Gut microbiome alterations precede graft rejection in kidney transplantation patients

From BugSigDB
Needs review
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Holle J, Reitmeir R, Behrens F, Singh D, Schindler D, Potapenko O, McParland V, Anandakumar H, Kanzelmeyer N, Sommerer C, Hartleif S, Andrassy J, Heemann U, Neuenhahn M, Forslund-Startceva SK, Gerhard M, Oh J, Wilck N, Löber U, Bartolomaeus H
Journal
American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons
Year
2025
Keywords:
graft rejection, gut microbiome, kidney transplantation, short-chain fatty acids
Kidney transplantation (KT) is the best treatment for end-stage kidney disease, with graft survival critically affected by the recipient's immune response. The role of the gut microbiome in modulating this immune response remains underexplored. Our study investigates how microbiome alterations might be associated with allograft rejection by analyzing the gut microbiome using 16S rRNA gene amplicon sequencing of a multicenter prospective study involving 562 samples from 245 individuals of whom 217 received KT. Overall, gut microbiome composition showed gradual recovery post-KT, mirroring chronic kidney disease (CKD)-to-health transition as indicated by an increase in Shannon diversity. Prior to graft rejection, we observed a decrease in microbial diversity and short-chain fatty acid-producing taxa. Functional analysis highlighted a decreased potential for short-chain fatty acid production in patients preceding the rejection event, validated by quantitative PCR for the production potential of propionate and butyrate. Postrejection analysis revealed normalization of these microbiome features. Comparison to published microbiome signatures from CKD patients demonstrated a partial overlap of the microbiome alterations preceding graft rejection with the alterations typically found in CKD. Our findings suggest that alterations in gut microbiome composition and function may precede and influence KT rejection, suggesting potential implications as biomarkers or for early therapeutic microbiome-targeting interventions.

Experiment 1


Needs review

Curated date: 2025/04/06

Curator: MyleeeA

Revision editor(s): MyleeeA

Subjects

Location of subjects
Germany
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
Response to transplant Response to transplant,response to transplant
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Non Rejection (Pre Rejection)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Rejection (Pre Rejection)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Participants in the Rejection group were those who underwent kidney transplantation prior to rejection.
Group 0 sample size Number of subjects in the control (unexposed) group
60
Group 1 sample size Number of subjects in the case (exposed) group
32

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V3-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
Kruskall-Wallis
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
Matched on Factors on which subjects have been matched on in a case-control study
age, chronic kidney disease, time, sex, Matched on: "Donor type" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.Donor type

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
decreased
Richness Number of species
unchanged

Signature 1

Needs review

Curated date: 2025/04/07

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 2F

Description: Differential abundance analysis of bacterial taxa between Rejection (Pre Rejection) and Non-Rejection (Pre Rejection).

Abundance in Group 1: increased abundance in Rejection (Pre Rejection)

NCBI Quality ControlLinks
Anaerosporobacter
Fusobacterium
Helicobacter
Neisseria
Porphyromonas
Prevotella
Ralstonia
Streptococcus

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2025/04/07

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 2F

Description: Differential abundance analysis of bacterial taxa between Rejection (Pre Rejection) and Non-Rejection (Pre Rejection).

Abundance in Group 1: decreased abundance in Rejection (Pre Rejection)

NCBI Quality ControlLinks
Bacteroides
Blautia
Faecalibacterium
Lachnoclostridium
Lachnospira
Ruminococcus t.g.Ruminococcus t.g.
Eubacterium e.g.Eubacterium e.g.
Lachnospiraceae Unknown GenusLachnospiraceae Unknown Genus

Revision editor(s): MyleeeA

Experiment 2


Needs review

Curated date: 2025/04/06

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Non Rejection (Post Rejection)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Rejection (Post Rejection)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Participants in the Rejection group were those who showed rejection after kidney transplantation within a timeframe of 90 to 1000 days.
Group 0 sample size Number of subjects in the control (unexposed) group
54
Group 1 sample size Number of subjects in the case (exposed) group
21

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/04/07

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 5c

Description: Differential abundance analysis of bacterial taxa between Rejection (Post Rejection) and Non-Rejection (Post Rejection).

