Bifidobacterium apis sp. nov., isolated from the gut of honeybee (Apis mellifera)

References

1. Li TT, Liu DD, Fu ML, Gu CT. Proposal of Lactobacillus kosoi Chiou et al. 2018 as a later heterotypic synonym of Lactobacillus micheneri Mcfrederick et al. 2018, elevation of Lactobacillus plantarum subsp, argentoratensis to the species level as Lactobacillus argentoratensis sp. nov., and Lactobacillus zhaodongensis sp. nov., isolated from traditional Chinese pickle and the intestinal tract of a honey bee (Apis mellifera). Int J Syst Evol Microbiol 2020; 70:3123–3133
   [Google Scholar]
2. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article] [PubMed]
   [Google Scholar]
3. Kishino H, Hasegawa M. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J Mol Evol 1989; 29:170–179 [View Article] [PubMed]
   [Google Scholar]
4. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article] [PubMed]
   [Google Scholar]
5. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article] [PubMed]
   [Google Scholar]
6. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genom 2008; 9:75 [View Article] [PubMed]
   [Google Scholar]
7. 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] [PubMed]
   [Google Scholar]
8. Alanjary M, Steinke K, Ziemert N. AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential. Nucleic Acids Res 2019; 47:W276–W282 [View Article] [PubMed]
   [Google Scholar]
9. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article] [PubMed]
   [Google Scholar]
10. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article] [PubMed]
    [Google Scholar]
11. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article] [PubMed]
    [Google Scholar]
12. 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]
13. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article] [PubMed]
    [Google Scholar]
14. Ventura M, Canchaya C, Casale AD, Dellaglio F, Neviani E et al. Analysis of bifidobacterial evolution using a multilocus approach. Int J Syst Evol Microbiol 2006; 56:2783–2792 [View Article] [PubMed]
    [Google Scholar]
15. Neuzil-Bunesova V, Lugli GA, Modrackova N, Makovska M, Mrazek J et al. Bifidobacterium canis sp. nov., a novel member of the Bifidobacterium pseudolongum phylogenetic group isolated from faeces of a dog (Canis lupus f. familiaris). Int J Syst Evol Microbiol 2020; 70:5040–5047 [View Article]
    [Google Scholar]
16. Ventura M, Zink R. Comparative sequence analysis of the tuf and recA genes and restriction fragment length polymorphism of the internal transcribed spacer region sequences supply additional tools for discriminating Bifidobacterium lactis from Bifidobacterium animalis. Appl Environ Microbiol 2003; 69:7517–7522 [View Article] [PubMed]
    [Google Scholar]
17. Ventura M, Zink R, Fitzgerald GF, van Sinderen D. Gene structure and transcriptional organization of the dnaK operon of Bifidobacterium breve UCC 2003 and application of the operon in bifidobacterial tracing. Appl Environ Microbiol 2005; 71:487–500 [View Article] [PubMed]
    [Google Scholar]
18. Mekadim C, Bunešová V, Vlková E, Hroncová Z, Killer J. Genetic marker-based multi-locus sequence analysis for classification, genotyping, and phylogenetics of the family Bifidobacteriaceae as an alternative approach to phylogenomics. Antonie van Leeuwenhoek 2019; 112:1785–1800 [View Article] [PubMed]
    [Google Scholar]
19. Killer J, Mekadim C, Pechar R, Bunešová V, Vlková E. The threonine-tRNA ligase gene region is applicable in classification, typing, and phylogenetic analysis of bifidobacteria. J Microbiol 2018; 56:713–721 [View Article] [PubMed]
    [Google Scholar]
20. Killer J, Mekadim C, Bunešová V, Mrázek J, Hroncová Z et al. Glutamine synthetase type I (glnAI) represents a rewarding molecular marker in the classification of bifidobacteria and related genera. Folia Microbiol 2020; 65:143–151 [View Article]
    [Google Scholar]
21. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101 Newark, DE, USA: Microbial ID Inc; 1990
    [Google Scholar]
22. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
    [Google Scholar]
23. Modesto M, Checcucci A, Mattarelli P. Identification of bifidobacteria by the Phosphoketolase assay. Methods Mol Biol 2021; 2278:141–148 [View Article] [PubMed]
    [Google Scholar]