Prevotella mikamonis sp. nov., isolated from equine clinical specimens

References

1. Shah HN, Collins DM. Prevotella, a new genus to include Bacteroides melaninogenicus and related species formerly classified in the genus Bacteroides. Int J Syst Bacteriol 1990; 40:205–208 [View Article] [PubMed]
   [Google Scholar]
2. Mehmood M, Jaffar NA, Nazim M, Khasawneh FA. Bacteremic skin and soft tissue infection caused by Prevotella loescheii. BMC Infect Dis 2014; 14:162 [View Article] [PubMed]
   [Google Scholar]
3. Le Moal G, Landron C, Grollier G, Bataille B, Roblot F et al. Characteristics of brain abscess with isolation of anaerobic bacteria. Scand J Infect Dis 2003; 35:318–321 [View Article] [PubMed]
   [Google Scholar]
4. Könönen E, Gursoy UK. Oral Prevotella species and their connection to events of clinical relevance in gastrointestinal and respiratory tracts. Front Microbiol 2021; 12:798763 [View Article] [PubMed]
   [Google Scholar]
5. Kinoshita Y, Niwa H, Katayama Y, Hariu K. Dominant obligate anaerobes revealed in lower respiratory tract infection in horses by 16S rRNA gene sequencing. J Vet Med Sci 2014; 76:587–591 [View Article] [PubMed]
   [Google Scholar]
6. Occhiogrosso L, Capozza P, Buonavoglia A, Decaro N, Trotta A et al. Bacterial periodontitis in horses: an epidemiological study in southern Italy. Animals 2023; 13:1814 [View Article] [PubMed]
   [Google Scholar]
7. Afouda P, Ndongo S, Khelaifia S, Labas N, Cadoret F et al. Noncontiguous finished genome sequence and description of Prevotella phocaeensis sp. nov., a new anaerobic species isolated from human gut infected by Clostridium difficile. New Microbes New Infect 2017; 15:117–127 [View Article] [PubMed]
   [Google Scholar]
8. Maaloum M, Afouda P, Lo CI, Dubourg G, Nguyen TT et al. Prevotella merdae sp. nov., a new bacterial species isolated from human faeces. FEMS Microbiol Lett 2022; 369:fnac001 [View Article]
   [Google Scholar]
9. Willems A, Collins MD. 16S rRNA gene similarities indicate that Hallella seregens (Moore and Moore) and Mitsuokella dentalis (Haapsalo et al.) are genealogically highly related and are members of the genus Prevotella: emended description of the genus Prevotella (Shah and Collins) and description of Prevotella dentalis comb. nov. Int J Syst Bacteriol 1995; 45:832–836 [View Article] [PubMed]
   [Google Scholar]
10. Grabner E, Stare E, Fanedl L, Zorec M, Jones DS et al. Expanding the rumen Prevotella collection: the description of Prevotella communis, sp. nov. of ovine origin. Syst Appl Microbiol 2023; 46:126437 [View Article] [PubMed]
    [Google Scholar]
11. Hutter G, Schlagenhauf U, Valenza G, Horn M, Burgemeister S et al. Molecular analysis of bacteria in periodontitis: evaluation of clone libraries, novel phylotypes and putative pathogens. Microbiology 2003; 149:67–75 [View Article] [PubMed]
    [Google Scholar]
12. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article] [PubMed]
    [Google Scholar]
13. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
    [Google Scholar]
14. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
15. Ko KS, Kuwahara T, Haehwa L, Yoon Y-J, Kim B-J et al. RNA polymerase beta-subunit gene (rpoB) sequence analysis for the identification of Bacteroides spp. Clin Microbiol Infect 2007; 13:48–54 [View Article] [PubMed]
    [Google Scholar]
16. Stackebrandt E, Goebel BM. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 1994; 44:846–849 [View Article]
    [Google Scholar]
17. Seng P, Drancourt M, Gouriet F, La Scola B, Fournier P-E et al. Ongoing revolution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Clin Infect Dis 2009; 49:543–551 [View Article] [PubMed]
    [Google Scholar]
18. Bizzini A, Greub G. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry, a revolution in clinical microbial identification. Clin Microbiol Infect 2010; 16:1614–1619 [View Article] [PubMed]
    [Google Scholar]
19. Vu H, Muto Y, Hayashi M, Noguchi H, Tanaka K et al. Complete genome sequences of three Phocaeicola vulgatus strains isolated from a healthy Japanese individual. Microbiol Resour Announc 2022; 11:e0112421 [View Article] [PubMed]
    [Google Scholar]
20. Hayashi M, Yonetamari J, Muto Y, Tanaka K. Complete genome sequence of Peptostreptococcus porci isolated from porcine endocarditis in Japan. Microbiol Resour Announc 2024; 13:e0020124 [View Article] [PubMed]
    [Google Scholar]
21. De Coster W, D’Hert S, Schultz DT, Cruts M, Van Broeckhoven C. NanoPack: visualizing and processing long-read sequencing data. Bioinformatics 2018; 34:2666–2669 [View Article] [PubMed]
    [Google Scholar]
22. Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 2018; 34:i884–i890 [View Article] [PubMed]
    [Google Scholar]
23. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article] [PubMed]
    [Google Scholar]
24. Wick RR, Schultz MB, Zobel J, Holt KE. Bandage: interactive visualization of de novo genome assemblies. Bioinformatics 2015; 31:3350–3352 [View Article] [PubMed]
    [Google Scholar]
25. Laetsch DR, Blaxter ML. BlobTools: interrogation of genome assemblies. F1000Res 2017; 6:1287 [View Article]
    [Google Scholar]
26. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article]
    [Google Scholar]
27. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article] [PubMed]
    [Google Scholar]
28. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 2005; 102:2567–2572 [View Article]
    [Google Scholar]
29. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article]
    [Google Scholar]
30. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article]
    [Google Scholar]
31. Pritchard L, Glover RH, Humphris S, Elphinstone JG, Toth IK. Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens. Anal Methods 2016; 8:12–24 [View Article]
    [Google Scholar]
32. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article] [PubMed]
    [Google Scholar]