Abundance in Group 1: increased abundance in Rejection (Post Rejection)

NCBI Quality ControlLinks
Actinobacillus
Actinomyces
Alloprevotella
Anaerosporobacter
Butyricicoccus
Campylobacter
Candidatus Saccharimonas
Capnocytophaga
Fretibacterium
Fusobacterium
Gemella
Granulicatella
Haemophilus
Helicobacter
Lautropia
Leptotrichia
Neisseria
Parvimonas
Peptococcus
Peptostreptococcus
Porphyromonas
Prevotella
Pseudomonas
Ralstonia
Rothia
Sediminibacterium
Selenomonas
Streptococcus
Veillonella
unclassified Acidaminococcaceae
unclassified Actinomycetaceae
uncultured actinomycete
Prevotella 7Prevotella 7
UCG-008UCG-008
Unknown UCG-010_1Unknown UCG-010_1
Unknown Clostridiales oral taxon 075Unknown Clostridiales oral taxon 075
unclassified Candidatus Saccharimonadales

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2025/04/07

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 5c

Description: Differential abundance analysis of bacterial taxa between Rejection (Post Rejection) and Non-Rejection (Post Rejection).

Abundance in Group 1: decreased abundance in Rejection (Post Rejection)

NCBI Quality ControlLinks
Bacteroides
Blautia
Clostridium
Coprococcus
Diplocloster
Eggerthella
Faecalibacterium
Faecalibacterium sp. UBA1819
Flavonifractor
Klebsiella
Lachnoclostridium
Lachnospira
Lachnospira eligens
Mediterraneibacter gnavus
Romboutsia
[Ruminococcus] torques
bacterium
unclassified Clostridia
unclassified Lachnospiraceae
unclassified Lachnospirales
unidentified proteobacterium
Bacteria incertae sedis
unclassified Eubacteriales

Revision editor(s): MyleeeA

Experiment 3


Needs review

Curated date: 2025/04/06

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Transplant outcome measurement Transplant outcome measurement,transplant outcome measurement
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Rejection (Sample 1-Pre rejection)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Rejection (Sample 2-Post rejection)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Participants in the Rejection group were those who showed rejection after kidney transplantation within a timeframe of 90 to 1000 days post rejection.
Group 0 sample size Number of subjects in the control (unexposed) group
32

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
Richness Number of species
unchanged

Signature 1

Needs review

Curated date: 2025/04/07

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 5c

Description: Differential abundance analysis of bacterial taxa between Rejection (Pre Rejection) and Rejection (Post Rejection).

Abundance in Group 1: increased abundance in Rejection (Sample 2-Post rejection)

NCBI Quality ControlLinks
Bacteroides
Blautia
Clostridium
Coprococcus
Eggerthella
Faecalibacterium
Faecalibacterium sp. UBA1819
Lachnoclostridium
Lachnospira
Lachnospira eligens
Lachnospiraceae incertae sedis
Mediterraneibacter gnavus
[Ruminococcus] torques
unclassified Acidaminococcaceae
unclassified Lachnospirales
Bacteria incertae sedis

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2025/04/07

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 5c

Description: Differential abundance analysis of bacterial taxa between Rejection (Pre Rejection) and Rejection (Post Rejection).

Abundance in Group 1: decreased abundance in Rejection (Sample 2-Post rejection)

NCBI Quality ControlLinks
Actinobacillus
Actinomyces
Alloprevotella
Anaerosporobacter
Campylobacter
Candidatus Saccharimonas
Capnocytophaga
Fretibacterium
Fusobacterium
Gemella
Granulicatella
Haemophilus
Lautropia
Leptotrichia
Neisseria
Parvimonas
Peptococcus
Peptostreptococcus
Porphyromonas
Prevotella
Pseudomonas
Ralstonia
Rothia
Sediminibacterium
Selenomonas
Veillonella
unclassified Actinomycetaceae
uncultured actinomycete
Prevotella 7Prevotella 7
UCG-008UCG-008
Unknown Clostridiales oral taxon 075Unknown Clostridiales oral taxon 075
unclassified Candidatus Saccharimonadales

Revision editor(s): MyleeeA

Experiment 4


Needs review

Curated date: 2025/04/06

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

Subjects

Lab analysis

Statistical Analysis

Statistical test
Mann-Whitney (Wilcoxon)

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
Richness Number of species
unchanged

Signature 1

Needs review

Curated date: 2025/04/07

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 5d

Description: Differential abundance analysis of bacterial taxa between Rejection (Pre Rejection) and Rejection (Post Rejection).

