Latilactobacillus fragifolii sp. nov., isolated from leaves of a strawberry plant (Fragaria x ananassa)

References

1. Zheng J, Wittouck S, Salvetti E, Franz CMAP, Harris HMB et al. A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae . Int J Syst Evol Microbiol 2020; 70:2782–2858 [View Article] [PubMed]
   [Google Scholar]
2. Duar RM, Lin XB, Zheng J, Martino ME, Grenier T et al. Lifestyles in transition: evolution and natural history of the genus Lactobacillus . FEMS Microbiol Rev 2017; 41:S27–S48 [View Article] [PubMed]
   [Google Scholar]
3. Vorholt JA. Microbial life in the phyllosphere. Nat Rev Microbiol 2012; 10:828–840 [View Article] [PubMed]
   [Google Scholar]
4. Miller ER, Kearns PJ, Niccum BA, O’Mara Schwartz J, Ornstein A et al. Establishment limitation constrains the abundance of lactic acid bacteria in the napa cabbage phyllosphere. Appl Environ Microbiol 2019; 85:e00269-19 [View Article] [PubMed]
   [Google Scholar]
5. Pontonio E, Di Cagno R, Tarraf W, Filannino P, De Mastro G et al. Dynamic and assembly of epiphyte and endophyte lactic acid bacteria during the life cycle of Origanum vulgare L. Front Microbiol 2018; 9:1372 [View Article] [PubMed]
   [Google Scholar]
6. Vokou D, Vareli K, Zarali E, Karamanoli K, Constantinidou H-IA et al. Exploring biodiversity in the bacterial community of the Mediterranean phyllosphere and its relationship with airborne bacteria. Microb Ecol 2012; 64:714–724 [View Article] [PubMed]
   [Google Scholar]
7. Lamont JR, Wilkins O, Bywater-Ekegärd M, Smith DL. From yogurt to yield: Potential applications of lactic acid bacteria in plant production. Soil Biol Biochem 2017; 111:1–9 [View Article]
   [Google Scholar]
8. Redford AJ, Fierer N. Bacterial succession on the leaf surface: a novel system for studying successional dynamics. Microb Ecol 2009; 58:189–198 [View Article] [PubMed]
   [Google Scholar]
9. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article] [PubMed]
   [Google Scholar]
10. Naser SM, Dawyndt P, Hoste B, Gevers D, Vandemeulebroecke K et al. Identification of lactobacilli by pheS and rpoA gene sequence analyses. Int J Syst Evol Microbiol 2007; 57:2777–2789 [View Article] [PubMed]
    [Google Scholar]
11. Mattarelli P, Holzapfel W, Franz CMAP, Endo A, Felis GE et al. Recommended minimal standards for description of new taxa of the genera Bifidobacterium, Lactobacillus and related genera. Int J Syst Evol Microbiol 2014; 64:1434–1451 [View Article] [PubMed]
    [Google Scholar]
12. Alimolaei M, Golchin M. An efficientEfficient DNA extraction method foExtraction Method for Lactobacillus casei, a difficult-to-lyse bacteriumDifficult-to-Lyse Bacterium. Int J Enteric Pathog 2016; 4:e32472 [View Article]
    [Google Scholar]
13. Nurk S, Bankevich A, Antipov D, Gurevich A, Korobeynikov A et al. Assembling genomes and mini-metagenomes from highly chimeric reads. Lect Notes Comput Sci 2013; 7821:158–170 [View Article]
    [Google Scholar]
14. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
    [Google Scholar]
15. Wittouck S, Wuyts S, Meehan CJ, van Noort V, Lebeer S. A genome-based species taxonomy of the Lactobacillus genus complex. mSystems 2019; 4:e00264-19 [View Article] [PubMed]
    [Google Scholar]
16. Wittouck S, Wuyts S, Meehan CJ, van Noort V, Lebeer S. A genome-based species taxonomy of the Lactobacillus genus complex. mSystems 2019; 4:e00264-19 [View Article] [PubMed]
    [Google Scholar]
17. 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; 14:141 [View Article] [PubMed]
    [Google Scholar]
18. Parks DH, Chuvochina M, Chaumeil P-A, Rinke C, Mussig AJ et al. A complete domain-to-species taxonomy for Bacteria and Archaea. Nat Biotechnol 2020; 38:1079–1086 [View Article] [PubMed]
    [Google Scholar]
19. Wood BJB, Holzapfel WH. The Genera of Lactic Acid Bacteria Berlin: Springer; 2020
    [Google Scholar]
20. Zotta T, Ricciardi A, Ianniello RG, Parente E, Reale A et al. Assessment of aerobic and respiratory growth in the Lactobacillus casei group. PLoS One 2014; 9:e99189 [View Article] [PubMed]
    [Google Scholar]
21. Wuyts S, Wittouck S, De Boeck I, Allonsius CN, Pasolli E et al. Large-Scale phylogenomics of the Lactobacillus casei group highlights taxonomic inconsistencies and reveals novel clade-associated features. mSystems 2017; 2:e00061-17 [View Article] [PubMed]
    [Google Scholar]
22. Abriouel H, Herrmann A, Stärke J, Yousif NMK, Wijaya A et al. Cloning and heterologous expression of hematin-dependent catalase produced by Lactobacillus plantarum CNRZ 1228. Appl Environ Microbiol 2004; 70:603–606 [View Article] [PubMed]
    [Google Scholar]
23. Igarashi T, Kono Y, Tanaka K. Molecular cloning of manganese catalase from Lactobacillus plantarum . J Biol Chem 1996; 271:29521–29524 [View Article] [PubMed]
    [Google Scholar]
24. Knauf HJ, Vogel RF, Hammes WP. Cloning, sequence, and phenotypic expression of katA, which encodes the catalase of Lactobacillus sake LTH677. Appl Environ Microbiol 1992; 58:832–839 [View Article]
    [Google Scholar]
25. Finn RD, Clements J, Eddy SR. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 2011; 39:W29–37 [View Article] [PubMed]
    [Google Scholar]
26. Siezen RJ, Bayjanov JR, Felis GE, van der Sijde MR, Starrenburg M et al. Genome-scale diversity and niche adaptation analysis of Lactococcus lactis by comparative genome hybridization using multi-strain arrays. Microb Biotechnol 2011; 4:383–402 [View Article] [PubMed]
    [Google Scholar]
27. Kawaguchi H, Sasaki M, Vertès AA, Inui M, Yukawa H. Identification and functional analysis of the gene cluster for l-arabinose utilization in Corynebacterium glutamicum . Appl Environ Microbiol 2009; 75:3419–3429 [View Article] [PubMed]
    [Google Scholar]
28. Sasser M. Identification of bacteria by gas chromatography of cellular fatty abacteria by gas chromatography of cellular fatty acids. Tech Note 2001; 101:1–6
    [Google Scholar]
29. Seemann T. tseemann/barrnap: Bacterial ribosomal RNA predictor Github; 2021 https://github.com/tseemann/barrnap
30. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article] [PubMed]
    [Google Scholar]
31. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article] [PubMed]
    [Google Scholar]
32. Yu G, Smith DK, Zhu H, Guan Y, Lam TT et al. ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol Evol 2016; 8:28–36 [View Article]
    [Google Scholar]
33. Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:111 [View Article] [PubMed]
    [Google Scholar]
34. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 2009; 25:1972–1973 [View Article] [PubMed]
    [Google Scholar]