Gut microbiota dysbiosis and diarrhea in kidney transplant recipients

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Reviewed Marked as Reviewed by Atrayees on 2023-6-6

Curated date: 2023/03/29

Curator: Ufuoma Ejite

Revision editor(s): Ufuoma Ejite

Subjects

Location of subjects: United States of America

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: Diarrhea Diarrhea,Diarrhoea,Watery stool,diarrhea

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Controls (No Diarrhea Group)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Diarrhea Group

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Kidney transplant recipients that developed post-transplant diarrhea within the first 3 months after transplantation

Group 0 sample size Number of subjects in the control (unexposed) group: 46

Group 1 sample size Number of subjects in the case (exposed) group: 18

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): Applicable, but exact duration not specified

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V4-V5

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)

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: decreased

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-6

Curated date: 2023/03/29

Curator: Ufuoma Ejite

Revision editor(s): Ufuoma Ejite, Atrayees

Source: Figure 2, Table 2

Description: Differential microbial abundance between Controls and Diarrhea group

Abundance in Group 1: decreased abundance in Diarrhea Group

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Anaerostipes
Bacteroides
Bifidobacterium
Blautia
Coprobacillus
Dorea
Eubacterium
Faecalibacterium
Fusicatenibacter
Oscillibacter
Romboutsia
Ruminiclostridium
Ruminococcus
Coprococcus

Revision editor(s): Ufuoma Ejite, Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-6

Curated date: 2023/03/29

Curator: Ufuoma Ejite

Revision editor(s): Ufuoma Ejite

Source: Figure 2

Description: Differential microbial abundance between Controls and Diarrhea group

Abundance in Group 1: increased abundance in Diarrhea Group

NCBI	Quality Control	Links
Enterococcus
Escherichia
Lachnoclostridium

Revision editor(s): Ufuoma Ejite

Experiment 2

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Reviewed Marked as Reviewed by Atrayees on 2023-6-6

Curated date: 2023/04/17

Curator: Ufuoma Ejite

Revision editor(s): Ufuoma Ejite

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Antibiotic-excluded Controls (No Diarrhea Group)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Antibiotic-excluded Diarrhea Group

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Antibiotic-excluded diarrheal group; Kidney transplant recipients that developed post-transplant diarrhea within the first 3 months after transplantation

Group 1 sample size Number of subjects in the case (exposed) group: 13

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): Applicable; but exact duration not specified

Lab analysis

Statistical Analysis

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.15

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: antibiotic exposure

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-6

Curated date: 2023/04/18

Curator: Ufuoma Ejite

Revision editor(s): Ufuoma Ejite, Atrayees

Source: Table S2

Description: Differential microbial abundance between Antibiotic-excluded Controls and Antibiotic-excluded Diarrhea group

Abundance in Group 1: decreased abundance in Antibiotic-excluded Diarrhea Group

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Eubacterium
Coprococcus
Anaerostipes
Romboutsia
Dorea
Faecalibacterium
Ruminococcus
Fusicatenibacter
Bifidobacterium
Oscillibacter
Ruminiclostridium
Bacteroides
Gemmiger
Coprobacillus

Revision editor(s): Ufuoma Ejite, Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-6

Curated date: 2023/04/18

Curator: Ufuoma Ejite

Revision editor(s): Ufuoma Ejite, Atrayees

Source: Table S2

Description: Differential microbial abundance between Antibiotic-excluded Controls and Antibiotic-excluded Diarrhea group

Abundance in Group 1: increased abundance in Antibiotic-excluded Diarrhea Group

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Lachnoclostridium
Escherichia
Thomasclavelia
Blautia
Streptococcus

Revision editor(s): Ufuoma Ejite, Atrayees

Experiment 3

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Reviewed Marked as Reviewed by Atrayees on 2023-6-6