Abundance in Group 1: increased abundance in Rejection (Sample 2-Post rejection)

NCBI Quality ControlLinks
Blautia
Faecalibacterium

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2025/04/08

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 5d

Description: Differential abundance analysis of bacterial taxa between Rejection (Pre Rejection) and Rejection (Post Rejection).

Abundance in Group 1: decreased abundance in Rejection (Sample 2-Post rejection)

NCBI Quality ControlLinks
Fusobacterium
Streptococcus

Revision editor(s): MyleeeA

Experiment 5


Needs review

Curated date: 2025/04/06

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Chronic kidney disease chronic kidney disease,chronic kidney failure,Chronic Kidney Insufficiencies,Chronic Kidney Insufficiency,chronic renal disease,Chronic Renal Failure,chronic renal failure syndrome,Chronic Renal Insufficiencies,chronic renal insufficiency,CKD,CKD - chronic kidney disease,Disease, End-Stage Kidney,Disease, End-Stage Renal,END STAGE KIDNEY DIS,End Stage Kidney Disease,END STAGE RENAL DIS,End Stage Renal Disease,End-Stage Kidney Disease,End-Stage Renal Disease,End-Stage Renal Failure,ESRD,kidney disease, chronic,Kidney Disease, End-Stage,Kidney Failure, Chronic,Kidney Insufficiencies, Chronic,Kidney Insufficiency, Chronic,RENAL DIS END STAGE,Renal Disease, End Stage,Renal Disease, End-Stage,renal failure - chronic,Renal Failure, Chronic,Renal Failure, End Stage,Renal Failure, End-Stage,Renal Insufficiencies, Chronic,Renal Insufficiency, Chronic,Chronic kidney disease
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Healthy controls
Group 1 name Corresponds to the case (exposed) group for case-control studies
Chronic Kidney Disease (CKD)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients with Chronic Kidney Disease (CKD) from an already published datasets.
Group 0 sample size Number of subjects in the control (unexposed) group
479
Group 1 sample size Number of subjects in the case (exposed) group
217

Lab analysis

Statistical Analysis

Matched on Factors on which subjects have been matched on in a case-control study
Not specified


Signature 1

Needs review

Curated date: 2025/04/08

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 6B

Description: Differential abundance analysis of bacterial taxa between Chronic Kidney Disease (CKD) and Healthy Controls.

Abundance in Group 1: increased abundance in Chronic Kidney Disease (CKD)

NCBI Quality ControlLinks
Streptococcus

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2025/04/08

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 6B

Description: Differential abundance analysis of bacterial taxa between Chronic Kidney Disease (CKD) and Healthy Controls.

Abundance in Group 1: decreased abundance in Chronic Kidney Disease (CKD)

NCBI Quality ControlLinks
Blautia
Faecalibacterium

Revision editor(s): MyleeeA

Experiment 6


Needs review

Curated date: 2025/04/06

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Response to transplant Response to transplant,response to transplant
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Non Rejection
Group 1 name Corresponds to the case (exposed) group for case-control studies
Rejection
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Participants in the rejection group were Propensity score matched and samples were obtained after Kidney Transplantation prior to rejection.
Group 0 sample size Number of subjects in the control (unexposed) group
60
Group 1 sample size Number of subjects in the case (exposed) group
32

Lab analysis

Statistical Analysis

Matched on Factors on which subjects have been matched on in a case-control study
Matched on: "propensity score" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.propensity score


Signature 1

Needs review

Curated date: 2025/04/08

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 6B

Description: Differential abundance analysis of bacterial taxa between Rejection and Non-Rejection.

Abundance in Group 1: increased abundance in Rejection

NCBI Quality ControlLinks
Fusobacterium
Streptococcus

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2025/04/08

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 6B

Description: Differential abundance analysis of bacterial taxa between Rejection and Non-Rejection.

