An alternative molecular marker with respect to the 16S rRNA gene demonstrating better identification and phylogenetic parameters has not been designed for the whole Bifidobacteriaceae family, which includes the genus Bifidobacterium and scardovial genera. Therefore, the aim of the study was to find such a gene in available genomic sequences, suggest appropriate means and conditions for asmplification and sequencing of the desired region of the selected gene in various strains of the bacterial family and verify the importance in classification and phylogeny. Specific primers flanking the variable region (~800 pb) within the pyrG gene encoding the CTP synthetase were designed by means of gene sequences retrieved from the genomes of strains belonging to the family Bifidobacteriaceae. The functionality and specificity of the primers were subsequently tested on the wild (7) and type strains of bifidobacteria (36) and scardovia (7). Comparative and phylogenetic studies based on obtained sequences revealed actual significance in classification and phylogeny of the Bifidobacteriaceae family. Gene statistics (percentages of mean sequence similarities and identical sites, mean number of nucleotide differences, P- and K-distances) and phylogenetic analyses (congruence between tree topologies, percentages of bootstrap values >50 and 70%) indicate that the pyrG gene represents an alternative identification and phylogenetic marker exhibiting higher discriminatory power among strains, (sub)species, and genera than the 16S rRNA gene. Sequences of the particular gene fragment, simply achieved through specific primers, enable more precisely to classify and evaluate phylogeny of the family Bifidobacteriaceae including, with some exceptions, health-promoting probiotic bacteria.

Faculty of Agrobiology Food and Natural Resources Department of Microbiology Nutrition and Dietetics Czech University of Life Sciences Prague 6 Suchdol Czechia

Institute of Animal Physiology and Genetics of the Czech Academy of Sciences Prague 4 Krč Czechia

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Abayneh, T. , Colquhoun, D. J. , & Sørum, H. (2012). Multi‐locus Sequence Analysis (MLSA) of Edwardsiella tarda isolates from fish. Veterinary Microbiology, 158, 367–375. 10.1016/j.vetmic.2012.03.006 PubMed DOI

Adékambi, T. , Butler, R. W. , Hanrahan, F. , Delcher, A. L. , Drancourt, M. , & Shinnick, T. M. (2011). Core gene set as the basis of multilocus sequence analysis of the subclass Actinobacteridae. PLoS ONE, 6, e14792 10.1371/journal.pone.0014792 PubMed DOI PMC

Avcin, S. L. , Pokorn, M. , Kitanovski, L. , Premru, M. M. , & Jazbec, J. (2015). Bifidobacterium breve sepsis in child with high‐risk acute lymphoblastic leukemia. Emerging Infectious Diseases, 21, 1674–1675. 10.3201/eid2109.150097 PubMed DOI PMC

Barberis, C. M. , Cittadini, R. M. , Almuzara, M. N. , Feinsilberg, A. , Famiglietti, A. M. , Ramírez, M. S. , & Vay, C. A. (2012). Recurrent urinary infection with Bifidobacterium scardovii . Journal of Clinical Microbiology, 50, 1086–1088. 10.1128/JCM.06027-11 PubMed DOI PMC

Biavati, B. , & Mattarelli, P. (2012). Genus Bifidobacterium In Whitman W., Goodfellow M., Kämpfer P., Busse H.‐J., Trujillo M., Ludwig W., Suzuki K. & Parte A. Bergey′s manual of systematic bacteriology (pp. 171–206). New York: Springer.

Bunesova, V. , Vlkova, E. , Rada, V. , Killer, J. , & Musilova, S. (2014). Bifidobacteria from the gastrointestinal tract of animals: Differences and similarities. Beneficial Microbes, 5, 377–388. 10.3920/BM2013.0081 PubMed DOI

Castresana, J. (2000). Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution, 17, 540–552. 10.1093/oxfordjournals.molbev.a026334 PubMed DOI

Delcenserie, V. , Gavini, F. , Beerens, H. , Tresse, O. , Franssen, C. , & Daube, G. (2007). Description of a new species, Bifidobacterium crudilactis sp. nov., isolated from raw milk and raw milk cheeses. Systematic and Applied Microbiology, 30, 381–389. 10.1016/j.syapm.2007.01.004 PubMed DOI

Delétoile, A. , Passet, V. , Aires, J. , Chambaud, I. , Butel, M. J. , Smokvina, T. , & Brisse, S. (2010). Species delineation and clonal diversity in four Bifidobacterium species as revealed by multilocus sequencing. Research in Microbiology, 161, 82–90. 10.1016/j.resmic.2009.12.006 PubMed DOI

