Skip to main content

CORRECTION article

Front. Microbiol., 12 June 2023
Sec. Evolutionary and Genomic Microbiology
Volume 14 - 2023 | https://doi.org/10.3389/fmicb.2023.1231746

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

This article is a correction to:

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

    1. Read original article
\r\nJohn A. Chmiel,John A. Chmiel1,2Charles CarrCharles Carr3Gerrit A. Stuivenberg,Gerrit A. Stuivenberg1,2Robertson VenemaRobertson Venema4Ryan M. ChanyiRyan M. Chanyi5Kait F. Al,Kait F. Al1,2Daniel GiguereDaniel Giguere6Henry SayHenry Say6Polycronis P. Akouris,Polycronis P. Akouris1,2Sergio Ari Domínguez RomeroSergio Ari Domínguez Romero6Aaron KwongAaron Kwong7Vera TaiVera Tai6Susan F. KovalSusan F. Koval1Hassan RazviHassan Razvi8Jennifer BjazevicJennifer Bjazevic8Jeremy P. Burton,, Jeremy P. Burton1,2,8*
  • 1Department of Microbiology and Immunology, Western University, London, ON, Canada
  • 2Canadian Centre for Human Microbiome and Probiotics Research, London, ON, Canada
  • 3Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
  • 4Department of Medicine, The University of British Columbia, Vancouver, BC, Canada
  • 5School of Veterinary Science, Massey University, Palmerston North, New Zealand
  • 6Department of Biology, Western University, London, ON, Canada
  • 7Department of Medicine, Western University, London, ON, Canada
  • 8Division of Urology, Department of Surgery, Western University, London, ON, Canada

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

by Chmiel, J. A., Carr, C., Stuivenberg, G. A., Venema, R., Chanyi, R. M., Al, K. F., Giguere, D., Say, H., Akouris, P. P., Domínguez Romero, S. A., Kwong, A., Tai, V., Koval, S. F., Razvi, H., Bjazevic, J., and Burton, J. P. (2022). Front. Microbiol. 13:1011102. doi: 10.3389/fmicb.2022.1011102

In the published article, there was an error in the protologues in which the newly proposed species Oxalobacter aliiformigenes sp. nov, Oxalobacter paeniformigenes sp. nov, and Oxalobacter paraformigenes sp. nov. that were described omitted the information on the culture collection accession identifiers for the three respective type strains. These identifiers are now available and so, to comply with Rule 27(3) of the International Code of Nomenclature of Prokaryotes (Oren et al., 2023), these three protologues are reprinted here in full.

A correction has been made to Taxonomic and Nomenclature Proposals, Description of Oxalobacter aliiformigenes sp. nov. The section previously stated:

Oxalobacter aliiformigenes (a.li.i.for.mi'ge.nes. L. masc. adj. alius, other; N.L. part. adj. formigenes, formic acid producing, and specific epithet of an Oxalobacter species; N.L. part. adj. aliiformigenes, meaning that this species is related to but distinct from Oxalobacter formigenes).

Cells are Gram-stain negative, rod-shaped with rounded ends typically measuring 1.6 – 2.1 × 0.8 – 1.1 μm on average (estimated from Gram stain), and occurring in singles, pairs, or sometimes in chains. Cells occasionally present as curved. Endospores not found. Flagella not detected. Anaerobic, but aerotolerant with chemotrophic metabolism. Oxalate is useda a major carbon and energy source but typically slow growing in oxalate broth. Optimal growth is at 37°C. Indole not formed. Does not appear to reduce nitrate or sulfate. High levels of the fatty acid C19:0 cyclopropane are present and diagnostically useful (Allison et al., 1985). Members of O. aliiformigenes can be distinguished from other species in the genus Oxalobacter based on phylogenetic analysis and overall genome relatedness indices. Average genome size ranges from 2.2 – 2.4 Mbp and G+C content of the DNA ranges from 50.9 – 51.5%.

