Profiling the urinary microbiome in men with calcium-based kidney stones

From BugSigDB
Reviewed Marked as Reviewed by Peace Sandy on 2024-6-24
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Xie J, Huang JS, Huang XJ, Peng JM, Yu Z, Yuan YQ, Xiao KF, Guo JN
Journal
BMC microbiology
Year
2020
Keywords:
Calcium-based, Kidney stone, Microbiome, Renal pelvis, Urine
BACKGROUND: The dogma that urine is sterile in healthy individuals has been overturned by recent studies applying molecular-based methods. Mounting evidences indicate that dysbiosis of the urinary microbiota is associated with several urological diseases. In this study, we aimed to investigate the urinary microbiome of male patients with calcium-based kidney stones and compare it with those of healthy individuals. RESULTS: The diversity of the urinary microbiota in kidney stone patients was significantly lower than that of healthy controls based on the Shannon and Simpson index (P < 0.001 for both indices). The urinary microbiota structure also significantly differed between kidney stone patients and healthy controls (ANOSIM, R = 0.11, P < 0.001). Differential representation of inflammation associated bacteria (e.g., Acinetobacter) and several enriched functional pathways were identified in the urine of kidney stones patients. Meanwhile, we found the species diversity, overall composition of microbiota and predicted functional pathways were similar between bladder urine and renal pelvis urine in kidney stone patients. CONCLUSIONS: A marked dysbiosis of urinary microbiota in male patients with calcium-based kidney stones was observed, which may be helpful to interpret the association between bacteria and calcium-based kidney stones.

Experiment 1


Reviewed Marked as Reviewed by Peace Sandy on 2024-6-24

Curated date: 2024/03/21

Curator: Victoria

Revision editor(s): Victoria

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
Urinary bladder Bladder,Urocyst,Vesica,Vesica urinaria,Urinary bladder,urinary bladder
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Nephrolithiasis Calculi, Kidney,Calculi, Renal,calculus of kidney and ureter,Calculus, Kidney,Calculus, Renal,CAON,Kidney Calculi,Kidney Calculus,kidney stone,Kidney Stones,Kidney stones,kidney stones,nephrolithiasis,nephrolithiasis, calcium oxalate,Renal Calculi,Renal calculi,renal calculi,Renal Calculus,Renal stones,Stone - kidney/ureter,Stone, Kidney,Stones, Kidney,urolithiasis, calcium oxalate,Nephrolithiasis
Group 0 name Corresponds to the control (unexposed) group for case-control studies
HB group - Bladder urine from healthy controls.
Group 1 name Corresponds to the case (exposed) group for case-control studies
KB group - Bladder urine from kidney stone patients.
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Bladder urine collected from nephrolithiasis (Kidney stone) patients.
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
22
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
30 days.

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)?
No
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
2
Matched on Factors on which subjects have been matched on in a case-control study
age

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
increased
Richness Number of species
decreased

Signature 1

Reviewed Marked as Reviewed by Peace Sandy on 2024-6-24

Curated date: 2024/03/22

Curator: Victoria

Revision editor(s): Victoria

Source: Fig. 5A & 5B

Description: A Cladogram and LEfSe analyses of microbiomes among HB (red), KB (green), and KP (blue) groups. Taxa in graph were with LDA score threshold > 2.0 and statistically significant (p < 0.05).

Abundance in Group 1: increased abundance in KB group - Bladder urine from kidney stone patients.

NCBI Quality ControlLinks
Bacteroidota
Bacillota
Prevotella
Prevotellaceae
Faecalibacterium
Peptococcaceae
Dyella
Fusobacteriales
Fusobacteriia
Fusobacteriota
Rahnella
Peptococcus
Sphingopyxis
Aminobacter
Paenibacillus
Porphyromonadaceae
Aeromonadales
Parabacteroides
Odoribacter
Odoribacteraceae

Revision editor(s): Victoria

Signature 2

Reviewed Marked as Reviewed by Peace Sandy on 2024-6-24

Curated date: 2024/03/22

Curator: Victoria

Revision editor(s): Victoria

Source: Fig. 5A & 5B

Description: A Cladogram and LEfSe analyses of microbiomes among HB (red), KB (green) and KP (blue) groups. Taxa in graph were with LDA score threshold > 2.0 and statistically significant (p < 0.05)

Abundance in Group 1: decreased abundance in KB group - Bladder urine from kidney stone patients.

NCBI Quality ControlLinks
Moraxellaceae
Acinetobacter
Pseudomonadales
Gammaproteobacteria
Pseudomonadota
Fusobacterium
Fusobacteriaceae

Revision editor(s): Victoria

Experiment 2


Reviewed Marked as Reviewed by Peace Sandy on 2024-6-24

Curated date: 2024/03/21

Curator: Victoria

Revision editor(s): Victoria

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Renal pelvis/ureter Renal pelvis and ureter,Renal pelvis plus ureter,Renal pelvis/ureter,renal pelvis/ureter
Group 0 name Corresponds to the control (unexposed) group for case-control studies
KB group - Bladder urine from kidney stone patients.
Group 1 name Corresponds to the case (exposed) group for case-control studies
KP group - Renal pelvis urine from kidney stone patients.
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Renal pelvis urine collected from nephrolithiasis (Kidney stone) patients.
Group 0 sample size Number of subjects in the control (unexposed) group
22
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
Participants using antibiotics within 30days were excluded.

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Peace Sandy on 2024-6-24

Curated date: 2024/03/22

Curator: Victoria

Revision editor(s): Victoria

Source: Fig. 5A & 5B

Description: A Cladogram and LEfSe analyses of microbiomes among HB (red), KB (green) and KP (blue) groups. Taxa in graph were with LDA score threshold > 2.0 and statistically significant (p < 0.05)

Abundance in Group 1: increased abundance in KP group - Renal pelvis urine from kidney stone patients.

NCBI Quality ControlLinks
Fusobacteriaceae
Fusobacterium
Pseudomonadota
Gammaproteobacteria
Moraxellaceae
Acinetobacter
Pseudomonadales

Revision editor(s): Victoria

Signature 2

Reviewed Marked as Reviewed by Peace Sandy on 2024-6-24

Curated date: 2024/03/22

Curator: Victoria

Revision editor(s): Victoria

Source: Fig. 5A & 5B

Description: A Cladogram and LEfSe analyses of microbiomes among HB (red), KB (green) and KP (blue) groups. Taxa in graph were with LDA score threshold > 2.0 and statistically significant (p < 0.05)

Abundance in Group 1: decreased abundance in KP group - Renal pelvis urine from kidney stone patients.

NCBI Quality ControlLinks
Actinomycetales
Anoxybacillus

Revision editor(s): Victoria