New perspectives on an old grouping: The genomic and phenotypic variability of Oxalobacter formigenes and the implications for calcium oxalate stone prevention.

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dc.citation.volume13
dc.contributor.authorChmiel JA
dc.contributor.authorCarr C
dc.contributor.authorStuivenberg GA
dc.contributor.authorVenema R
dc.contributor.authorChanyi RM
dc.contributor.authorAl KF
dc.contributor.authorGiguere D
dc.contributor.authorSay H
dc.contributor.authorAkouris PP
dc.contributor.authorDomínguez Romero SA
dc.contributor.authorKwong A
dc.contributor.authorTai V
dc.contributor.authorKoval SF
dc.contributor.authorRazvi H
dc.contributor.authorBjazevic J
dc.contributor.authorBurton JP
dc.contributor.editorSutcliffe I
dc.coverage.spatialSwitzerland
dc.date.accessioned2024-08-08T23:16:27Z
dc.date.available2024-08-08T23:16:27Z
dc.date.issued2022-12-21
dc.description.abstractOxalobacter formigenes is a unique bacterium with the ability to metabolize oxalate as a primary carbon source. Most kidney stones in humans are composed of calcium and oxalate. Therefore, supplementation with an oxalate-degrading bacterium may reduce stone burden in patients suffering from recurrent calcium oxalate-based urolithiasis. Strains of O. formigenes are divided into two groups: group I and group II. However, the differences between strains from each group remain unclear and elucidating these distinctions will provide a better understanding of their physiology and potential clinical applications. Here, genomes from multiple O. formigenes strains underwent whole genome sequencing followed by phylogenetic and functional analyses. Genetic differences suggest that the O. formigenes taxon should be divided into an additional three species: Oxalobacter aliiformigenes sp. nov, Oxalobacter paeniformigenes sp. nov, and Oxalobacter paraformigenes sp. nov. Despite the similarities in the oxalyl-CoA gene (oxc), which is essential for oxalate degradation, these strains have multiple unique genetic features that may be potential exploited for clinical use. Further investigation into the growth of these strains in a simulated fecal environment revealed that O. aliiformigenes strains are capable of thriving within the human gut microbiota. O. aliiformigenes may be a better therapeutic candidate than current group I strains (retaining the name O. formigenes), which have been previously tested and shown to be ineffective as an oral supplement to mitigate stone disease. By performing genomic analyses and identifying these novel characteristics, Oxalobacter strains better suited to mitigation of calcium oxalate-based urolithiasis may be identified in the future.
dc.description.confidentialfalse
dc.edition.edition2022
dc.format.pagination1011102-
dc.identifier.author-urlhttps://www.ncbi.nlm.nih.gov/pubmed/36620050
dc.identifier.citationChmiel JA, Carr C, Stuivenberg GA, Venema R, Chanyi RM, Al KF, Giguere D, Say H, Akouris PP, Domínguez Romero SA, Kwong A, Tai V, Koval SF, Razvi H, Bjazevic J, Burton JP. (2022). New perspectives on an old grouping: The genomic and phenotypic variability of Oxalobacter formigenes and the implications for calcium oxalate stone prevention.. Front Microbiol. 13. (pp. 1011102-).
dc.identifier.doi10.3389/fmicb.2022.1011102
dc.identifier.eissn1664-302X
dc.identifier.elements-typejournal-article
dc.identifier.issn1664-302X
dc.identifier.number1011102
dc.identifier.urihttps://mro.massey.ac.nz/handle/10179/71243
dc.languageeng
dc.publisherFrontiers Media S.A.
dc.publisher.urihttps://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2022.1011102/full
dc.relation.isPartOfFront Microbiol
dc.rights(c) 2022 The Author/s
dc.rightsCC BY 4.0
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectOxalobacter formigenes
dc.subjectgut microbiome
dc.subjectkidney stone disease
dc.subjectnephrolithiasis and hyperoxaluria
dc.subjectoxalate degradation
dc.subjectphylogenomic and comparative genomic analyses
dc.subjectrevised taxonomy
dc.titleNew perspectives on an old grouping: The genomic and phenotypic variability of Oxalobacter formigenes and the implications for calcium oxalate stone prevention.
dc.typeJournal article
pubs.elements-id458889
pubs.organisational-groupOther
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