The type strain Va3T (=ATCC XXXX =DSM XXXX) was isolated from a human fecal sample (Duncan et al., 2002).

The corrected section appears below:

Oxalobacter aliiformigenes (a.li.i.for.mi'ge.nes. L. masc. adj. alius, other; N.L. part. adj. formigenes, formic acid producing, and specific epithet of an Oxalobacter species; N.L. part. adj. aliiformigenes, meaning that this species is related to but distinct from Oxalobacter formigenes).

Cells are Gram-stain negative, rod-shaped with rounded ends typically measuring 1.6 – 2.1 × 0.8 – 1.1 μm on average (estimated from Gram stain), and occurring in singles, pairs, or sometimes in chains. Cells occasionally present as curved. Endospores not found. Flagella not detected. Anaerobic, but aerotolerant with chemotrophic metabolism. Oxalate is used as a major carbon and energy source but can be slow growing in oxalate broth. Optimal growth is at 37°C. Indole not formed. Does not appear to reduce nitrate or sulfate. High levels of the fatty acid C19:0 cyclopropane are present and diagnostically useful (Allison et al., 1985). Members of O. aliiformigenes can be distinguished from other species in the genus Oxalobacter based on phylogenetic analysis and overall genome relatedness indices. Average genome size ranges from 2.2 to 2.4 Mbp and G+C content of the DNA ranges from 50.9–51.5%.

The type strain Va3T (=ATCC TSD-348 =DSM 115068) was isolated from a human fecal sample (Duncan et al., 2002).

A correction has been made to Taxonomic and Nomenclature Proposals, Description of Oxalobacter paeniformigenes sp. nov. The section previously stated:

Oxalobacter paeniformigenes (pae.ni.for.mi'ge.nes. L. adv. paene, almost; N.L. part. adj. formigenes, formic acid producing, and specific epithet of an Oxalobacter species; N.L. part. adj. paeniformigenes, meaning that this species is related to but distinct from Oxalobacter formigenes).

Cells are Gram-stain negative, rod-shaped with rounded ends typically measuring 1.4 – 2.2 × 0.8 – 1.2 μm on average (estimated from Gram stain), and occurring in singles, pairs, or sometimes in chains. Cells occasionally present as curved. Endospores not found. Flagella not detected. Anaerobic, but aerotolerant with chemotrophic metabolism. Oxalate is used a major carbon and energy source. Optimal growth is at 37 °C. Indole not formed. Does not appear to reduce nitrate or sulfate. Members of O. paeniformigenes can be distinguished from other species in the genus Oxalobacter based on phylogenetic analysis and overall genome relatedness indices. The genome size of the type strain is 1.93 Mb and the G+C content is 53.8%.

The type strain OxGP1T (=ATCC XXXX =DSM XXXX) was isolated from guinea pig cecum.

The corrected section appears below:

Oxalobacter paeniformigenes (pae.ni.for.mi'ge.nes. L. adv. paene, almost; N.L. part. adj. formigenes, formic acid producing, and specific epithet of an Oxalobacter species; N.L. part. adj. paeniformigenes, meaning that this species is related to but distinct from Oxalobacter formigenes).

Cells are Gram-stain negative, rod-shaped with rounded ends typically measuring 1.4 – 2.2 × 0.8 – 1.2 μm on average (estimated from Gram stain), and occurring in singles, pairs, or sometimes in chains. Cells occasionally present as curved. Endospores not found. Flagella not detected. Anaerobic, but aerotolerant with chemotrophic metabolism. Oxalate is used as a major carbon and energy source. Optimal growth is at 37°C. Indole not formed. Does not appear to reduce nitrate or sulfate. Members of O. paeniformigenes can be distinguished from other species in the genus Oxalobacter based on phylogenetic analysis and overall genome relatedness indices. The genome size of the type strain is 1.93 Mb and the G+C content is 53.8%.

The type strain OxGP1T (=ATCC TSD-347=DSM 115066) was isolated from guinea pig cecum.

