Reclassification of Paenibacillus riograndensis as a genomovar of Paenibacillus sonchi: genome-based metrics improve bacterial taxonomic classification

Sant'Anna F, Ambrosini A, de Souza R, Fernandes GD, Bach E, Balsanelli E, Baura V, Fernandes de Brito L, Wendisch VF, de Oliveira Pedrosa F, de Souza EM, et al. (2017)
Frontiers in Microbiology 8: 1849.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
OA 3.23 MB
Autor*in
Sant'Anna, F.; Ambrosini, Adriana; de Souza, Rocheli; Fernandes, Gabriela D.; Bach, Evelise; Balsanelli, Eduardo; Baura, Valter; Fernandes de Brito, LucianaUniBi; Wendisch, Volker F.UniBi ; de Oliveira Pedrosa, Fabio; de Souza, Emanuel M.; Passaglia, LucianeUniBi
Erscheinungsjahr
2017
Zeitschriftentitel
Frontiers in Microbiology
Band
8
Art.-Nr.
1849
ISSN
1664-302X
Page URI
https://pub.uni-bielefeld.de/record/2913749

Zitieren

Sant'Anna F, Ambrosini A, de Souza R, et al. Reclassification of Paenibacillus riograndensis as a genomovar of Paenibacillus sonchi: genome-based metrics improve bacterial taxonomic classification. Frontiers in Microbiology. 2017;8: 1849.
Sant'Anna, F., Ambrosini, A., de Souza, R., Fernandes, G. D., Bach, E., Balsanelli, E., Baura, V., et al. (2017). Reclassification of Paenibacillus riograndensis as a genomovar of Paenibacillus sonchi: genome-based metrics improve bacterial taxonomic classification. Frontiers in Microbiology, 8, 1849. https://doi.org/10.3389/fmicb.2017.01849
Sant'Anna, F., Ambrosini, Adriana, de Souza, Rocheli, Fernandes, Gabriela D., Bach, Evelise, Balsanelli, Eduardo, Baura, Valter, et al. 2017. “Reclassification of Paenibacillus riograndensis as a genomovar of Paenibacillus sonchi: genome-based metrics improve bacterial taxonomic classification”. Frontiers in Microbiology 8: 1849.
Sant'Anna, F., Ambrosini, A., de Souza, R., Fernandes, G. D., Bach, E., Balsanelli, E., Baura, V., Fernandes de Brito, L., Wendisch, V. F., de Oliveira Pedrosa, F., et al. (2017). Reclassification of Paenibacillus riograndensis as a genomovar of Paenibacillus sonchi: genome-based metrics improve bacterial taxonomic classification. Frontiers in Microbiology 8:1849.
Sant'Anna, F., et al., 2017. Reclassification of Paenibacillus riograndensis as a genomovar of Paenibacillus sonchi: genome-based metrics improve bacterial taxonomic classification. Frontiers in Microbiology, 8: 1849.
F. Sant'Anna, et al., “Reclassification of Paenibacillus riograndensis as a genomovar of Paenibacillus sonchi: genome-based metrics improve bacterial taxonomic classification”, Frontiers in Microbiology, vol. 8, 2017, : 1849.
Sant'Anna, F., Ambrosini, A., de Souza, R., Fernandes, G.D., Bach, E., Balsanelli, E., Baura, V., Fernandes de Brito, L., Wendisch, V.F., de Oliveira Pedrosa, F., de Souza, E.M., Passaglia, L.: Reclassification of Paenibacillus riograndensis as a genomovar of Paenibacillus sonchi: genome-based metrics improve bacterial taxonomic classification. Frontiers in Microbiology. 8, : 1849 (2017).
Sant'Anna, F., Ambrosini, Adriana, de Souza, Rocheli, Fernandes, Gabriela D., Bach, Evelise, Balsanelli, Eduardo, Baura, Valter, Fernandes de Brito, Luciana, Wendisch, Volker F., de Oliveira Pedrosa, Fabio, de Souza, Emanuel M., and Passaglia, Luciane. “Reclassification of Paenibacillus riograndensis as a genomovar of Paenibacillus sonchi: genome-based metrics improve bacterial taxonomic classification”. Frontiers in Microbiology 8 (2017): 1849.
Alle Dateien verfügbar unter der/den folgenden Lizenz(en):
Creative Commons Namensnennung 4.0 International Public License (CC-BY 4.0):
Volltext(e)
Access Level
OA Open Access
Zuletzt Hochgeladen
2021-01-27T10:51:20Z
MD5 Prüfsumme
d93a13c653425643326ba06ba546cc76


1 Zitation in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Paenibacillus helianthi sp. nov., a nitrogen fixing species isolated from the rhizosphere of Helianthus annuus L.
Ambrosini A, Sant'Anna FH, Heinzmann J, de Carvalho Fernandes G, Bach E, Passaglia LMP., Antonie Van Leeuwenhoek 111(12), 2018
PMID: 30073429

57 References

Daten bereitgestellt von Europe PubMed Central.

