1,081
Views
0
CrossRef citations to date
0
Altmetric
Original Article

Site-specialization of human oral Gemella species

ORCID Icon, ORCID Icon, ORCID Icon & ORCID Icon
Article: 2225261 | Received 21 May 2021, Accepted 08 Jun 2023, Published online: 22 Jun 2023

References

  • Dewhirst FE, Chen T, Izard J, et al. The human oral microbiome. J Bacteriol. 2010;192(19):5002–15. doi: 10.1128/JB.00542-10
  • Collins MD, Hutson RA, Falsen E, et al. Description of Gemella sanguinis sp. nov., isolated from human clinical specimens. J Clin Microbiol. 1998;36(10):3090–3093. doi: 10.1128/JCM.36.10.3090-3093.1998
  • Collins MD, Hutson RA, Falsen E, et al. Gemella bergeriae sp. nov., isolated from human clinical specimens. J Clin Microbiol. 1998;36(5):1290–1293. doi: 10.1128/JCM.36.5.1290-1293.1998
  • Stackebrandt E, Wittek B, Seewaldt E, et al. Physiological, biochemical and phylogenetic studies on Gemella haemolysans. FEMS Microbiol Lett. 1982;13(4):361–365. doi: 10.1111/j.1574-6968.1982.tb08288.x
  • Kilpper-Balz R, Schleifer KH. Transfer of streptococcus morbillorum to the genus gemella as Gemella morbillorum comb. nov. Int J Syst Bacteriol. 1988;38(4):442–443. doi: 10.1099/00207713-38-4-442
  • Thjotta T, Boe J. Neisseria haemolysans. A haemolytic species of Neisseria trevisan. Acta Path Microbiol Scand. 1938;37:527–531.
  • Berger U. A proposed new genus of gram-negative cocci: gemella. Int Bull Bacteriol Nomencl Taxon. 1961;11(1):17–19. doi: 10.1099/0096266X-11-1-17
  • Ruoff KL. Miscellaneous catalase-negative, Gram-positive cocci: emerging opportunists. J Clin Microbiol. 2002;40(4):1129–1133. doi: 10.1128/JCM.40.4.1129-1133.2002
  • Chen T, Yu WH, Izard J, et al. The human oral microbiome database: a web accessible resource for investigating oral microbe taxonomic and genomic information. Database (Oxford). 2010;2010:1–10. doi: 10.1093/database/baq013
  • Escapa IF, Chen T, Huang Y, et al. New insights into human nostril microbiome from the expanded human oral microbiome database (eHOMD): a resource for the microbiome of the human aerodigestive tract. Msystems. 2018;3(6):1–20.9. doi: 10.1128/mSystems.00187-18
  • Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, et al. List of prokaryotic names with standing in nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol. 2020;70(11):5607–5612. doi: 10.1099/ijsem.0.004332.
  • Hoyles L, Foster G, Falsen E, et al. Characterization of a Gemella-like organism isolated from an abscess of a rabbit: description of Gemella cuniculi sp. nov. Int J Syst Evol Microbiol. 2000;50:2037–2041. doi: 10.1099/00207713-50-6-2037
  • Ulger-Toprak N, Summanen PH, Liu C, et al. Gemella asaccharolytica sp. nov., isolated from human clinical specimens. Int J Syst Evol Microbiol. 2010;60(5):1023–1026. doi: 10.1099/ijs.0.001966-0
  • Hung WC, Chen HJ, Tsai JC, et al. Gemella parahaemolysans sp. nov. and Gemella taiwanensis sp. nov., isolated from human clinical specimens. Int J Syst Evol Microbiol. 2014;64(Pt_6):2060–2065. doi: 10.1099/ijs.0.052795-0
  • Fonkou MD, Bilen M, Cadoret F, et al. Gemella massiliensis’ sp. nov., new bacterial species isolated from the human respiratory microbiome. New Microbe And New Infect. 2017;22:37–43. doi: 10.1016/j.nmni.2017.12.005
  • Mark Welch JL, Dewhirst FE, Borisy GG. Biogeography of the oral microbiome: the site-specialist hypothesis. Annu Rev Microbiol. 2019;73(1):335–358. doi: 10.1146/annurev-micro-090817-062503
  • Eren AM, Borisy GG, Huse SM, et al. Oligotyping analysis of the human oral microbiome. Proc Natl Acad Sci, USA. 2014;111(28):E2875–84. doi: 10.1073/pnas.1409644111
  • Socransky SS, Manganiello SD. The oral microbiota of man from birth to senility. J Periodontol. 1971;42(8):485–496. doi: 10.1902/jop.1971.42.8.485
  • Tettelin H, Masignani V, Cieslewicz MJ, et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome”. Proc Natl Acad Sci, USA. 2005;102(39):13950–13955.doi: 10.1073/pnas.0506758102
