Front. Microbiol. Frontiers in Microbiology Front. Microbiol. 1664-302X Frontiers Media S.A. 10.3389/fmicb.2023.1231746 Microbiology Correction Corrigendum: New perspectives on an old grouping: the genomic and phenotypic variability of Oxalobacter formigenes and the implications for calcium oxalate stone prevention Chmiel John A. 1 2 Carr Charles 3 Stuivenberg Gerrit A. 1 2 Venema Robertson 4 Chanyi Ryan M. 5 Al Kait F. 1 2 Giguere Daniel 6 Say Henry 6 Akouris Polycronis P. 1 2 Domínguez Romero Sergio Ari 6 Kwong Aaron 7 Tai Vera 6 Koval Susan F. 1 Razvi Hassan 8 Bjazevic Jennifer 8 Burton Jeremy P. 1 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

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 *Correspondence: Jeremy P. Burton Jeremy.Burton@LawsonResearch.com 12 06 2023 2023 14 1231746 30 05 2023 31 05 2023 Copyright © 2023 Chmiel, Carr, Stuivenberg, Venema, Chanyi, Al, Giguere, Say, Akouris, Domínguez Romero, Kwong, Tai, Koval, Razvi, Bjazevic and Burton. 2023 Chmiel, Carr, Stuivenberg, Venema, Chanyi, Al, Giguere, Say, Akouris, Domínguez Romero, Kwong, Tai, Koval, Razvi, Bjazevic and Burton

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 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 oxalate degradation Oxalobacter formigenes kidney stone disease gut microbiome revised taxonomy phylogenomic and comparative genomic analyses nephrolithiasis hyperoxaluria section-at-acceptance Evolutionary and Genomic Microbiology

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.

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 References Oren A. Arahal D. R. Göker M. Moore E. R. B. Rossello-Mora R. Sutcliffe I. C. (2023). International Code of Nomenclature of Prokaryotes. Prokaryotic Code (2022 revision). Int J Syst Evol Microbiol. 10.5281/zenodo.777013537219928 [Epubh ahead of print].