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons.
Alikhan NF, Petty NK, Ben Zakour NL, Beatson SA., BMC Genomics 12(), 2011
PMID: 21824423
Screening of plant growth promoting Rhizobacteria isolated from sunflower (Helianthus annuus L.).
Ambrosini A., Beneduzi A., Stefanski T., Pinheiro F., Vargas L., Passaglia L.., 2012
Diazotrophic bacilli isolated from the sunflower rhizosphere and the potential of Bacillus mycoides B38V as biofertiliser
Ambrosini A, Stefanski T, Lisboa BB, Beneduzi A, Vargas LK, Passaglia LMP., Ann. Appl. Biol. 168(1), 2016
PMID: IND604789235
Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation.
Angiuoli SV, Gussman A, Klimke W, Cochrane G, Field D, Garrity G, Kodira CD, Kyrpides N, Madupu R, Markowitz V, Tatusova T, Thomson N, White O., OMICS 12(2), 2008
PMID: 18416670
SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA., J. Comput. Biol. 19(5), 2012
PMID: 22506599
Paenibacillus riograndensis sp. nov., a nitrogen-fixing species isolated from the rhizosphere of Triticum aestivum.
Beneduzi A, Costa PB, Parma M, Melo IS, Bodanese-Zanettini MH, Passaglia LM., Int. J. Syst. Evol. Microbiol. 60(Pt 1), 2009
PMID: 19648317
Evaluation of genetic diversity and plant growth promoting activities of nitrogen-fixing bacilli isolated from rice fields in South Brazil
Beneduzi Anelise, Peres Daiane, Vargas LucianoK, Bodanese-Zanettini MariaHelena, Passaglia LucianeMariaP., Agric., Ecosyst. Environ., Appl. Soil Ecol. 39(3), 2008
PMID: IND44050237
Paenibacillus graminis sp. nov. and Paenibacillus odorifer sp. nov., isolated from plant roots, soil and food.
Berge O, Guinebretiere MH, Achouak W, Normand P, Heulin T., Int. J. Syst. Evol. Microbiol. 52(Pt 2), 2002
PMID: 11931174
EDGAR: a software framework for the comparative analysis of prokaryotic genomes.
Blom J, Albaum SP, Doppmeier D, Puhler A, Vorholter FJ, Zakrzewski M, Goesmann A., BMC Bioinformatics 10(), 2009
PMID: 19457249
Methods for quantification of nitrogen fixation associated with gramineae.
Boddey R., Knowles R.., 2008
Complete genome sequence of Paenibacillus riograndensis SBR5(T), a Gram-positive diazotrophic rhizobacterium.
Brito LF, Bach E, Kalinowski J, Ruckert C, Wibberg D, Passaglia LM, Wendisch VF., J. Biotechnol. 207(), 2015
PMID: 25959170
Defining bacterial species in the genomic era: insights from the genus Acinetobacter.
Chan JZ, Halachev MR, Loman NJ, Constantinidou C, Pallen MJ., BMC Microbiol. 12(), 2012
PMID: 23259572
Biopython: freely available Python tools for computational molecular biology and bioinformatics.
Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B, de Hoon MJ., Bioinformatics 25(11), 2009
PMID: 19304878
Ribosomal Database Project: data and tools for high throughput rRNA analysis.
Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, Brown CT, Porras-Alfaro A, Kuske CR, Tiedje JM., Nucleic Acids Res. 42(Database issue), 2013
PMID: 24288368
Characterization of plant growth-promoting bacteria associated with rice cropped in iron-stressed soils.
de R., Meyer J., Schoenfeld R., da P., Passaglia L.., 2014
Phylogeny.fr: robust phylogenetic analysis for the non-specialist.
Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, Chevenet F, Dufayard JF, Guindon S, Lefort V, Lescot M, Claverie JM, Gascuel O., Nucleic Acids Res. 36(Web Server issue), 2008
PMID: 18424797
How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity.
Fox GE, Wisotzkey JD, Jurtshuk P Jr, Fox GE., Int. J. Syst. Bacteriol. 42(1), 1992
PMID: 1371061
Opinion: Re-evaluating prokaryotic species.
Gevers D, Cohan FM, Lawrence JG, Spratt BG, Coenye T, Feil EJ, Stackebrandt E, Van de Peer Y, Vandamme P, Thompson FL, Swings J., Nat. Rev. Microbiol. 3(9), 2005
PMID: 16138101
QUAST: quality assessment tool for genome assemblies.
Gurevich A, Saveliev V, Vyahhi N, Tesler G., Bioinformatics 29(8), 2013
PMID: 23422339
PAST: paleontological statistics software package for education and data analysis.
Hammer Ø., Harper D., Ryan P.., 2001

