Perturbations of the Gut Microbiome and Metabolome in Children with Calcium Oxalate Kidney Stone Disease
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Denburg MR, Koepsell K, Lee JJ, Gerber J, Bittinger K, Tasian GE
Journal of the American Society of Nephrology : JASN
intestine, kidney stones, metabolism, pediatric nephrology
BACKGROUND: The relationship between the composition and function of gut microbial communities and early-onset calcium oxalate kidney stone disease is unknown. METHODS: We conducted a case-control study of 88 individuals aged 4-18 years, which included 44 individuals with kidney stones containing ≥50% calcium oxalate and 44 controls matched for age, sex, and race. Shotgun metagenomic sequencing and untargeted metabolomics were performed on stool samples. RESULTS: Participants who were kidney stone formers had a significantly less diverse gut microbiome compared with controls. Among bacterial taxa with a prevalence >0.1%, 31 taxa were less abundant among individuals with nephrolithiasis. These included seven taxa that produce butyrate and three taxa that degrade oxalate. The lower abundance of these bacteria was reflected in decreased abundance of the gene encoding butyryl-coA dehydrogenase (P=0.02). The relative abundance of these bacteria was correlated with the levels of 18 fecal metabolites, and levels of these metabolites differed in individuals with kidney stones compared with controls. The oxalate-degrading bacterial taxa identified as decreased in those who were kidney stone formers were components of a larger abundance correlation network that included Eggerthella lenta and several Lactobacillus species. The microbial (α) diversity was associated with age of stone onset, first decreasing and then increasing with age. For the individuals who were stone formers, we found the lowest α diversity among individuals who first formed stones at age 9-14 years, whereas controls displayed no age-related differences in diversity. CONCLUSIONS: Loss of gut bacteria, particularly loss of those that produce butyrate and degrade oxalate, associates with perturbations of the metabolome that may be upstream determinants of early-onset calcium oxalate kidney stone disease.
Reviewed Marked as Reviewed by Atrayees on 2023-6-8
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- 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
- 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
- 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
- Patients with kidney stones
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The patients suffering from Kidney Stones (nephrolithiasis) are individuals with incident and recurrent kidney stones consisting of 100% calcium (of which at least 50% was calcium oxalate) that spontaneously passed or were removed surgically within the prior 3 years.
- Group 0 sample size Number of subjects in the control (unexposed) group
- Group 1 sample size Number of subjects in the case (exposed) group
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
- Sequencing type
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Matched on Factors on which subjects have been matched on in a case-control study
- age, race, sex
- Shannon Estimator of species richness and species evenness: more weight on species richness
- Richness Number of species
Reviewed Marked as Reviewed by Atrayees on 2023-6-8
Source: figure 1
Description: The relative abundance of bacterial taxa among participants with kidney stone disease.
Abundance in Group 1: decreased abundance in Patients with kidney stones
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