Characteristics and Dysbiosis of the Gut Microbiome in Renal Transplant Recipients/Experiment 1

From BugSigDB


Needs review

Curated date: 2025/04/15

Curator: Agatha

Revision editor(s): Agatha, Montana-D

Subjects

Location of subjects
Netherlands
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
Renal transplant outcome measurement Renal transplant outcome measurement,renal transplant outcome measurement
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
RTR (Renal Transplant Recipients)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
These are renal transplant recipients that were at least one year post transplantation
Group 0 sample size Number of subjects in the control (unexposed) group
105
Group 1 sample size Number of subjects in the case (exposed) group
139

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
MaAsLin2
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.1
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
Yes
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
age, body mass index, smoking behavior, sex, Confounders controlled for: "medication use" 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.medication use

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2025/04/19

Curator: Agatha

Revision editor(s): Agatha, Montana-D

Source: Figure 4

Description: Significantly differential abundant taxa between RTRs and healthy controls.

Abundance in Group 1: increased abundance in RTR (Renal Transplant Recipients)

NCBI Quality ControlLinks
Blautia glucerasea
Blautia wexlerae
Eggerthella lenta
Escherichia coli
Rothia mucilaginosa
Schaalia odontolytica
Streptococcus mitis
Streptococcus parasanguinis
Streptococcus thermophilus

Revision editor(s): Agatha, Montana-D

Signature 2

Needs review

Curated date: 2025/04/22

Curator: Agatha

Revision editor(s): Agatha, Montana-D

Source: Figure 4

Description: Significantly differential abundant taxa between RTRS and healthy controls.

Abundance in Group 1: decreased abundance in RTR (Renal Transplant Recipients)

NCBI Quality ControlLinks
Bifidobacterium ruminantium
Collinsella aerofaciens
Coprococcus eutactus
Dorea longicatena
Faecalibacterium prausnitzii
Holdemanella biformis
Ruminococcus bromii
Slackia isoflavoniconvertens
[Eubacterium] siraeum
Bifidobacterium adolescentis
Bifidobacterium catenulatum subsp. kashiwanohense

Revision editor(s): Agatha, Montana-D