Rare phylotypes in stone, stool, and urine microbiomes are associated with urinary stone disease
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Study information
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Suryavanshi M, Agudelo J, Miller A
Journal
Frontiers in molecular biosciences
Year
2023
Keywords:
human microbiome, kidney stones, rare phylotype, reference database, urinary stone disease, urobiome, urology
Introduction: In complex microbial communities, the importance of microbial species at very low abundance levels and their prevalence for overall community structure and function is increasingly being recognized. Clinical microbiome studies on urinary stone disease (USD) have indicated that both the gut and urinary tract microbiota are associated with the onset of the disease and that kidney stones them-selves harbor a complex, yet consistent and viable, microbiome. However, how rare phylotypes contribute to this association remains unclear. Delineating the contribution of rare and common phylotypes to urinary stone disease is important for the development of bacteriotherapies to promote urologic health. Methods: The objectives of the current report were to conduct a metaanalysis of 16S rRNA datasets derived from the kidney stone, stool, and urine samples of participants with or without urinary stone disease. To delineate the impact of rare and common phylotypes, metaanalyses were conducted by first separating rare and common taxa determined by both the frequency and abundance of amplicon sequence variants. Results: Consistent with previous analyses, we found that gut, upper urinary, and lower urinary tract microbiomes were all unique. Rare phylotypes comprised the majority of species observed in all sample types, with kidney stones exhibiting the greatest bias toward rarity, followed by urine and stool. Both rare and common fractions contributed significantly to the differences observed between sample types and health disparity. Furthermore, the rare and common fractions were taxonomically unique across all sample types. A total of 222 and 320 unique rare phylotypes from urine and stool samples were found to be significantly associated with USD. A co-occurrence correlation analysis revealed that rare phylotypes are most important for microbiome structure in stones, followed by urine and stool. Discussion: Collectively, the results indicate that rare phylotypes may be important for the pathophysiology of USD, particularly in the kidney stone matrix, which is inherently a very low microbial biomass niche that can have implications for the diagnosis and treatment of kidney stones. Further studies are needed to investigate the functional significance of rare phylotypes in kidney stone pathogenesis.
Experiment 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-26
Subjects
- 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
- Urolithiasis calculus,kidney stone,urinary stones,urolithiasis,Urolithiasis
- 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
- urinary stone disease patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients with urinary stone disease
- Group 0 sample size Number of subjects in the control (unexposed) group
- 136
- Group 1 sample size Number of subjects in the case (exposed) group
- 201
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- DESeq2
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
Signature 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-26
Source: Figure 6
Description: Bubble plot showing the fold change of differentially abundant common rare (B) taxa associated with health disparities (control and USD phenotypes) in stool samples. Selection of taxa is defined using DESeq2 differential abundance analysis with a false discovery rate-corrected p-value <0.05. Taxa are listed as the number of ASVs within the lowest assigned taxonomy as a means to elucidate the most important taxa associated with USD.
Abundance in Group 1: increased abundance in urinary stone disease patients
Revision editor(s): Joju, Iram jamshed, MyleeeA
Experiment 2
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-26
Differences from previous experiment shown
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Urine Urine,urine
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- TEST
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-26
Source: Figure 7
Description: Bubble plot showing the fold change of differentially abundant rare (B) taxa associated with health disparities (control and USD phenotypes) in urine samples.
Abundance in Group 1: increased abundance in urinary stone disease patients
Revision editor(s): Joju
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