

Curator: Glorious

Revision editor(s): Glorious, Fiddyhamma

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 ControlLinks
Bacilli
Bacillus
Enterococcaceae
Enterococcus
Lacticaseibacillus
Lactobacillales
Streptococcus
Streptococcaceae
Enterobacteriaceae
Lactobacillaceae

Revision editor(s): Glorious, Fiddyhamma

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2024-5-14

Curated date: 2024/03/18

Curator: Glorious

Revision editor(s): Glorious, Fiddyhamma

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)

NCBI Quality ControlLinks
Bacteroidaceae
Bacteroidales
Bacteroides
Bacteroidia
Bacteroidota
Candidatus Epulonipiscium
Clostridia
Eubacteriales
Faecalibacterium
Fusobacteriaceae
Fusobacteriales
Fusobacteriia
Fusobacteriota
Lachnospiraceae
Lachnospirales
Leyella stercorea
Negativicutes
Oscillospiraceae
Phocaeicola coprocola
Phocaeicola dorei
Phocaeicola plebeius
Prevotella
Prevotellaceae
veillonellales selenomonadalesveillonellales selenomonadales
prevotella 9prevotella 9

Revision editor(s): Glorious, Fiddyhamma

Experiment 3


Reviewed Marked as Reviewed by Folakunmi on 2024-5-14

Curated date: 2024/04/10

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma

Differences from previous experiment shown

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

Reviewed Marked as Reviewed by Folakunmi on 2024-5-14

Curated date: 2024/04/10

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, Folakunmi

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 ControlLinks
Mediterraneibacter gnavus

Revision editor(s): Fiddyhamma, Folakunmi