Abundance in Group 1: decreased abundance in Rejection

NCBI Quality ControlLinks
Blautia
Faecalibacterium

Revision editor(s): MyleeeA

Experiment 7


Needs review

Curated date: 2025/04/06

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Transplant outcome measurement Transplant outcome measurement,transplant outcome measurement
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Rejection (Decreased)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Rejection (Increased)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients experiencing kidney transplantation rejection at any time
Group 0 sample size Number of subjects in the control (unexposed) group
Not specified
Group 1 sample size Number of subjects in the case (exposed) group
Not specified

Lab analysis

Statistical Analysis

Statistical test
Kruskall-Wallis
Matched on Factors on which subjects have been matched on in a case-control study
Not specified


Signature 1

Needs review

Curated date: 2025/04/08

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Supplementary Figure 4

Description: Heatmap showing associations of bacterial genera with kidney transplant rejection.

Abundance in Group 1: increased abundance in Rejection (Increased)

NCBI Quality ControlLinks
Acidaminococcaceae incertae sedis
Alloprevotella
Butyricicoccus
Campylobacter
Fusobacterium
Gemella
Helicobacter
Leptotrichia
Negativibacillus
Neisseria
Parvimonas
Porphyromonas
Prevotella
Ralstonia
Rothia
unclassified Actinomycetaceae
unclassified Actinomycetales
unclassified Monoglobaceae
unclassified Muribaculaceae
unclassified Rikenellaceae
uncultured organism
unknown uncultured organismunknown uncultured organism
Unknown Clostridia UCG-014 1Unknown Clostridia UCG-014 1
Family XIII UCG-001Family XIII UCG-001
Defulviitaleaceae UCG 011Defulviitaleaceae UCG 011
Christensenellaceae R-7 groupChristensenellaceae R-7 group
Unknown UCG-010 1Unknown UCG-010 1
Unknown UCG-010Unknown UCG-010
UCG-009UCG-009
unknown Clostridia vadinBB60 groupunknown Clostridia vadinBB60 group
unknown genusunknown genus
Prevotella 7Prevotella 7
Actinobacillus

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2025/04/08

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Supplementary Figure 4

Description: Heatmap showing associations of bacterial genera with kidney transplant rejection.

Abundance in Group 1: decreased abundance in Rejection (Increased)

NCBI Quality ControlLinks
Bacteroides
Blautia
Clostridium
Dielma
Diplocloster
Eggerthella
Escherichia/Shigella sp.
Faecalibacterium
Faecalibacterium sp. UBA1819
Flavonifractor
Lachnoclostridium
Lachnospira
Lachnospira eligens
Mediterraneibacter gnavus
Romboutsia
[Ruminococcus] torques
unclassified Clostridia
unclassified Lachnospiraceae
unclassified Pseudomonadota
unclassified Tannerellaceae
unclassified Eubacteriales

Revision editor(s): MyleeeA

Experiment 8


Needs review

Curated date: 2025/04/06

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Reaction time measurement Reaction time measurement,reaction time measurement
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Distance to Rejection (Decreasing)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Distance to Rejection (Increasing)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Participants grouped based on Distance to rejection of kidney transplantation at any sampling time

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/04/08

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Supplementary Figure 4

Description: Heatmap showing associations of bacterial genera with kidney transplant rejection.

Abundance in Group 1: increased abundance in Distance to Rejection (Increasing)

NCBI Quality ControlLinks
Anaerofilum
Bacteroides
Blautia
Diplocloster
Eggerthella
Eubacterium ventriosum
Faecalibacterium sp. UBA1819
Faecalitalea
Flavonifractor
Holdemania
Lachnoclostridium
Oscillibacter
Paraprevotella
Sutterella
[Eubacterium] siraeum
unclassified Bacteroidaceae
unclassified Bacteroidales
unclassified Bacteroidia
unclassified Clostridia
unclassified Rickenellaceae
unclassified Tannerellaceae
Lachnospiraceae UCG-008Lachnospiraceae UCG-008
Bacteria incertae sedis
unclassified Eubacteriales

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2025/04/08

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Supplementary Figure 4

Description: Heatmap showing associations of bacterial genera with kidney transplant rejection.

