1887

Abstract

Isolates LMG 28357 ( = R-53146) and LMG 28623 were obtained from gut samples of bumblebees caught in Ghent, Belgium. They had identical 16S rRNA gene sequences which were 95.7 % identical to that of wkB301, a member of the family Both isolates had highly similar matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS and randomly amplified polymorphic DNA (RAPD) profiles. A draft genome sequence was obtained for strain LMG 28357 (Gold ID Gp0108260); its DNA G+C content was 30.4 %, which is within the range reported for members of the family (27 to 56 mol%) and which is similar to that of the type strain of (29.0 mol%). Whole-cell fatty acid methyl ester analysis of strain LMG 28357 revealed many branched-chain fatty acids, a typical characteristic of bacteria of the family and a profile that was similar to that reported for wkB301. MK6 was the major respiratory quinone, again conforming to bacteria of the family . The isolates LMG 28357 and LMG 28623 could be distinguished from strains through their oxidase activity. On the basis of phylogenetic, genotypic and phenotypic data, we propose to classify both isolates as representatives of a novel species of the genus , sp. nov., with LMG 28357 ( = DSM 100903 = R-53146) as the type strain.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.000921
2016-04-01
2020-08-05
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/66/4/1645.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.000921&mimeType=html&fmt=ahah

References

  1. Aslam Z., Im W. T., Kim M. K., Lee S. T.. 2005; Flavobacterium granuli sp. nov., isolated from granules used in a wastewater treatment plant. Int J Syst Evol Microbiol55:747–751 [CrossRef][PubMed]
    [Google Scholar]
  2. Aziz R. K., Bartels D., Best A. A., DeJongh M., Disz T., Edwards R. A., Formsma K., Gerdes S., Glass E. M., other authors. 2008; The rast Server: rapid annotations using subsystems technology. BMC Genomics9:75 [CrossRef][PubMed]
    [Google Scholar]
  3. Bernardet J.-F.. 2010; Family I. Flavobacteriaceae Reichenbach 1992b, 327VP (effective publication: Reichenbach 1989b, 2013.) emend. Bernardet, Segers, Vancanneyt, Berthe, Kersters and Vandamme 1996, 145 emend. Bernardet, Nakagawa and Holmes 2002, 1057. In Bergey's Manual of Systematic Bacteriology, 2nd edn.vol. 4 pp106–111Edited by Krieg N. R., Ludwig W., Whitman W. B., Hedlund B. P., Paster B. J., Staley J. T., Ward N. L., Brown D. R., Parte A.. New York: Springer;
    [Google Scholar]
  4. Bernardet J.-F., Nakagawa Y.. 2006; An introduction to the family Flavobacteriaceae . In The Prokaryotes: a Handbook on the Biology of Bacteria, 3rd edn.vol. 7 pp455–480Edited by Dworkin M., Falkow S., Rosenberg E., Schleifer K. H., Stackebrandt E.. New York: Springer;
    [Google Scholar]
  5. Cariveau D. P., Elijah Powell J., Koch H., Winfree R., Moran N. A.. 2014; Variation in gut microbial communities and its association with pathogen infection in wild bumble bees (Bombus). ISME J8:2369–2379 [CrossRef][PubMed]
    [Google Scholar]
  6. da Costa M. S., Albuquerque L., Nobre M. F., Wait R.. 2011; The extraction and identification of respiratory lipoquinones of prokaryotes and their use in taxonomy. Methods Microbiol38:197–206 [CrossRef]
    [Google Scholar]
  7. De Bruyne K., Schillinger U., Caroline L., Boehringer B., Cleenwerck I., Vancanneyt M., De Vuyst L., Franz C. M., Vandamme P.. 2007; Leuconostoc holzapfelii sp. nov., isolated from Ethiopian coffee fermentation and assessment of sequence analysis of housekeeping genes for delineation of Leuconostoc species. Int J Syst Evol Microbiol57:2952–2959 [CrossRef][PubMed]
    [Google Scholar]
  8. Felsenstein J.. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution39:783–791[CrossRef]
    [Google Scholar]
  9. Gallai N., Salles J.-M., Settele J., Vaissière B. E.. 2009; Economic valuation of the vulnerability of world agriculture confronted with pollinator decline. Ecol Econ68:810–821 [CrossRef]
    [Google Scholar]
  10. Ghyselinck J., Van Hoorde K., Hoste B., Heylen K., De Vos P.. 2011; Evaluation of MALDI-TOF MS as a tool for high-throughput dereplication. J Microbiol Methods86:327–336 [CrossRef][PubMed]
    [Google Scholar]
  11. Gnerre S., Maccallum I., Przybylski D., Ribeiro F. J., Burton J. N., Walker B. J., Sharpe T., Hall G., Shea T. P., other authors. 2011; High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A108:1513–1518 [CrossRef][PubMed]
    [Google Scholar]
  12. Goulson D., Lye G. C., Darvill B.. 2008; Decline and conservation of bumble bees. Annu Rev Entomol53:191–208 [CrossRef][PubMed]
    [Google Scholar]
  13. Killer J., Kopecný J., Mrázek J., Rada V., Benada O., Koppová I., Havlík J., Straka J.. 2009; Bifidobacterium bombi sp. nov., from the bumblebee digestive tract. Int J Syst Evol Microbiol59:2020–2024 [CrossRef][PubMed]