  • Vernikos G, Medini D, Riley DR, et al. Ten Years of pan-genome analyses. Curr Opin Microbiol. 2015;23:148–154. doi: 10.1016/j.mib.2014.11.016
  • Handelsman J. Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev. 2004;68(4):669–685. doi: 10.1128/MMBR.68.4.669-685.2004
  • Quince C, Walker AW, Simpson JT, et al. Shotgun metagenomics, from sampling to analysis. Nature Biotechnol. 2017;35(9):833–844. doi: 10.1038/nbt.3935
  • Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486(7402): 207–214. doi: 10.1038/nature11234
  • Delmont TO, Eren AM. Linking pangenomes and metagenomes: the prochlorococcus metapangenome. PeerJ. 2018;6:e4320. doi: 10.7717/peerj.4320
  • Nayfach S, Rodriguez-Mueller B, Garud N, et al. An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography. Genome Res. 2016;26(11):1612–1625. doi: 10.1101/gr.201863.115
  • Kraal L, Abubucker S, Kota K, et al. The prevalence of species and strains in the human microbiome: a resource for experimental efforts. PLoS ONE. 2014;9(5):e97279. doi: 10.1371/journal.pone.0097279
  • Lloyd-Price J, Mahurkar A, Rahnavard G, et al. Strains, functions and dynamics in the expanded human microbiome project. Nature. 2017;550(7674):61. doi: 10.1038/nature23889
  • Truong DT, Tett A, Pasolli E, et al. Microbial strain-level population structure and genetic diversity from metagenomes. Genome Res. 2017;27(4):626–638. doi: 10.1101/gr.216242.116
  • Donati C, Zolfo M, Albanese D, et al. Uncovering oral Neisseria tropism and persistence using metagenomic sequencing. Nat Microbiol. 2016;1(7):16070. doi: 10.1038/nmicrobiol.2016.70
  • Shaiber A, Willis AD, Delmont TO, et al. Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome. 2020. Genome Biol. 2020;21(1):292. doi: 10.1186/s13059-020-02195-w
  • Utter DR, Borisy GG, Eren AM, et al. Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity. Genome Bio. 2020;21(1):293. doi: 10.1186/s13059-020-02200-2
  • Eren AM, Öc E, Quince C, et al. Anvi’o: an advanced analysis and visualization platform for ‘Omics Data. Peer J. 2015;3:e1319. doi: 10.7717/peerj.1319
  • Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci, USA. 2005;102(7):2567–2572. doi: 10.1073/pnas.0409727102
  • Kim M, Oh HS, Park SC, et al. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol. 2014;64(Pt_2):346–351. doi: 10.1099/ijs.0.059774-0
  • García López E, Martín-Galiano AJ. The versatility of opportunistic infections caused by gemella isolates is supported by the carriage of virulence factors from multiple origins. Front Microbiol. 2020;11(March):1–16. doi: 10.3389/fmicb.2020.00524
  • Nguyen L-T, Schmidt HA, von Haeseler A, et al. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. Mol Biol Evol. 2015;32:268–274. doi: 10.1093/molbev/msu300
  • Reyn A, Birch-Andersen A, Berger U. Fine structure and taxonomic position of Neisseria haemolysans (Thjotta and Boe 1938) or Gemella haemolysans (Berger 1960). Acta Pathol Microbiol Scand B Microbiol Immunol. 1970;78(3):375–389. doi: 10.1111/j.1699-0463.1970.tb04317.x
  • Olm MR, Crits-Christoph A, Bouma-Gregson K, et al. In Strain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains. Nature Biotechnol. 2021;39(6):727–736. doi: 10.1038/s41587-020-00797-0
  • Bacher A, Eberhardt S, Fischer M, et al. Biosynthesis of vitamin b2 (riboflavin). Annu Rev Nutr. 2000;20:153–167. doi: 10.1146/annurev.nutr.20.1.153
  • Rodionov DA, Arzamasov AA, Koroshkin MS, et al. Micronutrient requirements and sharing capabilities of the human gut microbiome. Front Microbiol. 2019;10. doi: 10.3389/fmicb.2019.01316
  • Sideris AC, Zimmermann E, Ogami T, et al. A rare case of isolated mitral valve endocarditis by Gemella sanguinis: case report and review of the literature. Int J Surg Case Rep. 2020 [Epub 2020 Mar 7];69:51–54.
