Many ecological experiments are based on the extraction and downstream analyses of microorganisms from different environmental samples. Due to its high throughput, cost-effectiveness and rapid performance, Matrix Assisted Laser Desorption/Ionization Mass Spectrometry with Time-of-Flight detector (MALDI-TOF MS), which has been proposed as a promising tool for bacterial identification and classification, could be advantageously used for dereplication of recurrent bacterial isolates. In this study, we compared whole-cell MALDI-TOF MS-based analyses of 49 bacterial cultures to two well-established bacterial identification and classification methods based on nearly complete 16S rRNA gene sequence analyses: a phylotype-based approach, using a closest type strain assignment, and a sequence similarity-based approach involving a 98.65% sequence similarity threshold, which has been found to best delineate bacterial species. Culture classification using reference-based MALDI-TOF MS was comparable to that yielded by phylotype assignment up to the genus level. At the species level, agreement between 16S rRNA gene analysis and MALDI-TOF MS was found to be limited, potentially indicating that spectral reference databases need to be improved. We also evaluated the mass spectral similarity technique for species-level delineation which can be used independently of reference databases. We established optimal mass spectral similarity thresholds which group MALDI-TOF mass spectra of common environmental isolates analogically to phylotype- and sequence similarity-based approaches. When using a mass spectrum similarity approach, we recommend a mass range of 4-10 kDa for analysis, which is populated with stable mass signals and contains the majority of phylotype-determining peaks. We show that a cosine similarity (CS) threshold of 0.79 differentiate mass spectra analogously to 98.65% species-level delineation sequence similarity threshold, with corresponding precision and recall values of 0.70 and 0.73, respectively. When matched to species-level phylotype assignment, an optimal CS threshold of 0.92 was calculated, with associated precision and recall values of 0.83 and 0.64, respectively. Overall, our research indicates that a similarity-based MALDI-TOF MS approach can be routinely used for efficient dereplication of isolates for downstream analyses, with minimal loss of unique organisms. In addition, MALDI-TOF MS analysis has further improvement potential unlike 16S rRNA gene analysis, whose methodological limits have reached a plateau.

Department of Biochemistry and Microbiology Faculty of Food and Biochemical Technology University of Chemistry and Technology Prague Czechia

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Ahdesmaki M., Strimmer K. (2010). Feature selection in omics prediction problems using cat scores and false nondiscovery rate control. Ann. Appl. Stat. 4, 503–519. 10.1214/09-AOAS277 DOI

Ahdesmaki M., Zuber V., Gibb S., Strimmer K. (2015). sda: Shrinkage Discriminant Analysis and CAT Score Variable Selection. R package version 1.3.7 [Online]. Available online at: https://CRAN.R-project.org/package=sda.

Alatoom A. A., Cunningham S. A., Ihde S. M., Mandrekar J., Patel R. (2011). Comparison of direct colony method versus extraction method for identification of gram-positive cocci by use of Bruker Biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometry. J. Clin. Microbiol. 49, 2868–2873. 10.1128/JCM.00506-11 PubMed DOI PMC

Arnold R. J., Karty J. A., Ellington A. D., Reilly J. P. (1999). Monitoring the growth of a bacteria culture by MALDI-MS of whole cells. Anal. Chem. 71, 1990–1996. 10.1021/ac981196c PubMed DOI

Arnold R. J., Reilly J. P. (1998). Fingerprint matching of E.coli strains with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of whole cells using a modified correlation approach. Rapid Commun. Mass Spectrom. 12, 630–636. PubMed

Bizzini A., Jaton K., Romo D., Bille J., Prod'hom G., Greub G. (2011). Matrix-assisted laser desorption ionization-time of flight mass spectrometry as an alternative to 16S rRNA gene sequencing for identification of difficult-to-identify bacterial strains. J. Clin. Microbiol. 49, 693–696. 10.1128/JCM.01463-10 PubMed DOI PMC

