1887

Abstract

A novel predatory bacterium, strain LBG001, has been isolated from Reynosa, Mexico. The 16S rRNA shares approximately 97 % sequence identity with many reported strains in the genus including the type strain HD100. Phylogenetic trees based on the 16S rRNA gene and on 30 concatenated housekeeping genes or core genes showed that LBG001 is on a separate branch from the group. LBG0001 has a genome size of 3 582 323 bp with a G+C content of 43.1 mol %. The average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values with other members of the genus (<79, <72 and <17 %, respectively) qualifies the strain to represent a new species in the genus. Strain LBG001 formed visible plaques on all 10 tested Gram-negative bacterial species. The phenotypic characteristics, phylogenetic analysis and genomic taxonomic studies support the classification of the strain as representing a new species for which the name sp. nov. is proposed. The type strain is LBG001(=ATCC TSD-288 CM-CNRG 0932).

Funding
This study was supported by the:
  • Secretaría de Investigación y Posgrado, Instituto Politécnico Nacional (Award 20202202)
    • Principle Award Recipient: XianwuGuo
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005608
2022-12-14
2024-02-27
Loading full text...

Full text loading...

References

  1. Hahn MW, Schmidt J, Koll U, Rohde M, Verbarg S et al. Silvanigrella aquatica gen. nov., sp. nov., isolated from a freshwater lake, description of Silvanigrellaceae fam. nov. and Silvanigrellales ord. nov., reclassification of the order Bdellovibrionales in the class Oligoflexia, reclassification of the families Bacteriovoracaceae and Halobacteriovoraceae in the new order Bacteriovoracales ord. nov., and reclassification of the family Pseudobacteriovoracaceae in the order Oligoflexales. Int J Syst Evol Microbiol 2017; 67:2555–2568 [View Article] [PubMed]
    [Google Scholar]
  2. Pitt A, Koll U, Schmidt J, Hahn MW. Fluviispira multicolorata gen. nov., sp. nov. and Silvanigrella paludirubra sp. nov., isolated from freshwater habitats. Int J Syst Evol Microbiol 2020; 70:1630–1638 [View Article]
    [Google Scholar]
  3. Nakai R, Nishijima M, Tazato N, Handa Y, Karray F et al. Oligoflexus tunisiensis gen. nov., sp. nov., a Gram-negative, aerobic, filamentous bacterium of a novel proteobacterial lineage, and description of Oligoflexaceae fam. nov., Oligoflexales ord. nov. and Oligoflexia classis nov. Int J Syst Evol Microbiol 2014; 64:3353–3359 [View Article]
    [Google Scholar]
  4. Williams HN, Chen H. Environmental regulation of the distribution and ecology of Bdellovibrio and like organisms. Front Microbiol 2020; 11:545070 [View Article]
    [Google Scholar]
  5. Stolp H, Starr MP. Bdellovibrio bacteriovorus gen. et sp. n., a predatory, ectoparasitic, and bacteriolytic microorganism. Antonie van Leeuwenhoek 1963; 29:217–248 [View Article]
    [Google Scholar]
  6. Bratanis E, Andersson T, Lood R, Bukowska-Faniband E. Biotechnological potential of Bdellovibrio and like organisms and their secreted enzymes. Front Microbiol 2020; 11:662 [View Article]
    [Google Scholar]
  7. Pérez J, Moraleda-Muñoz A, Marcos-Torres FJ, Muñoz-Dorado J. Bacterial predation: 75 years and counting!. Environ Microbiol 2016; 18:766–779 [View Article] [PubMed]
    [Google Scholar]
  8. Waite DW, Chuvochina M, Pelikan C, Parks DH, Yilmaz P et al. Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities. Int J Syst Evol Microbiol 2020; 70:5972–6016 [View Article] [PubMed]
    [Google Scholar]
  9. Jurkevitch E. Isolation and classification of Bdellovibrio and like organisms. Curr Protoc Microbiol 2012; 7:Unit7B.1 [View Article]
    [Google Scholar]
  10. Van Essche M, Sliepen I, Loozen G, Van Eldere J, Quirynen M et al. Development and performance of a quantitative PCR for the enumeration of Bdellovibrionaceae. Environ Microbiol Rep 2009; 1:228–233 [View Article] [PubMed]