A correction has been made to Taxonomic and Nomenclature Proposals, Description of Oxalobacter paraformigenes sp. nov. The section previously stated:

Oxalobacter paraformigenes (pa.ra.for.mi'ge.nes. Gr. pref. para, beside; N.L. part. adj. formigenes, formic acid producing, and specific epithet of an Oxalobacter species; N.L. part. adj. paraformigenes, meaning that this species is related to but distinct from Oxalobacter formigenes).

Cells are Gram-stain negative, rod-shaped with rounded ends typically measuring 1.6 – 2.4 × 0.8 – 1.1 μm on average (estimated from Gram stain), and occurring in singles, pairs, or sometimes in chains. Cells occasionally present as curved. Endospores not found. Flagella not detected. Anaerobic, but aerotolerant with chemotrophic metabolism. Oxalate is used a major carbon and energy source. Optimal growth is at 37°C. Indole not formed. Does not appear to reduce nitrate or sulfate. Members of O. paraformigenes can be distinguished from other species in the Oxalobacter genus based on phylogenetic analysis and overall genome relatedness indices. The genome size of the type strain is 2.49 Mb and the G+C content is 52.7%.

The type strain O. paraformigenes HOxBLST (=ATCC XXXX =DSM XXXX) was isolated from human fecal material.

The corrected section appears below:

Oxalobacter paraformigenes (pa.ra.for.mi'ge.nes. Gr. pref. para, beside; N.L. part. adj. formigenes, formic acid producing, and specific epithet of an Oxalobacter species; N.L. part. adj. paraformigenes, meaning that this species is related to but distinct from Oxalobacter formigenes).

Cells are Gram-stain negative, rod-shaped with rounded ends typically measuring 1.6 – 2.4 × 0.8 – 1.1 μm on average (estimated from Gram stain), and occurring in singles, pairs, or sometimes in chains. Cells occasionally present as curved. Endospores not found. Flagella not detected. Anaerobic, but aerotolerant with chemotrophic metabolism. Oxalate is used as a major carbon and energy source. Optimal growth is at 37°C. Indole not formed. Does not appear to reduce nitrate or sulfate. Members of O. paraformigenes can be distinguished from other species in the Oxalobacter genus based on phylogenetic analysis and overall genome relatedness indices. The genome size of the type strain is 2.49 Mb and the G+C content is 52.7%.

The type strain O. paraformigenes HOxBLST (=ATCC TSD-346=DSM 115067) was isolated from human fecal material.

The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way.

Publisher's note

All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.

References

Oren, A., Arahal, D. R., Göker, M., Moore, E. R. B., Rossello-Mora, R. and Sutcliffe, I. C. (2023). International Code of Nomenclature of Prokaryotes. Prokaryotic Code (2022 revision). Int J Syst Evol Microbiol. doi: 10.5281/zenodo.7770135 [Epubh ahead of print].

PubMed Abstract | CrossRef Full Text | Google Scholar

Keywords: oxalate degradation, Oxalobacter formigenes, kidney stone disease, gut microbiome, revised taxonomy, phylogenomic and comparative genomic analyses, nephrolithiasis, hyperoxaluria

Citation: Chmiel 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 and Burton JP (2023) Corrigendum: New perspectives on an old grouping: the genomic and phenotypic variability of Oxalobacter formigenes and the implications for calcium oxalate stone prevention. Front. Microbiol. 14:1231746. doi: 10.3389/fmicb.2023.1231746

Received: 30 May 2023; Accepted: 31 May 2023;
Published: 12 June 2023.

Approved by:

Frontiers Editorial Office, Frontiers Media SA, Switzerland

Copyright © 2023 Chmiel, Carr, Stuivenberg, Venema, Chanyi, Al, Giguere, Say, Akouris, Domínguez Romero, Kwong, Tai, Koval, Razvi, Bjazevic and Burton. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

*Correspondence: Jeremy P. Burton, Jeremy.Burton@LawsonResearch.com

Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.