Böhme K., Fernández-No I. C., Barros-Velázquez J., Gallardo J. M., Cañas B., Calo-Mata P. (2012). SpectraBank: an open access tool for rapid microbial identification by MALDI-TOF MS fingerprinting. Electrophoresis 33, 2138–2142. 10.1002/elps.201200074 PubMed DOI

Böhme K., Fernández-No I. C., Pazos M., Gallardo J. M., Barros-Velázquez J., Cañas B., et al. . (2013). Identification and classification of seafood-borne pathogenic and spoilage bacteria: 16S rRNA sequencing versus MALDI-TOF MS fingerprinting. Electrophoresis 34, 877–887. 10.1002/elps.201200532 PubMed DOI

Buckwalter S. P., Olson S. L., Connelly B. J., Lucas B. C., Rodning A. A., Walchak R. C., et al. . (2016). Evaluation of matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of Mycobacterium species, Nocardia species, and other aerobic Actinomycetes. J. Clin. Microbiol. 54, 376–384. 10.1128/JCM.02128-15 PubMed DOI PMC

Busse H. J. (2016). Review of the taxonomy of the genus Arthrobacter, emendation of the genus Arthrobacter sensu lato, proposal to reclassify selected species of the genus Arthrobacter in the novel genera Glutamicibacter gen. nov., Paeniglutamicibacter gen. nov., Pseudoglutamicibacter gen. nov., Paenarthrobacter gen. nov. and Pseudarthrobacter gen. nov., and emended description of Arthrobacter roseus. Int. J. Syst. Evol. Microbiol. 66, 9–37. 10.1099/ijsem.0.000702 PubMed DOI

Cheng W. C., Jan I. S., Chen J. M., Teng S. H., Teng L. J., Sheng W. H., et al. . (2015). Evaluation of the Bruker Biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometry system for identification of blood isolates of Vibrio species. J. Clin. Microbiol. 53, 1741–1744. 10.1128/JCM.00105-15 PubMed DOI PMC

Claydon M. A., Davey S. N., Edwards-Jones V., Gordon D. B. (1996). The rapid identification of intact microorganisms using mass spectrometry. Nat. Biotechnol. 14, 1584–1586. 10.1038/nbt1196-1584 PubMed DOI

Cole J. R., Wang Q., Fish J. A., Chai B., Mcgarrell D. M., Sun Y., et al. . (2014). Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res. 42, D633–D642. 10.1093/nar/gkt1244 PubMed DOI PMC

Coorevits A., De Jonghe V., Vandroemme J., Reekmans R., Heyrman J., Messens W., et al. . (2008). Comparative analysis of the diversity of aerobic spore-forming bacteria in raw milk from organic and conventional dairy farms. Syst. Appl. Microbiol. 31, 126–140. 10.1016/j.syapm.2008.03.002 PubMed DOI

Croxatto A., Prod'hom G., Greub G. (2012). Applications of MALDI-TOF mass spectrometry in clinical diagnostic microbiology. FEMS Microbiol. Rev. 36, 380–407. 10.1111/j.1574-6976.2011.00298.x PubMed DOI

Dai Y., Li L., Roser D. C., Long S. R. (1999). Detection and identification of low-mass peptides and proteins from solvent suspensions of Escherichia coli by high performance liquid chromatography fractionation and matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun. Mass Spectrom. 13, 73–78. 10.1002/(SICI)1097-0231(19990115)13:1<73::AID-RCM454>3.0.CO PubMed DOI

De Clerck E., De Vos P. (2002). Study of the bacterial load in a gelatine production process focussed on bacillus and related endosporeforming genera. Syst. Appl. Microbiol. 25, 611–617. 10.1078/07232020260517751 PubMed DOI

Dieckmann R., Graeber I., Kaesler I., Szewzyk U., von Döhren H. (2005). Rapid screening and dereplication of bacterial isolates from marine sponges of the Sula Ridge by Intact-Cell-MALDI-TOF mass spectrometry (ICM-MS). Appl. Microbiol. Biotechnol. 67, 539–548. 10.1007/s00253-004-1812-2 PubMed DOI