    [Google Scholar]
  11. Lambert C, Sockett RE. Laboratory maintenance of Bdellovibrio. Curr Protoc Microbiol 2008; 7:7B–2 [View Article]
    [Google Scholar]
  12. Bosi E, Donati B, Galardini M, Brunetti S, Sagot MF et al. MeDuSa: a multi-draft based scaffolder. Bioinformatics 2015; 31:2443–2451 [View Article] [PubMed]
    [Google Scholar]
  13. Davis JJ, Wattam AR, Aziz RK, Brettin T, Butler R et al. The PATRIC bioinformatics resource center: expanding data and analysis capabilities. Nucleic Acids Res 2020; 48:D606–D612 [View Article] [PubMed]
    [Google Scholar]
  14. Kim M, Oh HS, Park SC, Chun J. 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; 64:346–351 [View Article] [PubMed]
    [Google Scholar]
  15. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 2014; 12:635–645 [View Article] [PubMed]
    [Google Scholar]
  16. Meier-Kolthoff JP, Klenk HP, Göker M. Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int J Syst Evol Microbiol 2014; 64:352–356 [View Article] [PubMed]
    [Google Scholar]
  17. Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Preprints 2016 [View Article]
    [Google Scholar]
  18. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 2018; 9:1–8 [View Article] [PubMed]
    [Google Scholar]
  19. Thompson CC, Chimetto L, Edwards RA, Swings J, Stackebrandt E et al. Microbial genomic taxonomy. BMC Genomics 2013; 14:1–8 [View Article] [PubMed]
    [Google Scholar]
  20. Arndt D, Grant JR, Marcu A, Sajed T, Pon A et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res 2016; 44:W16–21 [View Article] [PubMed]
    [Google Scholar]
  21. Bertelli C, Laird MR, Williams KP. Simon Fraser University Research Computing Group Lau BY et al. IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Res 2017; 45:W30–W35 [View Article]
    [Google Scholar]
  22. Kanehisa M, Sato Y, Morishima K. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 2016; 428:726–731 [View Article] [PubMed]
    [Google Scholar]
  23. Gophna U, Charlebois RL, Doolittle WF. Ancient lateral gene transfer in the evolution of Bdellovibrio bacteriovorus. Trends Microbiol 2006; 14:64–69 [View Article]
    [Google Scholar]
  24. Pasternak Z, Pietrokovski S, Rotem O, Gophna U, Lurie-Weinberger MN et al. By their genes ye shall know them: genomic signatures of predatory bacteria. ISME J 2013; 7:756–769 [View Article] [PubMed]
    [Google Scholar]
  25. Cotter TW, Thomashow MF. Identification of a Bdellovibrio bacteriovorus genetic locus, hit, associated with the host-independent phenotype. J Bacteriol 1992; 174:6018–6024 [View Article] [PubMed]
    [Google Scholar]
  26. Seidler RJ, Starr MP. Isolation and characterization of host-independent Bdellovibrios. J Bacteriol 1969; 100:769–785 [View Article] [PubMed]
    [Google Scholar]
  27. Jurkevitch E, Minz D, Ramati B, Barel G. Prey range characterization, ribotyping, and diversity of soil and rhizosphere Bdellovibrio spp. isolated on phytopathogenic bacteria. Appl Environ Microbiol 2000; 66:2365–2371 [View Article] [PubMed]
    [Google Scholar]
  28. Schwudke D, Strauch E, Krueger M, Appel B. Taxonomic studies of predatory bdellovibrios based on 16S rRNA analysis, ribotyping and the hit locus and characterization of isolates from the gut of animals. Syst Appl Microbiol 2001; 24:385–394 [View Article] [PubMed]
    [Google Scholar]
  29. Rendulic S, Jagtap P, Rosinus A, Eppinger M, Baar C et al. A predator unmasked: life cycle of Bdellovibrio bacteriovorus from a genomic perspective. Science 2004; 303:689–692 [View Article] [PubMed]
    [Google Scholar]
  30. Duncan MC, Gillette RK, Maglasang MA, Corn EA, Tai AK et al. High-throughput analysis of gene function in the bacterial predator Bdellovibrio bacteriovorus. mBio 2019; 10:1–12 [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005608
Loading
/content/journal/ijsem/10.1099/ijsem.0.005608
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error