Curated date: 2023/04/19

Curator: Ufuoma Ejite

Revision editor(s): Ufuoma Ejite

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: 1000 mg/day MMF Dosage No Diarrhea Group

Group 1 name Corresponds to the case (exposed) group for case-control studies: 2000 mg/day MMF Dosage No Diarrhea Group

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: 2000 mg/day MMF Dosage administered to the No Diarrhea Group

Group 0 sample size Number of subjects in the control (unexposed) group: 21

Group 1 sample size Number of subjects in the case (exposed) group: 25

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): Not specified

Lab analysis

Statistical Analysis

Matched on Factors on which subjects have been matched on in a case-control study: intake of diabetes medication

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-6

Curated date: 2023/04/19

Curator: Ufuoma Ejite

Revision editor(s): Ufuoma Ejite, Atrayees

Source: Table S4

Description: Differential microbial abundance between 1000 mg/day MMF Dosage No Diarrhea Group and 2000 mg/day MMF Dosage No Diarrhea Group

Abundance in Group 1: decreased abundance in 2000 mg/day MMF Dosage No Diarrhea Group

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Erysipelotrichaceae
Romboutsia
Coprococcus
Fusicatenibacter
Dorea
Intestinibacter
Eubacterium
Streptococcus
Anaerostipes

Revision editor(s): Ufuoma Ejite, Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-6

Curated date: 2023/06/06

Curator: Atrayees

Revision editor(s): Atrayees

Source: Table S4

Description: Differential microbial abundance between 1000 mg/day MMF Dosage No Diarrhea Group and 2000 mg/day MMF Dosage No Diarrhea Group

Abundance in Group 1: increased abundance in 2000 mg/day MMF Dosage No Diarrhea Group

NCBI	Quality Control	Links
Ruminococcus
Ruminiclostridium
Blautia
Bacteroides
Bifidobacterium
Faecalibacterium
Lachnoclostridium
Gemmiger

Revision editor(s): Atrayees

Experiment 4

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Atrayees on 2023-6-7

Curated date: 2023/04/19

Curator: Ufuoma Ejite

Revision editor(s): Ufuoma Ejite, Victoria

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies: 1000 mg/day MMF Dosage Diarrhea Group

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: 1000 mg/day MMF Dosage administered to the Diarrhea Group

Group 1 sample size Number of subjects in the case (exposed) group: 4

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-7

Curated date: 2023/04/19

Curator: Ufuoma Ejite

Revision editor(s): Ufuoma Ejite, Atrayees

Source: Table S5

Description: Differential microbial abundance between 1000 mg/day MMF Dosage No Diarrhea Group and 1000 mg/day MMF Dosage Diarrhea Group

Abundance in Group 1: decreased abundance in 1000 mg/day MMF Dosage Diarrhea Group

NCBI	Quality Control	Links
Bacteroides
Eubacterium
Oscillibacter
Dorea
Ruminococcus
Anaerostipes
Faecalibacterium
Romboutsia
Fusicatenibacter
Ruminiclostridium
Gemmiger
Coprococcus
Thomasclavelia
Blautia
Intestinibacter

Revision editor(s): Ufuoma Ejite, Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-7

Curated date: 2023/04/19

Curator: Ufuoma Ejite

Revision editor(s): Ufuoma Ejite, Atrayees

Source: Table S5

Description: Differential microbial abundance between 1000 mg/day MMF Dosage No Diarrhea Group and 1000 mg/day MMF Dosage Diarrhea Group

Abundance in Group 1: increased abundance in 1000 mg/day MMF Dosage Diarrhea Group

NCBI	Quality Control	Links
Enterococcus
Escherichia
Streptococcus
Lachnoclostridium
Coprobacillus

Revision editor(s): Ufuoma Ejite, Atrayees

Experiment 5

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Atrayees on 2023-6-7

Curated date: 2023/04/19

Curator: Ufuoma Ejite

Revision editor(s): Ufuoma Ejite, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: 2000 mg/day MMF Dosage No Diarrhea Group