Fenselau C., Demirev P. A. (2001). Characterization of intact microorganisms by MALDI mass spectrometry. Mass Spectrom. Rev. 20, 157–171. 10.1002/mas.10004 PubMed DOI

Fox G. E., Wisotzkey J. D., Jurtshuk P. (1992). How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int. J. Syst. Evol. Microbiol. 42, 166–170. 10.1099/00207713-42-1-166 PubMed DOI

Fraraccio S., Strejcek M., Dolinova I., Macek T., Uhlik O. (2017). Secondary compound hypothesis revisited: selected plant secondary metabolites promote bacterial degradation of cis-1,2-dichloroethylene (cDCE). Sci. Rep. 7:8406. 10.1038/s41598-017-07760-1 PubMed DOI PMC

Friedman J. H. (1984). “A Variable Span Smoother”. Stanford University; Available online at: http://www.dtic.mil/docs/citations/ADA148241.

Fykse E. M., Tjarnhage T., Humppi T., Eggen V. S., Ingebretsen A., Skogan G., et al. (2015). Identification of airborne bacteria by 16S rDNA sequencing, MALDI-TOF MS and the MIDI microbial identification system. Aerobiologia 31, 271–281. 10.1007/s10453-015-9363-9 PubMed DOI PMC

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. Methods 86, 327–336. 10.1016/j.mimet.2011.06.004 PubMed DOI

Gibb S., Strimmer K. (2012). MALDIquant: a versatile R package for the analysis of mass spectrometry data. Bioinformatics 28, 2270–2271. 10.1093/bioinformatics/bts447 PubMed DOI

Holland R. D., Wilkes J. G., Rafii F., Sutherland J. B., Persons C. C., Voorhees K. J., et al. . (1996). Rapid identification of intact whole bacteria based on spectral patterns using matrix-assisted laser desorption/ionization with time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 10, 1227–1232. 10.1002/(SICI)1097-0231(19960731)10:10<1227::AID-RCM659>3.0.CO;2-6 PubMed DOI

Huber W., Carey V. J., Gentleman R., Anders S., Carlson M., Carvalho B. S., et al. . (2015). Orchestrating high-throughput genomic analysis with Bioconductor. Nat. Methods 12, 115–121. 10.1038/nmeth.3252 PubMed DOI PMC

Janda J. M., Abbott S. L. (2007). 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls. J. Clin. Microbiol. 45, 2761–2764. 10.1128/JCM.01228-07 PubMed DOI PMC

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. Microbiol. 64, 346–351. 10.1099/ijs.0.059774-0 PubMed DOI

Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., et al. . (2012). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int. J. Syst. Evol. Microbiol. 62, 716–721. 10.1099/ijs.0.038075-0 PubMed DOI

Konstantinidis K. T., Ramette A., Tiedje J. M. (2006). The bacterial species definition in the genomic era. Philos. Trans. R. Soc. Lond. B Biol. Sci. 361, 1929–1940. 10.1098/rstb.2006.1920 PubMed DOI PMC

Koubek J., Uhlík O., Ječná K., Junková P., Vrkoslavová J., Lipov J., et al. (2012). Whole-cell MALDI-TOF: rapid screening method in environmental microbiology. Int. Biodeterior. Biodegradation 69, 82–86. 10.1016/j.ibiod.2011.12.007 DOI

Kumar S., Stecher G., Tamura K. (2016). MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33, 1870–1874. 10.1093/molbev/msw054 PubMed DOI PMC

Kurzawova V., Stursa P., Uhlik O., Norkova K., Strohalm M., Lipov J., et al. . (2012). Plant-microorganism interactions in bioremediation of polychlorinated biphenyl-contaminated soil. N. Biotechnol. 30, 15–22. 10.1016/j.nbt.2012.06.004 PubMed DOI

Lane D. J. (1991). 16S/23S rRNA sequencing, in Nucleic Acid Techniques in Bacterial Systematics, eds Stackebrandt E., Goodfellow M. (New York, NY: John Wiley and Sons; ), 115–175.

