The Presence of Oxalobacter formigenes in the Microbiome of Healthy Young Adults

J Urol. 2016 Feb;195(2):499-506. doi: 10.1016/j.juro.2015.08.070. Epub 2015 Aug 17.


Purpose: Oxalobacter formigenes, a member of the human colonic microbiota with a major role in net colonic oxalate transport and secretion, is protective against the formation of calcium oxalate kidney stones. We describe the prevalence, relative abundance and stability of O. formigenes in healthy young adults in the United States.

Materials and methods: We used HMP (Human Microbiome Project) data on fecal samples from 242 healthy young adults who had 1 to 3 study visits. Samples underwent whole genomic shotgun sequencing and/or 16S rRNA sequencing. Three data sets available from the processed sequence data were studied, including whole genomic shotgun metagenomic analysis by alignment to reference genomes using shotgun community profiling, or MetaPhlAn ( or QIIME ( analysis of the V1-3 or V3-5 16S sequences.

Results: O. formigenes was detected in fecal samples using whole genomic shotgun and 16S rRNA data. Analysis of the whole genomic shotgun data set using shotgun community profiling showed that 29 of 94 subjects (31%) were O. formigenes positive. V1-3 and V3-5 analyses were less sensitive for O. formigenes detection. When present, O. formigenes relative abundance varied over 3 log10 and was normally distributed. All assays agreed in 58 of 66 samples (88%) studied by all 3 methods. Of 14 subjects who were O. formigenes positive at baseline 13 (93%) were positive at the followup visit, indicating the stability of colonization.

Conclusions: O. formigenes appears to be stably present in fewer than half of healthy young adults in the United States. It is most sensitively detected by whole genomic shotgun.

Keywords: Oxalobacter formigenes; kidney calculi; metagenomics; microbiota; oxalates.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Adolescent
  • Adult
  • Feces / microbiology
  • Female
  • Healthy Volunteers
  • Humans
  • Male
  • Metagenome / genetics
  • Microbiota*
  • Oxalobacter formigenes / classification
  • Oxalobacter formigenes / genetics
  • Oxalobacter formigenes / isolation & purification*
  • United States