Abundance in Group 1: decreased abundance in Distance to Rejection (Increasing)

NCBI Quality ControlLinks
Actinobacillus
Anaerosporobacter
Campylobacter
Candidatus Nanosynbacter lyticus
Enterococcus
Fusobacterium
Gemella
Granulicatella
Haemophilus
Lactococcus
Leptotrichia
Parvimonas
Prevotella
Selenomonas
Streptococcus
Veillonella
unclassified Actinomycetaceae
UCG-008UCG-008
unclassified Candidatus Saccharimonadales

Revision editor(s): MyleeeA

Experiment 9


Needs review

Curated date: 2025/04/06

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Distance to Kidney Transplantation (Decreasing)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Distance to Kidney Transplantation (Increasing)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Participants grouped based on Distance to kidney transplantation at any sampling time

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/04/09

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Supplementary Figure 4

Description: Heatmap showing associations of bacterial genera with kidney transplant rejection.

Abundance in Group 1: increased abundance in Distance to Kidney Transplantation (Increasing)

NCBI Quality ControlLinks
Akkermansia
Butyricicoccus
Coprococcus
Eubacterium ventriosum
Faecalibacterium
Lachnospira
Lachnospira eligens
Mediterraneibacter gnavus
Monoglobus
Parasutterella
Roseburia
Sutterella
Tyzzerella
[Ruminococcus] torques
unclassified Actinomycetota
unclassified Bacillota
unclassified Bacteria
unclassified Bacteroidaceae
unclassified Bacteroidales
unclassified Bacteroidota
unclassified Lachnospiraceae
unclassified Lachnospirales
unclassified Monoglobaceae
Unknown Clostridia UCG-014 1Unknown Clostridia UCG-014 1
Lachnospiraceae UCG-008Lachnospiraceae UCG-008
Family XIII AD3011Family XIII AD3011
Unknown Eubacterium coprostanoligenes groupUnknown Eubacterium coprostanoligenes group
Lachnospiraceae UCG-004Lachnospiraceae UCG-004

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2025/04/09

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Supplementary Figure 4

Description: Heatmap showing associations of bacterial genera with kidney transplant rejection.

Abundance in Group 1: decreased abundance in Distance to Kidney Transplantation (Increasing)

NCBI Quality ControlLinks
Actinomyces
Alloprevotella
Campylobacter
Fusobacterium
Granulicatella
Neisseria
Ralstonia
Rothia
Streptococcus
Prevotella 7Prevotella 7
unknown genusunknown genus
UCG-008UCG-008
unclassified Candidatus Saccharimonadales

Revision editor(s): MyleeeA

Experiment 10


Needs review

Curated date: 2025/04/07

Curator: Victoria

Revision editor(s): Victoria

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Age Age,age
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Age (Decreasing)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Age (Increasing)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Participants here were grouped by age.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/04/08

Curator: Victoria

Revision editor(s): Victoria

Source: Supplementary figure S4

Description: Heatmap showing associations of bacterial genera with kidney transplant rejection.

Abundance in Group 1: increased abundance in Age (Increasing)

NCBI Quality ControlLinks
Alistipes
Anaerotruncus
Bacillus
Butyricimonas
Colidextribacter
Desulfovibrio
Dielma
Harryflintia
Lactobacillus
Limosilactobacillus
Merdimmobilis
Monoglobus
Negativibacillus
Oscillibacter
Paludicola
Ruminococcus
Slackia
Subdoligranulum
Thomasclavelia
unclassified Acidaminococcaceae
unclassified Bacilli
unclassified Bacteroidota
unclassified Lactobacillaceae
unclassified Oscillospiraceae
uncultured organism
unknown [Eubacterium] coprostanoligenes groupunknown [Eubacterium] coprostanoligenes group
unknown UCG-011unknown UCG-011
unknown UCG-010unknown UCG-010
UCG-009UCG-009
unknown UCG-010_1unknown UCG-010_1
Christensenellaceae R-7 groupChristensenellaceae R-7 group
Family XII AD3011 groupFamily XII AD3011 group
NK4A214 groupNK4A214 group
UCG-002UCG-002
UCG-005UCG-005
DTU089DTU089
Defluviitaleaceae UCG-011Defluviitaleaceae UCG-011
unknown Clostridia UCG-014_1unknown Clostridia UCG-014_1
Family XII UCG-001Family XII UCG-001
unknown Clostridia UCG-014unknown Clostridia UCG-014
unknown uncultured organismunknown uncultured organism
[Eubacterium] nodatum
Bacteria incertae sedis

Revision editor(s): Victoria

Signature 2

Needs review

Curated date: 2025/04/08

Curator: Victoria

Revision editor(s): Victoria

Source: Supplementary figure S4

Description: Heatmap showing associations of bacterial genera with kidney transplant rejection.