Lassalle F., Campillo T., Vial L., Baude J., Costechareyre D., Chapulliot D., et al. . (2011). Genomic species are ecological species as revealed by comparative genomics in Agrobacterium tumefaciens. Genome. Biol. Evol. 3, 762–781. 10.1093/gbe/evr070 PubMed DOI PMC

Lay J. O., Jr. (2001). MALDI-TOF mass spectrometry of bacteria. Mass Spectrom. Rev. 20, 172–194. 10.1002/mas.10003 PubMed DOI

Liu H., Du Z., Wang J., Yang R. (2007). Universal sample preparation method for characterization of bacteria by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Appl. Environ. Microbiol. 73, 1899–1907. 10.1128/AEM.02391-06 PubMed DOI PMC

Maier T., Klepel S., Renner U., Kostrzewa M. (2006). Fast and reliable MALDI-TOF MS-based microorganism identification. Nat. Methods 3:328 10.1038/nmeth870 DOI

Mellmann A., Bimet F., Bizet C., Borovskaya A. D., Drake R. R., Eigner U., et al. . (2009). High interlaboratory reproducibility of matrix-assisted laser desorption ionization-time of flight mass spectrometry-based species identification of nonfermenting bacteria. J. Clin. Microbiol. 47, 3732–3734. 10.1128/JCM.00921-09 PubMed DOI PMC

Mellmann A., Cloud J., Maier T., Keckevoet U., Ramminger I., Iwen P., et al. . (2008). Evaluation of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry in comparison to 16S rRNA gene sequencing for species identification of nonfermenting bacteria. J. Clin. Microbiol. 46, 1946–1954. 10.1128/JCM.00157-08 PubMed DOI PMC

Morhac M. (2009). An algorithm for determination of peak regions and baseline elimination in spectroscopic data. Nucl. Instrum. Methods Phys. Res. Sect. A 600, 478–487. 10.1016/j.nima.2008.11.132 DOI

Munoz R., Yarza P., Ludwig W., Euzeby J., Amann R., Schleifer K. H., et al. . (2011). Release LTPs104 of the All-species living tree. Syst. Appl. Microbiol. 34, 169–170. 10.1016/j.syapm.2011.03.001 PubMed DOI

Murray P. R. (2010). Matrix-assisted laser desorption ionization time-of-flight mass spectrometry: usefulness for taxonomy and epidemiology. Clin. Microbiol. Infect. 16, 1626–1630. 10.1111/j.1469-0691.2010.03364.x PubMed DOI

Needleman S. B., Wunsch C. D. (1970). A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48, 443–453. 10.1016/0022-2836(70)90057-4 PubMed DOI

Nováková H., Vošahliková M., Pazlarová J., Macková M., Burkhard J., Demnerová K. (2002). PCB metabolism by Pseudomonas sp. P2. Int. Biodeterior. Biodegradation 50, 47–54. 10.1016/S0964-8305(02)00058-6 DOI

Oberle M., Wohlwend N., Jonas D., Maurer F. P., Jost G., Tschudin-Sutter S., et al. . (2016). The Technical and Biological Reproducibility of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) based typing: employment of bioinformatics in a multicenter study. PLoS ONE 11:e0164260. 10.1371/journal.pone.0164260 PubMed DOI PMC

Quast C., Pruesse E., Yilmaz P., Gerken J., Schweer T., Yarza P., et al. . (2013). The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596. 10.1093/nar/gks1219 PubMed DOI PMC

R. Core Team (2017). R: A Language and Environment for Statistical Computing. Vienna: R Foundation for Statistical Computing; Available online at: https://www.R-project.org/.