Group 1 name Corresponds to the case (exposed) group for case-control studies: 2000 mg/day MMF Dosage Diarrhea Group

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: 2000 mg/day MMF Dosage administered to the Diarrhea Group

Group 0 sample size Number of subjects in the control (unexposed) group: 25

Group 1 sample size Number of subjects in the case (exposed) group: 13

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-7

Curated date: 2023/04/19

Curator: Ufuoma Ejite

Revision editor(s): Ufuoma Ejite, Atrayees

Source: Table S6

Description: Differential microbial abundance between 2000 mg/day MMF Dosage No Diarrhea Group and 2000 mg/day MMF Dosage Diarrhea Group

Abundance in Group 1: decreased abundance in 2000 mg/day MMF Dosage Diarrhea Group

NCBI	Quality Control	Links
Eubacterium
Coprococcus
Anaerostipes
Ruminococcus
Faecalibacterium
Romboutsia
Ruminiclostridium
Dorea
Oscillibacter
Bifidobacterium
Fusicatenibacter
Blautia
Bacteroides
Gemmiger
Coprobacillus
Thomasclavelia

Revision editor(s): Ufuoma Ejite, Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-7

Curated date: 2023/04/19

Curator: Ufuoma Ejite

Revision editor(s): Ufuoma Ejite, Atrayees

Source: Table S6

Description: Differential microbial abundance between 2000 mg/day MMF Dosage No Diarrhea Group and 2000 mg/day MMF Dosage Diarrhea Group

Abundance in Group 1: increased abundance in 2000 mg/day MMF Dosage Diarrhea Group

NCBI	Quality Control	Links
Enterococcus
Lachnoclostridium
Streptococcus
Intestinibacter

Revision editor(s): Ufuoma Ejite, Atrayees

Experiment 6

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Atrayees on 2023-6-7

Curated date: 2023/06/07

Curator: Atrayees

Revision editor(s): Atrayees, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Pre-Diarrheal specimens

Group 1 name Corresponds to the case (exposed) group for case-control studies: Diarrheal specimens

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Diarrheal specimens

Group 0 sample size Number of subjects in the control (unexposed) group: 14

Group 1 sample size Number of subjects in the case (exposed) group: 14

Lab analysis

Statistical Analysis

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

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-7

Curated date: 2023/06/07

Curator: Atrayees

Revision editor(s): Atrayees

Source: Table S7

Description: Relative abundance of taxa in Diarrheal specimens

Abundance in Group 1: decreased abundance in Diarrheal specimens

NCBI	Quality Control	Links
Gemmiger
Ruminococcus
Eubacterium
Anaerostipes
Thomasclavelia
Coprobacillus
Oscillibacter
Ruminiclostridium
Bifidobacterium
Coprococcus
Escherichia
Bacteroides
Dorea

Revision editor(s): Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-7

Curated date: 2023/06/07

Curator: Atrayees

Revision editor(s): Atrayees

Source: Table S7

Description: Relative abundance of taxa in Diarrheal specimens

Abundance in Group 1: increased abundance in Diarrheal specimens

NCBI	Quality Control	Links
Streptococcus
Lachnoclostridium

Revision editor(s): Atrayees

Experiment 7

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Atrayees on 2023-6-7

Curated date: 2023/06/07

Curator: Atrayees

Revision editor(s): Atrayees

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: First Diarrheal Specimens Time-Matched Fecal Specimens from the No Diarrhea Group

Group 1 name Corresponds to the case (exposed) group for case-control studies: First Diarrheal Specimens in the Diarrhea group

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: First Diarrheal Specimens in the Diarrhea group

Group 0 sample size Number of subjects in the control (unexposed) group: 46

Group 1 sample size Number of subjects in the case (exposed) group: 18

Lab analysis

Statistical Analysis

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: Not specified

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: decreased

Signature 1