Abundance in Group 1: decreased abundance in Age (Increasing)

NCBI Quality ControlLinks
Anaerotignum
Lachnoclostridium
Butyrivibrio

Revision editor(s): Victoria

Experiment 11


Needs review

Curated date: 2025/04/07

Curator: Victoria

Revision editor(s): Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Donor Age(10-15)/Decreasing
Group 1 name Corresponds to the case (exposed) group for case-control studies
Donor Age(10-15)/ Increasing
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Participants in this group are donors between the ages of 10 and 15 years.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/04/08

Curator: Victoria

Revision editor(s): Victoria

Source: Supplemental Figure S4

Description: Heatmap showing associations of bacterial genera with kidney transplant rejection.

Abundance in Group 1: increased abundance in Donor Age(10-15)/ Increasing

NCBI Quality ControlLinks
Enterococcus

Revision editor(s): Victoria

Signature 2

Needs review

Curated date: 2025/04/08

Curator: Victoria

Revision editor(s): Victoria

Source: Supplementary Figure S4

Description: Heatmap showing associations of bacterial genera with kidney transplant rejection.

Abundance in Group 1: decreased abundance in Donor Age(10-15)/ Increasing

NCBI Quality ControlLinks
[Ruminococcus] torques
Faecalibacterium sp. UBA1819

Revision editor(s): Victoria

Experiment 12


Needs review

Curated date: 2025/04/07

Curator: Victoria

Revision editor(s): Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Donor Age(15-20)/Decreasing
Group 1 name Corresponds to the case (exposed) group for case-control studies
Donor Age(15-20)/ Increasing
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Participants in this group are donors between the ages of 15 and 20 years.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/04/08

Curator: Victoria

Revision editor(s): Victoria

Source: Supplemental Figure S4

Description: Heatmap showing associations of bacterial genera with kidney transplant rejection.

Abundance in Group 1: increased abundance in Donor Age(15-20)/ Increasing

NCBI Quality ControlLinks
Desulfovibrio
Enterorhabdus

Revision editor(s): Victoria

Experiment 13


Needs review

Curated date: 2025/04/07

Curator: Victoria

Revision editor(s): Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Donor Age(20-25)/Decreasing
Group 1 name Corresponds to the case (exposed) group for case-control studies
Donor Age(20-25)/ Increasing
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Participants in this group are donors between the ages of 20 and 25 years.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/04/08

Curator: Victoria

Revision editor(s): Victoria

Source: Supplementary figure S4

Description: Heatmap showing associations of bacterial genera with kidney transplant rejection.

Abundance in Group 1: increased abundance in Donor Age(20-25)/ Increasing

NCBI Quality ControlLinks
unknown [Eubacterium] coprostanoligenes groupunknown [Eubacterium] coprostanoligenes group
Flavonifractor
Dialister
Acidaminococcus

Revision editor(s): Victoria

Signature 2

Needs review

Curated date: 2025/04/08

Curator: Victoria

Revision editor(s): Victoria

Source: Supplementary figure S4

Description: Heatmap showing associations of bacterial genera with kidney transplant rejection.

Abundance in Group 1: decreased abundance in Donor Age(20-25)/ Increasing

NCBI Quality ControlLinks
unclassified Bacteroidota

Revision editor(s): Victoria

Experiment 14


Needs review

Curated date: 2025/04/07

Curator: Victoria

Revision editor(s): Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Donor Age(35-40)/Decreasing
Group 1 name Corresponds to the case (exposed) group for case-control studies
Donor Age(35-40)/ Increasing
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Participants in this group are donors between the ages of 35 and 40 years.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/04/08

Curator: Victoria

Revision editor(s): Victoria

Source: Supplementary figure S4

Description: Heatmap showing associations of bacterial genera with kidney transplant rejection.