Ryzhov V., Fenselau C. (2001). Characterization of the protein subset desorbed by MALDI from whole bacterial cells. Anal. Chem. 73, 746–750. 10.1021/ac0008791 PubMed DOI

Savitzky A., Golay M. J. E. (1964). Smoothing + differentiation of data by simplified least squares procedures. Anal. Chem. 36, 1627–1639. 10.1021/ac60214a047 DOI

Sawana A., Adeolu M., Gupta R. S. (2014). Molecular signatures and phylogenomic analysis of the genus Burkholderia: proposal for division of this genus into the emended genus Burkholderia containing pathogenic organisms and a new genus Paraburkholderia gen. nov. harboring environmental species. Front. Genet. 5:429. 10.3389/fgene.2014.00429 PubMed DOI PMC

Schleifer K. H. (2009). Classification of bacteria and archaea: past, present and future. Syst. Appl. Microbiol. 32, 533–542. 10.1016/j.syapm.2009.09.002 PubMed DOI

Schmidt D. (2016). Co-Operation: Fast Correlation, Covariance, and Cosine Similarity. R package version 0.6-0. Available online at: https://cran.r-project.org/package=coop.

Schmitt B. H., Cunningham S. A., Dailey A. L., Gustafson D. R., Patel R. (2013). Identification of anaerobic bacteria by Bruker Biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometry with on-plate formic acid preparation. J. Clin. Microbiol. 51, 782–786. 10.1128/JCM.02420-12 PubMed DOI PMC

Schulthess B., Bloemberg G. V., Zbinden A., Mouttet F., Zbinden R., Bottger E. C., et al. . (2016). Evaluation of the Bruker MALDI biotyper for identification of fastidious gram-negative rods. J. Clin. Microbiol. 54, 543–548. 10.1128/JCM.03107-15 PubMed DOI PMC

Schulthess B., Brodner K., Bloemberg G. V., Zbinden R., Bttger E. C., Hombach M. (2013). Identification of gram-positive cocci by use of matrix-assisted laser desorption ionization-time of flight mass spectrometry: comparison of different preparation methods and implementation of a practical algorithm for routine diagnostics. J. Clin. Microbiol. 51, 1834–1840. 10.1128/JCM.02654-12 PubMed DOI PMC

Seng P., Abat C., Rolain J. M., Colson P., Lagier J.-C., Gouriet F., et al. (2013). Identification of rare pathogenic bacteria in a clinical microbiology laboratory: impact of MALDI-TOF mass spectrometry. J. Clin. Microbiol. 51, 2182–2194. 10.1128/JCM.00492-13 PubMed DOI PMC

Shin H. B., Yoon J., Lee Y., Kim M. S., Lee K. (2015). Comparison of MALDI-TOF MS, housekeeping gene sequencing, and 16S rRNA gene sequencing for identification of Aeromonas clinical isolates. Yonsei Med. J. 56, 550–555. 10.3349/ymj.2015.56.2.550 PubMed DOI PMC

Spitaels F., Wieme A. D., Vandamme P. (2016). MALDI-TOF MS as a Novel Tool for Dereplication and Characterization of Microbiota in Bacterial Diversity Studies, in Applications of Mass Spectrometry in Microbiology: From Strain Characterization to Rapid Screening for Antibiotic Resistance, eds Demirev P., Sandrin T.R. (Cham: Springer International Publishing; ), 235–256.

Stackebrandt E., Goebel B. (1994). Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Evol. Microbiol. 44, 846–849. 10.1099/00207713-44-4-846 DOI

Stein S. E., Scott D. R. (1994). Optimization and testing of mass spectral library search algorithms for compound identification. J. Am. Soc. Mass Spectrom. 5, 859–866. 10.1016/1044-0305(94)87009-8 PubMed DOI

Strimmer K. (2015). crossval: Generic Functions for Cross Validation. R Package Version 1.0.3. Available online at: https://CRAN.R-project.org/package=crossval

