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Phylogenomic and molecular markers based studies on Staphylococcaceae and Gemella species. Proposals for an emended family Staphylococcaceae and three new families (Abyssicoccaceae fam. nov., Salinicoccaceae fam. nov. and Gemellaceae fam. nov.) harboring four new genera, Lacicoccus gen. nov., Macrococcoides gen. nov., Gemelliphila gen. nov., and Phocicoccus gen. nov.

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Abstract

The family Staphylococcacae and genus Gemella contain several organisms of clinical or biotechnological importance. We report here comprehensive phylogenomic and comparative analyses on 112 available genomes from species in these taxa to clarify their evolutionary relationships and classification. In a phylogenomic tree based on 678 core proteins, Gemella species were separated from Staphylococcacae by a long branch indicating that they constitute a distinct family (Gemellaceae fam. nov.). In this tree, Staphylococcacae species formed two main clades, one encompassing the genera Aliicoccus, Jeotgalicoccus, Nosocomiicoccus and Salinicoccus (Family “Salinicoccaceae”), while the other clade consisted of the genera Macrococcus, Mammaliicoccus and Staphylococcus (Family Staphylococcaceae emend.). In this tree, species from the genera Gemella, Jeotgalicoccus, Macrococcus and Salinicoccus each formed two distinct clades. Two species clades for these genera are also observed in 16S rRNA gene trees and supported by average amino acid identity analysis. We also report here detailed analyses on protein sequences from Staphylococcaceae and Gemella genomes to identify conserved signature indels (CSIs) which are specific for different genus and family-level clades. These analyses have identified 120 novel CSIs robustly demarcating different proposed families and genera. The identified CSIs provide independent evidence that the genera Gemella, Jeotgalicoccus, Macrococcus and Salinicoccus consist of two distinct clades, which can be reliably distinguished based on multiple exclusively shared CSIs. We are proposing transfers of the species from the novel clades of the above four genera into the genera Gemelliphila gen. nov., Phocicoccus gen. nov., Macrococcoides gen. nov. and Lacicoccus gen. nov., respectively. The identified CSIs also provide strong evidence for division of Staphylococcaceae into an emended family Staphylococcaceae and two new families, Abyssicoccaceae fam. nov. and Salinicoccaceae fam. nov. All of these families can be reliably demarcated based on several exclusively shared CSIs.

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Abbreviations

AAI:

Average amino acid identity

aa:

Amino acid

MSA:

Multiple sequence alignment

CSI:

Conserved signature indel (insert or deletion)

GTDB:

Genome taxonomy database

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Acknowledgements

We are grateful to Dr Aharon Oren for checking and making useful suggestions regarding the etymology and protologues for the names of new genera proposed here. We also thank Dr. Iain Sutcliffe for many useful suggestions for the improvement of this manuscript.

Funding

This work was supported by a research grant from the Natural Science and Engineering Research Council of Canada to Dr. Radhey S. Gupta, and an ORF grant from the Ontario Ministry of Research Innovation and Science.

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  1. Sarah Bello, Syed Huzaifa Mudassir and Bashudev Rudra have contributed equally to the work and their names are shown in alphabetical order.

Authors and Affiliations

  1. Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada

    Sarah Bello, Syed Huzaifa Mudassir, Bashudev Rudra & Radhey S. Gupta

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  1. Sarah Bello
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  2. Syed Huzaifa Mudassir
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  4. Radhey S. Gupta
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SB, SM, and RB were responsible for carrying out data analysis and in the preparation and revision of the manuscript. RSG conceptualized and supervised all of the work, obtained funding, checked the accuracy and interpretation of the data, and edited and finalized the manuscript

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Correspondence to Radhey S. Gupta.

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Bello, S., Mudassir, S.H., Rudra, B. et al. Phylogenomic and molecular markers based studies on Staphylococcaceae and Gemella species. Proposals for an emended family Staphylococcaceae and three new families (Abyssicoccaceae fam. nov., Salinicoccaceae fam. nov. and Gemellaceae fam. nov.) harboring four new genera, Lacicoccus gen. nov., Macrococcoides gen. nov., Gemelliphila gen. nov., and Phocicoccus gen. nov.. Antonie van Leeuwenhoek 116, 937–973 (2023). https://doi.org/10.1007/s10482-023-01857-6

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  • DOI: https://doi.org/10.1007/s10482-023-01857-6

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