Holt J.., 2000
“Gram-positive bacteria other than Actinomycetes,” in
Holt J.., 1986
Paenibacillus sonchi sp. nov., a nitrogen-fixing species isolated from the rhizosphere of Sonchus oleraceus.
Hong YY, Ma YC, Zhou YG, Gao F, Liu HC, Chen SF., Int. J. Syst. Evol. Microbiol. 59(Pt 11), 2009
PMID: 19625436
r2cat: synteny plots and comparative assembly.
Husemann P, Stoye J., Bioinformatics 26(4), 2009
PMID: 20015948
Paenibacillus jilunlii sp. nov., a nitrogen-fixing species isolated from the rhizosphere of Begonia semperflorens.
Jin HJ, Zhou YG, Liu HC, Chen SF., Int. J. Syst. Evol. Microbiol. 61(Pt 6), 2010
PMID: 20601486
Bacterial genospecies that are not ecologically coherent: population genomics of Rhizobium leguminosarum.
Kumar N, Lad G, Giuntini E, Kaye ME, Udomwong P, Shamsani NJ, Young JP, Bailly X., Open Biol 5(1), 2015
PMID: 25589577
Paenibacillus bovis sp. nov., isolated from raw yak (Bos grunniens) milk.
Gao C, Han J, Liu Z, Xu X, Hang F, Wu Z., Int. J. Syst. Evol. Microbiol. 66(3), 2016
PMID: 26769366
Proposed minimal standards for describing new taxa of aerobic, endospore-forming bacteria.
Logan NA, Berge O, Bishop AH, Busse HJ, De Vos P, Fritze D, Heyndrickx M, Kampfer P, Rabinovitch L, Salkinoja-Salonen MS, Seldin L, Ventosa A., Int. J. Syst. Evol. Microbiol. 59(Pt 8), 2009
PMID: 19567583
Plant-growth-promoting rhizobacteria.
Lugtenberg B, Kamilova F., Annu. Rev. Microbiol. 63(), 2009
PMID: 19575558

MacFaddin J.., 2000
Bacillus taxonomy in the genomic era finds phenotypes to be essential though often misleading.
Maughan H, Van der Auwera G., Infect. Genet. Evol. 11(5), 2011
PMID: 21334463
Genome sequence-based species delimitation with confidence intervals and improved distance functions.
Meier-Kolthoff JP, Auch AF, Klenk HP, Goker M., BMC Bioinformatics 14(), 2013
PMID: 23432962
When should a DDH experiment be mandatory in microbial taxonomy?
Meier-Kolthoff JP, Goker M, Sproer C, Klenk HP., Arch. Microbiol. 195(6), 2013
PMID: 23591456
Complete genome sequence of DSM 30083(T), the type strain (U5/41(T)) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy.
Meier-Kolthoff JP, Hahnke RL, Petersen J, Scheuner C, Michael V, Fiebig A, Rohde C, Rohde M, Fartmann B, Goodwin LA, Chertkov O, Reddy T, Pati A, Ivanova NN, Markowitz V, Kyrpides NC, Woyke T, Goker M, Klenk HP., Stand Genomic Sci 9(), 2014
PMID: 25780495
Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age.
Meier-Kolthoff JP, Klenk HP, Goker M., Int. J. Syst. Evol. Microbiol. 64(Pt 2), 2014
PMID: 24505073
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.
Parks D., Imelfort M., Skennerton C., Hugenholtz P., Tyson G.., 2014
SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes.
Pruesse E, Peplies J, Glockner FO., Bioinformatics 28(14), 2012
PMID: 22556368
Shifting the genomic gold standard for the prokaryotic species definition.
Richter M, Rossello-Mora R., Proc. Natl. Acad. Sci. U.S.A. 106(45), 2009
PMID: 19855009
Classification of Bacteria and Archaea: past, present and future.
Schleifer KH., Syst. Appl. Microbiol. 32(8), 2009
PMID: 19819658
Ecology and evolution of bacterial microdiversity.
Schloter M, Lebuhn M, Heulin T, Hartmann A., FEMS Microbiol. Rev. 24(5), 2000
PMID: 11077156
Universal chemical assay for the detection and determination of siderophores.
Schwyn B, Neilands JB., Anal. Biochem. 160(1), 1987
PMID: 2952030
“Paenibacillus, nitrogen fixation and soil fertility,” in
Seldin L.., 2011
Taxonomic parameters revisited: tarnished gold standards.
Stackebrandt E., Ebers J.., 2006
MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S., Mol. Biol. Evol. 30(12), 2013
PMID: 24132122
Microbial species delineation using whole genome sequences.
Varghese NJ, Mukherjee S, Ivanova N, Konstantinidis KT, Mavrommatis K, Kyrpides NC, Pati A., Nucleic Acids Res. 43(14), 2015
PMID: 26150420
A simple, fast, and accurate method of phylogenomic inference.
Wu M, Eisen JA., Genome Biol. 9(10), 2008
PMID: 18851752
Comparative genomic analysis of N2-fixing and non-N2-fixing Paenibacillus spp.: organization, evolution and expression of the nitrogen fixation genes.
Xie JB, Du Z, Bai L, Tian C, Zhang Y, Xie JY, Wang T, Liu X, Chen X, Cheng Q, Chen S, Li J., PLoS Genet. 10(3), 2014
PMID: 24651173
Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®
Quellen

PMID: 29046663
PubMed | Europe PMC

Suchen in

Google Scholar