Suarez S., Ferroni A., Lotz A., Jolley K. A., Guerin P., Leto J., et al. . (2013). Ribosomal proteins as biomarkers for bacterial identification by mass spectrometry in the clinical microbiology laboratory. J. Microbiol. Methods 94, 390–396. 10.1016/j.mimet.2013.07.021 PubMed DOI PMC

Svobodova B., Vlach J., Junkova P., Karamonova L., Blazkova M., Fukal L. (2017). Novel method for reliable identification of Siccibacter and Franconibacter strains: from “Pseudo-Cronobacter” to new Enterobacteriaceae genera. Appl. Environ. Microbiol. 83:e00234–17. 10.1128/AEM.00234-17 PubMed DOI PMC

Thompson J. R., Marcelino L. A., Polz M. F. (2002). Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by 'reconditioning PCR'. Nucleic Acids Res. 30, 2083–2088. 10.1093/nar/30.9.2083 PubMed DOI PMC

Tindall B. J., Rossello-Mora R., Busse H. J., Ludwig W., Kampfer P. (2010). Notes on the characterization of prokaryote strains for taxonomic purposes. Int. J. Syst. Evol. Microbiol. 60, 249–266. 10.1099/ijs.0.016949-0 PubMed DOI

Uhlík O., Strejček M., Junková P., Šanda M., Hroudová M., Vlček C., et al. . (2011). Matrix-assisted laser desorption ionization (MALDI)-time of flight mass spectrometry- and MALDI biotyper-based identification of cultured biphenyl-metabolizing bacteria from contaminated horseradish rhizosphere soil. Appl. Environ. Microbiol. 77, 6858–6866. 10.1128/AEM.05465-11 PubMed DOI PMC

UniProt Consortium (2017). UniProt: the universal protein knowledgebase. Nucleic Acids Res. 45, D158–D169. 10.1093/nar/gkw1099 PubMed DOI PMC

Vancanneyti M., Witt S., Abraham W.-R., Kersters K., Fredrickson H. L. (1996). Fatty acid content in whole-cell hydrolysates and phospholipid and phospholipid fractions of pseudomonads: a taxonomic evaluation. Syst. Appl. Microbiol. 19, 528–540. 10.1016/S0723-2020(96)80025-7 DOI

Versalovic J. (1994). Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction. Methods Mol. Cell. Biol. 5, 25–40.

Wald J., Hroudová M., Jansa J., Vrchotová B., Macek T., Uhlík O. (2015). Pseudomonads rule degradation of polyaromatic hydrocarbons in aerated sediment. Front. Microbiol. 6:1268. 10.3389/fmicb.2015.01268 PubMed DOI PMC

Wang Q., Garrity G. M., Tiedje J. M., Cole J. R. (2007). Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261–5267. 10.1128/AEM.00062-07 PubMed DOI PMC

Westblade L. F., Garner O. B., Macdonald K., Bradford C., Pincus D. H., Mochon A. B., et al. . (2015). Assessment of reproducibility of matrix-assisted laser desorption ionization-time of flight mass spectrometry for bacterial and yeast identification. J. Clin. Microbiol. 53, 2349–2352. 10.1128/JCM.00187-15 PubMed DOI PMC

Wieser A., Schneider L., Jung J., Schubert S. (2012). MALDI-TOF MS in microbiological diagnostics-identification of microorganisms and beyond (mini review). Appl. Microbiol. Biotechnol. 93, 965–974. 10.1007/s00253-011-3783-4 PubMed DOI

Woese C. R. (1987). Bacterial evolution. Microbiol. Rev. 51, 221–271. PubMed PMC

Yoon S. H., Ha S. M., Kwon S., Lim J., Kim Y., Seo H., et al. . (2017). Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int. J. Syst. Evol. Microbiol. 67, 1613–1617. 10.1099/ijsem.0.001755 PubMed DOI PMC

Yutin N., Puigbo P., Koonin E. V., Wolf Y. I. (2012). Phylogenomics of prokaryotic ribosomal proteins. PLoS ONE 7:e36972. 10.1371/journal.pone.0036972 PubMed DOI PMC

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