1887

Abstract

Four strains, SG5_A10, SGEP1_A5, SG4_D2, and SG4_A1, were isolated from the honey or homogenate of Australian stingless bee species and . Based on 16S rRNA gene phylogeny, core gene phylogenetics, whole genome analyses such as determination of amino acid identity (AAI), cAAI of conserved genes, average nucleotide identity (ANI), and digital DNA–DNA hybridization (dDDH), chemotaxonomic analyses, and the novel isolation sources and unique geography, we propose three new species and one genus with the names sp. nov. (SG5_A10 = LMG 32133 = NBRC 114991), sp. nov. (SG4_A1 = LMG 32125 = NBRC 114984), sp. nov. (SG4_D2 = LMG 32126 = NBRC 115004) and sp. nov. (SGEP1_A5 = LMG 32134 = NBRC 114992). Three out of the four strains were found to be fructophilic, where SG5_A10 and SGEP1_A5 belong to obligately fructophilic lactic acid bacteria, and SG4_D2 representing a new type denoted here as kinetically fructophilic. This study represents the first published lactic acid bacterial species associated with the unique niche of Australian stingless bees.

Funding
This study was supported by the:
  • Adelaide International Scholarship (Award N/A)
    • Principle Award Recipient: ScottA Oliphant
  • ARCTC for Innovative Wine Production (Award IC70100008)
    • Principle Award Recipient: VladimirJiranek
  • ARCTC for Innovative Wine Production (Award IC70100008)
    • Principle Award Recipient: KristaM Sumby
  • Wine Australia (Award UA 1803_2.1)
    • Principle Award Recipient: VladimirJiranek
  • Wine Australia (Award UA 1803_2.1)
    • Principle Award Recipient: JenniferGardner
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005588
2022-09-12
2022-12-01
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/72/9/ijsem005588.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.005588&mimeType=html&fmt=ahah

