Blood Microbiome Profile in CKD : A Pilot Study/Experiment 1

From BugSigDB


Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Victoria

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
Blood Portion of blood,Vertebrate blood,Whole blood,Blood,blood
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
controls
Group 1 name Corresponds to the case (exposed) group for case-control studies
CKD
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
20
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
current use

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
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)?
Yes
Matched on Factors on which subjects have been matched on in a case-control study
age
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
age, body mass index, hyperlipidemia, hypertension, leukocyte, immunosuppressant use measurement

Alpha Diversity

Chao1 Abundance-based estimator of species richness
decreased

Signature 1

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): Lwaldron, WikiWorks

Source: Figure 3 and Table 2

Description: Linear discriminant analysis Effect Size (LEfSe) showing microbiome differences between groups at various taxonomic levels.

Abundance in Group 1: increased abundance in CKD

NCBI Quality ControlLinks
Acetobacteraceae
Acinetobacter
Azotobacter group
Bacillus
Chitinophagaceae
Enterobacterales
Enterobacteriaceae
Gammaproteobacteria
Hyphomicrobiaceae
Hyphomicrobium
Legionella
Legionellaceae
Legionellales
Lysobacter
Peptostreptococcaceae
Pseudomonadota
Pseudarcicella
Pseudomonas
Sediminibacterium
Serratia
Yersinia
Yersinia intermedia
Rhodospirillales

Revision editor(s): Lwaldron, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): Lwaldron, Fatima, WikiWorks

Source: Figure 3 and Table 2

Description: Linear discriminant analysis Effect Size (LEfSe) showing microbiome differences between groups at various taxonomic levels.

Abundance in Group 1: decreased abundance in CKD

NCBI Quality ControlLinks
Acidimicrobiaceae
Acidimicrobiales
Terriglobia
Aurantimicrobium
Bryobacter
Bryobacterales
Corynebacterium
Desulfobulbaceae
Galloisiana yuasai
Lachnospiraceae
Microscillaceae
Ohtaekwangia
Paracoccus
Sphingomonas
Stenotrophomonas
Tyzzerella

Revision editor(s): Lwaldron, Fatima, WikiWorks