    [Google Scholar]
  14. Killer J., Kopečný J., Mrázek J., Havlík J., Koppová I., Benada O., Rada V., Kofronˇová O.. 2010; Bombiscardovia coagulans gen. nov., sp. nov., a new member of the family Bifidobacteriaceae isolated from the digestive tract of bumblebees. Syst Appl Microbiol33:359–366 [CrossRef][PubMed]
    [Google Scholar]
  15. Killer J., Kopečný J., Mrázek J., Koppová I., Havlík J., Benada O., Kott T.. 2011; Bifidobacterium actinocoloniiforme sp. nov. and Bifidobacterium bohemicum sp. nov., from the bumblebee digestive tract. Int J Syst Evol Microbiol61:1315–1321 [CrossRef][PubMed]
    [Google Scholar]
  16. Kim M., Oh H. S., Park S. C., Chun J.. 2014; Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol64:346–351 [CrossRef][PubMed]
    [Google Scholar]
  17. Klein A.-M., Vaissière B. E., Cane J. H., Steffan-Dewenter I., Cunningham S. A., Kremen C., Tscharntke T.. 2007; Importance of pollinators in changing landscapes for world crops. Proc Biol Sci274:303–313 [CrossRef][PubMed]
    [Google Scholar]
  18. Koch H., Schmid-Hempel P.. 2011a; Socially transmitted gut microbiota protect bumble bees against an intestinal parasite. Proc Natl Acad Sci U S A108:19288–19292 [CrossRef][PubMed]
    [Google Scholar]
  19. Koch H., Schmid-Hempel P.. 2011b; Bacterial communities in central European bumblebees: low diversity and high specificity. Microb Ecol62:121–133 [CrossRef][PubMed]
    [Google Scholar]
  20. Koch H., Schmid-Hempel P.. 2012; Gut microbiota instead of host genotype drive the specificity in the interaction of a natural host-parasite system. Ecol Lett15:1095–1103 [CrossRef][PubMed]
    [Google Scholar]
  21. Kwong W. K., Moran N. A.. 2013; Cultivation and characterization of the gut symbionts of honey bees and bumble bees: description of Snodgrassella alvi gen. nov., sp. nov., a member of the family Neisseriaceae of the Betaproteobacteria, and Gilliamella apicola gen. nov., sp. nov., a member of Orbaceae fam. nov., Orbales ord. nov., a sister taxon to the order ‘Enterobacteriales’ of the Gammaproteobacteria . Int J Syst Evol Microbiol63:2008–2018 [CrossRef][PubMed]
    [Google Scholar]
  22. Kwong W. K., Moran N. A.. 2013; Apibacter adventoris gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from honey bees. Int J Syst Evol Microbiol. (In Press) [CrossRef]
    [Google Scholar]
  23. MacFaddin J. F.. 1980; Biochemical Tests for Identification of Medical Bacteria Baltimore, MD: Williams & Wilkins;
    [Google Scholar]
  24. McCutcheon J. P., Moran N. A.. 2012; Extreme genome reduction in symbiotic bacteria. Nat Rev Microbiol10:13–26[PubMed]
    [Google Scholar]
  25. Meeus I., Brown M. J. F., De Graaf D. C., Smagghe G.. 2011; Effects of invasive parasites on bumble bee declines. Conserv Biol25:662–671 [CrossRef][PubMed]
    [Google Scholar]
  26. Meeus I., Parmentier L., Billiet A., Maebe K., Van Nieuwerburgh F., Deforce D., Wäckers F., Vandamme P., Smagghe G.. 2015; 16S rRNA amplicon sequencing demonstrates that indoor-reared bumblebees (Bombus terrestris) harbor a core subset of bacteria normally associated with the wild host. PLoS One10:e0125152 [CrossRef][PubMed]
    [Google Scholar]
  27. Pitcher D. G., Saunders N. A., Owen R. J.. 1989; Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett Appl Microbiol8:151–156 [CrossRef]
    [Google Scholar]
  28. Praet J., Meeus I., Cnockaert M., Houf K., Smagghe G., Vandamme P.. 2015; Novel lactic acid bacteria isolated from the bumble bee gut: Convivina intestini gen. nov., sp. nov., Lactobacillus bombicola sp. nov., and Weissella bombi sp. nov. Antonie van Leeuwenhoek107:1337–1349 [CrossRef][PubMed]
    [Google Scholar]
  29. Roulston T. H., Cane J. H.. 2000; Pollen nutritional content and digestibility for animals. Plant Syst Evol222:187–209 [CrossRef]
    [Google Scholar]
  30. Schmidt J. O.. 1997; Bee products: chemical composition and application. In Bee Products–Properties, Applications, and Apitherapy pp15–26Edited by Mizrahi L., Lensky Y.. New York: Springer;
    [Google Scholar]
  31. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S., Arabia S., Kumar S.. 2013; mega6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol30:2725–2729[CrossRef]
    [Google Scholar]
  32. Williams J. G. K., Kubelik A. R., Livak K. J., Rafalski J. A., Tingey S. V.. 1990; DNA polymorphisms amplified by arbitrary primers useful as genetic markers are. 18:6531–6535
    [Google Scholar]
  33. Zerbino D. R., Birney E.. 2008; Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res18:821–829 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.000921
Loading
/content/journal/ijsem/10.1099/ijsem.0.000921
Loading

Data & Media loading...

Supplements

Supplementary Data

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