References

  1. Gerez CL, Torres MJ, Font de Valdez G, Rollán G. Control of spoilage fungi by lactic acid bacteria. Biol Control 2013; 64:231–237 [View Article]
    [Google Scholar]
  2. Kwong WK, Moran NA. Gut microbial communities of social bees. Nat Rev Microbiol 2016; 14:374–384 [View Article]
    [Google Scholar]
  3. Rouse S, Harnett D, Vaughan A, van Sinderen D. Lactic acid bacteria with potential to eliminate fungal spoilage in foods. J Appl Microbiol 2008; 104:915–923 [View Article] [PubMed]
    [Google Scholar]
  4. Vásquez A, Forsgren E, Fries I, Paxton RJ, Flaberg E et al. Symbionts as major modulators of insect health: lactic acid bacteria and honeybees. PLoS One 2012; 7:e33188 [View Article]
    [Google Scholar]
  5. He H, Chen Y, Zhang Y, Wei C. Bacteria associated with gut lumen of Camponotus japonicus Mayr. Environ Entomol 2011; 40:1405–1409 [View Article] [PubMed]
    [Google Scholar]
  6. Koch H, Schmid-Hempel P. Socially transmitted gut microbiota protect bumble bees against an intestinal parasite. Proc Natl Acad Sci U S A 2011; 108:19288–19292 [View Article]
    [Google Scholar]
  7. Endo A, Salminen S. Honeybees and beehives are rich sources for fructophilic lactic acid bacteria. Syst Appl Microbiol 2013; 36:444–448 [View Article] [PubMed]
    [Google Scholar]
  8. Endo A, Maeno S, Tanizawa Y, Kneifel W, Arita M et al. Fructophilic lactic acid bacteria, a unique group of fructose-fermenting microbes. Appl Environ Microbiol 2018; 84:19 [View Article]
    [Google Scholar]
  9. McFrederick QS, Cannone JJ, Gutell RR, Kellner K, Plowes RM et al. Specificity between lactobacilli and hymenopteran hosts is the exception rather than the rule. Appl Environ Microbiol 2013; 79:1803–1812 [View Article]
    [Google Scholar]
  10. McFrederick QS, Thomas JM, Neff JL, Vuong HQ, Russell KA et al. Flowers and wild megachilid bees share microbes. Microb Ecol 2017; 73:188–200 [View Article]
    [Google Scholar]
  11. 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 2017; 70:2782–2858 [View Article]
    [Google Scholar]
  12. Maeno S, Nishimura H, Tanizawa Y, Dicks L, Arita M et al. Unique niche-specific adaptation of fructophilic lactic acid bacteria and proposal of three Apilactobacillus species as novel members of the group. BMC Microbiol 2017; 21:1–14 [View Article]
    [Google Scholar]
  13. Martinson VG, Danforth BN, Minckley RL, Rueppell O, Tingek S et al. A simple and distinctive microbiota associated with honey bees and bumble bees. Mol Ecol 2011; 20:619–628 [View Article] [PubMed]
    [Google Scholar]
  14. Kwong WK, Medina LA, Koch H, Sing K-W, Soh EJY et al. Dynamic microbiome evolution in social bees. Sci Adv 2017; 3:e1600513 [View Article] [PubMed]
    [Google Scholar]
  15. Zheng H, Powell JE, Steele MI, Dietrich C, Moran NA et al. Honeybee gut microbiota promotes host weight gain via bacterial metabolism and hormonal signaling. Proc Natl Acad Sci USA 2017; 114:4775–4780 [View Article]
    [Google Scholar]
  16. Nowak A, Szczuka D, Górczyńska A, Motyl I, Kręgiel D. Characterization of Apis mellifera gastrointestinal microbiota and lactic acid bacteria for honeybee protection-a review. Cells 2021; 10:701 [View Article]
    [Google Scholar]
  17. Martinson VG, Moy J, Moran NA. Establishment of characteristic gut bacteria during development of the honeybee worker. Appl Environ Microbiol 2012; 78:2830–2840 [View Article]
    [Google Scholar]
  18. Leonhardt SD, Kaltenpoth M. Microbial communities of three sympatric Australian stingless bee species. PLoS One 2014; 9:e105718 [View Article]
    [Google Scholar]
  19. Ellegaard KM, Tamarit D, Javelind E, Olofsson TC, Andersson SGE et al. Extensive intra-phylotype diversity in lactobacilli and bifidobacteria from the honeybee gut. BMC Genomics 2015; 16:284 [View Article]
    [Google Scholar]
  20. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article] [PubMed]
    [Google Scholar]
  21. Syed Yaacob SN, Huyop F, Kamarulzaman Raja Ibrahim R, Wahab RA. Identification of Lactobacillus spp. and Fructobacillus spp. isolated from fresh heterotrigona itama honey and their antagonistic activities against clinical pathogenic bacteria. J Apic Res 2018; 57:395–405 [View Article]
    [Google Scholar]
  22. Lamei S, Hu YOO, Olofsson TC, Andersson AF, Forsgren E et al. Improvement of identification methods for honeybee specific lactic acid bacteria; future approaches. PLoS ONE 2017; 12:e0174614 [View Article]
    [Google Scholar]
  23. Galkiewicz JP, Kellogg CA. Cross-kingdom amplification using bacteria-specific primers: complications for studies of coral microbial ecology. Appl Environ Microbiol 2008; 74:7828–7831 [View Article]
    [Google Scholar]
  24. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013; 29:1072–1075 [View Article] [PubMed]
    [Google Scholar]
  25. 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]
  26. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
    [Google Scholar]
  27. 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]
  28. Nawrocki EP. Structural RNA homology search and alignment using covariance models ProQuest Dissertations Publishing; 2009
    [Google Scholar]
  29. Bastolla U, Porto M, Roman HE, Vendruscolo M. Structural Approaches to Sequence Evolution. In SeqinR 1.0-2: A Contributed Package to the R Project for Statistical Computing Devoted to Biological Sequences Retrieval and Analysis. Biological and Medical Physics, Biomedical Engineering Berlin, Heidelberg: Springer Berlin Heidelberg; 2007 pp 207–232 [View Article]
    [Google Scholar]
  30. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006; 22:2688–2690 [View Article] [PubMed]
    [Google Scholar]
  31. McFrederick QS, Vuong HQ, Rothman JA. Lactobacillus micheneri sp. nov., Lactobacillus timberlakei sp. nov. and Lactobacillus quenuiae sp. nov., lactic acid bacteria isolated from wild bees and flowers. Int J Syst Evol Microbiol 2018; 68:1879–1884 [View Article] [PubMed]
