Abstract
We present genomic, phylogenomic, and phenotypic taxonomic data to demonstrate that three human ear isolates represent a novel species within the genus Gulosibacter. These isolates could not be identified reliably using MALDI-TOF mass spectrometry during routine diagnostic work, but partial 16S rRNA gene sequence analysis revealed that they belonged to the genus Gulosibacter. Overall genomic relatedness indices between the draft genome sequences of the three isolates and of the type strains of established Gulosibacter species confirmed that the three isolates represented a single novel Gulosibacter species. A biochemical characterisation yielded differential tests between the novel and established Gulosibacter species, which could also be differentiated using MALDI-TOF mass spectrometry. We propose to formally classify these three isolates into Gulosibacter hominis sp. nov., with 401352-2018 T (= LMG 31778 T, CCUG 74795 T) as the type strain. The whole-genome sequence of strain 401352-2018 T has a size of 2,340,181 bp and a G+C content of 62.04 mol%. A Gulosibacter pangenome analysis revealed 467 gene clusters that were exclusively present in G. hominis genomes. While these G. hominis specific gene clusters were enriched in several COG functional categories, this analysis did not reveal functions that suggested a role in the human microbiome, nor did it explain the occurrence of G. hominis in ear infections. The absence of acquired antimicrobial resistance determinants and virulence factors in the G. hominis genomes, and an analysis of publicly available 16S rRNA gene sequences and 16S rRNA amplicon sequencing data sets suggested that G. hominis is a member of the human skin microbiota that may occasionally be involved in opportunistic infections.
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Sequence data have been made public and the type strain was deposited into two culture collections.
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Acknowledgements
We thank Annegreth Dannacher, Clarisse Straub, Elisabeth Schultheiss, Berfin Kocyigit and Aline Cuénod for excellent technical assistance at University Hospital Basel.
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Conceptualization: PV, CP, DG; data curation: CP; formal analysis: PV, MC, CP, HSS; funding acquisition: PV; investigation: MC, CP, DG, GL; methodology: PV, CP, DG; project administration; MC, CP; software: CP, HSS; supervision: PV, DG, AE; writing – original draft: PV, DG; writing – review & editing: MC, CP, HSS, AE.
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Vandamme, P., Peeters, C., Seth-Smith, H.M.B. et al. Gulosibacter hominis sp. nov.: a novel human microbiome bacterium that may cause opportunistic infections. Antonie van Leeuwenhoek 114, 1841–1854 (2021). https://doi.org/10.1007/s10482-021-01644-1
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DOI: https://doi.org/10.1007/s10482-021-01644-1