Abundance in Group 1: increased abundance in Donor Age(35-40)/ Increasing

NCBI Quality ControlLinks
Dialister
unclassified Actinomycetota

Revision editor(s): Victoria

Experiment 15


Needs review

Curated date: 2025/04/07

Curator: Victoria

Revision editor(s): Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Donor Age(40-45)/Decreasing
Group 1 name Corresponds to the case (exposed) group for case-control studies
Donor Age(40-45)/ Increasing
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Participants in this group are donors between the ages of 40 and 45 years.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/04/08

Curator: Victoria

Revision editor(s): Victoria

Source: Supplementary figure S4

Description: Heatmap showing associations of bacterial genera with kidney transplant rejection.

Abundance in Group 1: increased abundance in Donor Age(40-45)/ Increasing

NCBI Quality ControlLinks
Butyrivibrio

Revision editor(s): Victoria

Experiment 16


Needs review

Curated date: 2025/04/07

Curator: Victoria

Revision editor(s): Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Donor Age(45-50)/ Decreasing
Group 1 name Corresponds to the case (exposed) group for case-control studies
Donor Age(45-50)/ Increasing
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Participants in this group are donors between the ages of 45 and 50 years.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/04/08

Curator: Victoria

Revision editor(s): Victoria

Source: Supplemental Figure S4

Description: Heatmap showing associations of bacterial genera with kidney transplant rejection.

Abundance in Group 1: increased abundance in Donor Age(45-50)/ Increasing

NCBI Quality ControlLinks
Prevotella 7Prevotella 7
Ralstonia

Revision editor(s): Victoria

Signature 2

Needs review

Curated date: 2025/04/08

Curator: Victoria

Revision editor(s): Victoria

Source: Supplemental Figure S4

Description: Heatmap showing associations of bacterial genera with kidney transplant rejection.

Abundance in Group 1: decreased abundance in Donor Age(45-50)/ Increasing

NCBI Quality ControlLinks
unclassified Oscillospiraceae

Revision editor(s): Victoria

Experiment 17


Needs review

Curated date: 2025/04/07

Curator: Victoria

Revision editor(s): Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Donor Age(70-75)/ Decreasing
Group 1 name Corresponds to the case (exposed) group for case-control studies
Donor Age(70-75)/ Increasing
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Participants in this group are donors between the ages of 70 and 75 years.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/04/08

Curator: Victoria

Revision editor(s): Victoria

Source: Supplemental Figure S4

Description: Heatmap showing associations of bacterial genera with kidney transplant rejection.

Abundance in Group 1: increased abundance in Donor Age(70-75)/ Increasing

NCBI Quality ControlLinks
Holdemania
unclassified Bacilli

Revision editor(s): Victoria

Experiment 18


Needs review

Curated date: 2025/04/07

Curator: Victoria

Revision editor(s): Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Donor Age(75-80)/ Decreasing
Group 1 name Corresponds to the case (exposed) group for case-control studies
Donor Age(75-80)/ Increasing
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Participants in this group are donors between the ages of 75 and 80 years.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/04/08

Curator: Victoria

Revision editor(s): Victoria

Source: Supplemental Figure S4

Description: Heatmap showing associations of bacterial genera with kidney transplant rejection.

Abundance in Group 1: increased abundance in Donor Age(75-80)/ Increasing

NCBI Quality ControlLinks
unknown UCG-010unknown UCG-010
Thomasclavelia
Enterobacter
Citrobacter

Revision editor(s): Victoria

Experiment 19


Needs review

Curated date: 2025/04/07

Curator: Victoria

Revision editor(s): Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Donor Age(>80)/ Decreasing
Group 1 name Corresponds to the case (exposed) group for case-control studies
Donor Age(>80)/ Increasing
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Participants in this group are donors above the age of 80.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/04/08

Curator: Victoria

Revision editor(s): Victoria

Source: Supplemental Figure S4

Description: Heatmap showing associations of bacterial genera with kidney transplant rejection.

Abundance in Group 1: increased abundance in Donor Age(>80)/ Increasing

NCBI Quality ControlLinks
Citrobacter
unclassified Lactobacillaceae
Escherichia/Shigella sp.

Revision editor(s): Victoria