  • Agrawal T, Irani M, Fuentes Rojas S, et al. A rare case of infective endocarditis caused by Gemella haemolysans. Cureus. 2019 Nov 26;11(11):e6234. doi: 10.7759/cureus.6234
  • Shahani L. Gemella morbillorum prosthetic aortic valve endocarditis.BMJ Case Rep. 2014 [Nov 18; 2014];2014(nov18 1):bcr2014207304. doi: 10.1136/bcr-2014-207304
  • García-Angulo VA. Overlapping riboflavin supply pathways in bacteria. Crit Rev Microbiol. 2017;43(2):196–209. doi: 10.1080/1040841X.2016.1192578
  • Vitreschak AG, Rodionov DA, Mironov AA, et al. Evidence for an ABC-type riboflavin transporter system in pathogenic spirochetes. Nucleic Acid Research. 2002;30(14):3141–3151. doi: 10.1093/nar/gkf433
  • Takenouchi-Ohkubu N, Mortensen LM, Drasbek KR, et al. Horizontal transfer of the immunoglobulin A1 protease gene (iga) from Streptococcus to Gemella haemolysans. Microbiology. 2006;152(7):2171–2180. doi: 10.1099/mic.0.28801-0
  • Hyatt D, Chen GL, LoCascio PF, et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinf. 2010;11:119. doi: 10.1186/1471-2105-11-119
  • Lee MD, Ponty Y. GToTree: a user-friendly workflow for phylogenomics. Bioinformatics. 2019 Oct 15;35(20):4162–4164.
  • Hug LA, Baker BJ, Anantharaman K, et al. A new view of the tree of life. Nat Microbiol. 2016 Apr 11;1(5):16048.
  • Seemann T. https://github.com/tseemann/barrnap/blob/master/README.md#barrnap
  • Galperin MY, Wolf YI, Makarova KS, et al. COG database update: focus on microbial diversity, model organisms, and widespread pathogens. Nucleic Acids Res. 2021 [2021 Jan 8];49(D1):D274–D281. doi: 10.1093/nar/gkaa1018
  • Mistry J, Chuguransky S, Williams L, et al. Pfam: the protein families database in 2021. Nucleic Acids Res. 2020;49(D1). doi: 10.1093/nar/gkaa913
  • Kanehisa M, Goto S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 2000;28:27–30. doi: 10.1093/nar/28.1.27
  • Kanehisa M. Toward understanding the origin and evolution of cellular organisms. Protein Sci. 2019;28:1947–1951. doi: 10.1002/pro.3715
  • Kanehisa M, Furumichi M, Sato Y, et al. KEGG: integrating viruses and cellular organisms. Nucleic Acids Res. 2021;49:D545–D551. doi: 10.1093/nar/gkaa970
  • Camacho C, Coulouris G, Avagyan V, et al. BLAST+: architecture and applications. BMC Bioinf. 2009;10:421. doi: 10.1186/1471-2105-10-421
  • Enright AJ, Van Dongen S, Ouzounis CA. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 2002 1 April 2002;30(7):1575–1584. 10.1093/nar/30.7.1575
  • Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinf. 2004;5:113. doi: 10.1186/1471-2105-5-113
  • Pritchard L, Glover RH, Humphris S, et al. Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens. Anal Methods. 2016;8:12–24. doi: 10.1039/C5AY02550H
  • Kalyaanamoorthy S, Minh BQ, Wong TKF, et al. ModelFinder: fast model selection for accurate phylogenetic estimates. Nature Methods. 2017;14(6):587–589. doi: 10.1038/nmeth.4285
  • Rambaut A. https://github.com/rambaut/figtree
  • IGS. https://github.com/IGS/portal_client
  • Entrez Programming Utilities Help [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2010. https://www.ncbi.nlm.nih.gov/books/NBK25501/
  • Minoche AE, Dohm JC, Himmelbauer H. Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and genome analyzer systems. Genome Biol. 2011;12(11):R112. doi: 10.1186/gb-2011-12-11-r112
  • Eren AM, Vineis JH, Morrison HG, et al. A Filtering Method to Generate High Quality Short Reads Using Illumina Paired-End Technology. PLoS ONE. 2013;8(6):e66643.
  • Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. 2012. Nature Methods. 2012;9(4):357–359. doi: 10.1038/nmeth.1923
  • Danecek BP, Liddle J, Marshall J, et al. Twelve years of SAMtools and BCFtools. Gigascience. 2021 February;10(2):giab008. doi: 10.1093/gigascience/giab008