Differences in gut microbiota structure in patients with stages 4-5 chronic kidney disease/Experiment 1

From BugSigDB


Reviewed Marked as Reviewed by Peace Sandy on 2024-3-27

Curated date: 2024/03/13

Curator: Sneha6003

Revision editor(s): Sneha6003, Peace Sandy

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
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
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Diagnosed with stage 4-5 Chronic Kidney Disease (CKD) based on established medical criteria and diagnostic assessments conducted by nephrology experts.
Group 0 sample size Number of subjects in the control (unexposed) group
40
Group 1 sample size Number of subjects in the case (exposed) group
39
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
4 weeks

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
MGISEQ-2000

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
Chao1 Abundance-based estimator of species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased
Richness Number of species
decreased
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
decreased

Signature 1

Reviewed Marked as Reviewed by Peace Sandy on 2024-3-27

Curated date: 2024/03/26

Curator: Sneha6003

Revision editor(s): Sneha6003, Peace Sandy

Source: Figure 4

Description: LEfSe analysis was used to statistically resolve the microbiota with significant effects in the different groups. The LDA threshold was set as 2. (A) The stage 4-5 CKD group and (B) the control group.

Abundance in Group 1: increased abundance in Chronic kidney disease

NCBI Quality ControlLinks
Abiotrophia
Acinetobacter
Actinomyces
Actinomycetaceae
Actinomycetales
Actinomycetota
Aerococcaceae
Atopobium
Bacillales
Bacilli
Betaproteobacteria
Burkholderiales
Candidatus Saccharibacteria
Candidatus Saccharibacteria incertae sedis
Carnobacteriaceae
Christensenella
Clostridium
Collinsella
Coprobacillus
Coprobacter
Corynebacteriaceae
Corynebacterium
Eggerthella
Enterobacterales
Enterobacteriaceae
Enterococcaceae
Enterococcus
Erysipelotrichaceae
Erysipelotrichaceae incertae sedis
Erysipelotrichales
Erysipelotrichia
Eubacteriaceae
Eubacterium
Gammaproteobacteria
Gemmiger
Granulicatella
Lactobacillaceae
Lactobacillales
Lactobacillus
Leptotrichia
Micrococcaceae
Moraxellaceae
Morganella
Neisseria
Neisseriaceae
Neisseriales
Olsenella
Paraprevotella
Peptostreptococcaceae
Peptostreptococcus
Pseudomonadaceae
Pseudomonadales
Pseudomonadota
Pseudomonas
Pyramidobacter
Rothia
Ruminococcus
Scardovia
Shuttleworthella
Solobacterium
Staphylococcaceae
Staphylococcus
Streptococcaceae
Streptococcus

Revision editor(s): Sneha6003, Peace Sandy

Signature 2

Reviewed Marked as Reviewed by Peace Sandy on 2024-3-27

Curated date: 2024/03/27

Curator: Peace Sandy

Revision editor(s): Peace Sandy

Source: Figure 4

Description: LEfSe analysis was used to statistically resolve the microbiota with significant effects in the different groups. The LDA threshold was set as 2. (A) The stage 4-5 CKD group and (B) the control group.

Abundance in Group 1: decreased abundance in Chronic kidney disease

NCBI Quality ControlLinks
Clostridia
Eubacteriales
Prevotella
Prevotellaceae
Faecalibacterium
Roseburia
Selenomonadales
Negativicutes
Lachnospiraceae
Acidaminococcaceae
Phascolarctobacterium
Lachnospiraceae incertae sedis
Veillonellaceae
Ruminococcus
Coprococcus
Dialister
Rikenellaceae
Alistipes
Oscillibacter
Sutterellaceae
Parasutterella
Rhodospirillaceae
Rhodospirillales
Asaccharobacter
Haemophilus
Oxalobacteraceae
Butyricicoccus
Oxalobacter
Slackia
Dorea
Fusicatenibacter
Holdemanella
Clostridium
Barnesiella
Romboutsia
Anaerostipes
Butyricimonas
Odoribacter
Acidaminococcus
Allisonella

Revision editor(s): Peace Sandy