    [Google Scholar]
  32. Rosselló-Móra R, Amann R. Past and future species definitions for Bacteria and Archaea. Syst Appl Microbiol 2015; 38:209–216 [View Article]
    [Google Scholar]
  33. Lei X, Sun G, Xie J, Wei D. Lactobacillus curieae sp. nov., isolated from stinky tofu brine. Int J Syst Evol Microbiol 2013; 63:2501–2505 [View Article] [PubMed]
    [Google Scholar]
  34. Watanabe K, Fujimoto J, Tomii Y, Sasamoto M, Makino H et al. Lactobacillus kisonensis sp. nov., Lactobacillus otakiensis sp. nov., Lactobacillus rapi sp. nov. and Lactobacillus sunkii sp. nov., heterofermentative species isolated from sunki, a traditional Japanese pickle. Int J Syst Evol Microbiol 2009; 59:754–760 [View Article]
    [Google Scholar]
  35. Kawasaki S, Kurosawa K, Miyazaki M, Sakamoto M, Ohkuma M et al. Lactobacillus ozensis sp. nov., isolated from mountain flowers. Int J Syst Evol Microbiol 2011; 61:2435–2438 [View Article] [PubMed]
    [Google Scholar]
  36. Killer J, Votavová A, Valterová I, Vlková E, Rada V et al. Lactobacillus bombi sp. nov., from the digestive tract of laboratory-reared bumblebee queens (Bombus terrestris). Int J Syst Evol Microbiol 2014; 64:2611–2617 [View Article] [PubMed]
    [Google Scholar]
  37. Olofsson TC, Alsterfjord M, Nilson B, Butler È, Vásquez A. Lactobacillus apinorum sp. nov., Lactobacillus mellifer sp. nov., Lactobacillus mellis sp. nov., Lactobacillus melliventris sp. nov., Lactobacillus kimbladii sp. nov., Lactobacillus helsingborgensis sp. nov. and Lactobacillus kullabergensis sp. nov., isolated from the honey stomach of the honeybee Apis mellifera. Int J Syst Evol Microbiol 2014; 64:3109–3119 [View Article]
    [Google Scholar]
  38. Kim J, Na S-I, Kim D, Chun J. UBCG2: Up-to-date bacterial core genes and pipeline for phylogenomic analysis. J Microbiol 2021; 59:609–615 [View Article]
    [Google Scholar]
  39. 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]
  40. Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010; 26:2460–2461 [View Article] [PubMed]
    [Google Scholar]
  41. Kim D, Park S, Chun J. Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity. J Microbiol 2021; 59:476–480 [View Article]
    [Google Scholar]
  42. 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; 11:119 [View Article]
    [Google Scholar]
  43. Steinegger M, Söding J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat Biotechnol 2017; 35:1026–1028 [View Article] [PubMed]
    [Google Scholar]
  44. Gu Z, Eils R, Schlesner M. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics 2016; 32:2847–2849 [View Article] [PubMed]
    [Google Scholar]
  45. 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]
  46. 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]
  47. Edgar RC. MUSCLE v5 enables improved estimates of phylogenetic tree confidence by ensemble bootstrapping. bioRxiv 2021 [View Article]
    [Google Scholar]
  48. Li W, O’Neill KR, Haft DH, DiCuccio M, Chetvernin V et al. RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation. Nucleic Acids Res 2021; 49:D1020–D1028 [View Article] [PubMed]
    [Google Scholar]
  49. Kim M, Oh H-S, Park S-C, 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]
    [Google Scholar]
  50. 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]
  51. 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]
  52. 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]
  53. Li F, Cheng CC, Zheng J, Liu J, Quevedo RM et al. Limosilactobacillus balticus sp. nov., Limosilactobacillus agrestis sp. nov., Limosilactobacillus albertensis sp. nov., Limosilactobacillus rudii sp. nov. and Limosilactobacillus fastidiosus sp. nov., five novel Limosilactobacillus species isolated from the vertebrate gastrointestinal tract, and proposal of six subspecies of Limosilactobacillus reuteri adapted to the gastrointestinal tract of specific vertebrate hosts. Int J Syst Evol Microbiol 2021; 71: [View Article]
    [Google Scholar]
  54. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article] [PubMed]
    [Google Scholar]
  55. Endo A, Okada S. Reclassification of the genus Leuconostoc and proposals of Fructobacillus fructosus gen. nov., comb. nov., Fructobacillus durionis comb. nov., Fructobacillus ficulneus comb. nov. and Fructobacillus pseudoficulneus comb. nov. Int J Syst Evol Microbiol 2008; 58:2195–2205 [View Article]
    [Google Scholar]
  56. Teusink B, Molenaar D. Systems biology of lactic acid bacteria: for food and thought. Curr Opin Syst Biol 2017; 6:7–13 [View Article]
    [Google Scholar]
  57. Endo A, Futagawa-Endo Y, Dicks LMT. Isolation and characterization of fructophilic lactic acid bacteria from fructose-rich niches. Syst Appl Microbiol 2009; 32:593–600 [View Article] [PubMed]
    [Google Scholar]
  58. Juergensmeyer MA, Nelson ES, Juergensmeyer EA. Shaking alone, without concurrent aeration, affects the growth characteristics of Escherichia coli. Lett Appl Microbiol 2007; 45:179–183 [View Article] [PubMed]
    [Google Scholar]
  59. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article]
    [Google Scholar]
  60. Sumby KM, Niimi J, Betteridge AL, Jiranek V. Ethanol‐tolerant lactic acid bacteria strains as a basis for efficient malolactic fermentation in wine: evaluation of experimentally evolved lactic acid bacteria and winery isolates. Aust J Grape Wine Res 2019; 25:404–413 [View Article]
    [Google Scholar]
  61. Schumann P. Peptidoglycan structure. In Methods in Microbiology Amsterdam: Elsevier Ltd; 2011 pp 101–129
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005588
Loading
/content/journal/ijsem/10.1099/ijsem.0.005588
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month Most Cited RSS feed

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