Diancourt, L. , Passet, V. , Chervaux, C. , Garault, P. , Smokvina, T. , & Brisse, S. (2007). Multilocus sequence typing of Lactobacillus casei reveals a clonal population structure with low levels of homologous recombination. Applied and Environmental Microbiology, 73, 6601–6611. 10.1128/AEM.01095-07 PubMed DOI PMC

Dong, X. , Xin, Y. , Jian, W. , Liu, X. , & Ling, D. (2000). Bifidobacterium thermacidophilum sp. nov., isolated from an anaerobic digester. International Journal of Systematic and Evolutionary Microbiology, 50, 119–125. 10.1099/00207713-50-1-119 PubMed DOI

Downes, J. , Mantzourani, M. , Beighton, D. , Hooper, S. , Wilson, M. J. , Nicholson, A. , & Wade, W. G. (2011). Scardovia wiggsiae sp. nov., isolated from the human oral cavity and clinical material, and emended descriptions of the genus Scardovia and Scardovia inopinata . International Journal of Systematic and Evolutionary Microbiology, 61, 25–29. 10.1099/ijs.0.019752-0 PubMed DOI

Fournier, P. E. , Suhre, K. , Fournous, G. , & Raoult, D. (2006). Estimation of prokaryote genomic DNA G+C content by sequencing universally conserved genes. International Journal of Systematic and Evolutionary Microbiology, 56, 1025–1029. 10.1099/ijs.0.63903-0 PubMed DOI

Glaeser, S. P. , & Kämpfer, P. (2015). Multilocus sequence analysis (MLSA) in prokaryotic taxonomy. Systematic and Applied Microbiology, 38, 237–245. 10.1016/j.syapm.2015.03.007 PubMed DOI

Gupta, R. S. , Nanda, A. , & Khadka, B. (2017). Novel molecular, structural and evolutionary characteristics of the phosphoketolases from bifidobacteria and Coriobacteriales. PLoS ONE, 12, e0172176 10.1371/journal.pone.0172176 PubMed DOI PMC

Huys, G. , Vancanneyt, M. , D′Haene, K. , Falsen, E. , Wauters, G. , & Vandamme, P. (2007). Alloscardovia omnicolens gen. nov., sp. nov., from human clinical samples. International Journal of Systematic and Evolutionary Microbiology, 57, 1442–1446. 10.1099/ijs.0.64812-0 PubMed DOI

Jian, W. , Zhu, L. , & Dong, X. (2001). New approach to phylogenetic analysis of the genus Bifidobacterium based on partial HSP60 gene sequences. International Journal of Systematic and Evolutionary Microbiology, 51, 1633–1638. 10.1099/00207713-51-5-1633 PubMed DOI

Killer, J. , Havlik, J. , Bunesova, V. , Vlkova, E. , & Benada, O. (2014). Pseudoscardovia radai sp. nov., another representative of a new genus within the family Bifidobacteriaceae isolated from the digestive tract of a wild pig (Sus scrofa scrofa). International Journal of Systematic and Evolutionary Microbiology, 64, 2932–2938. 10.1099/ijs.0.063230-0 PubMed DOI

Killer, J. , Kopečný, J. , Mrázek, J. , Havlík, J. , Koppová, I. , Benada, O. , … Kofroňová, O. (2010). Bombiscardovia coagulans gen. nov., sp. nov., a new member of the family Bifidobacteriaceae isolated from the digestive tract of bumblebees. Systematic and Applied Microbiology, 33, 359–366. 10.1016/j.syapm.2010.08.002 PubMed DOI

Killer, J. , Ročková, Š. , Vlková, E. , Rada, V. , Havlík, J. , Kopečný, J. , … Profousová, I. (2013a). Alloscardovia macacae sp. nov., isolated from the milk of a macaque (Macaca mulatta), emended description of the genus Alloscardovia and proposal of Alloscardovia criceti comb. nov. International Journal of Systematic and Evolutionary Microbiology, 63, 4439–4446. 10.1099/ijs.0.051326-0 PubMed DOI

Killer, J. , Sedláček, I. , Rada, V. , Havlík, J. , & Kopečný, J. (2013b). Reclassification of Bifidobacterium stercoris Kim et al. 2010 as a later heterotypic synonym of Bifidobacterium adolescentis . International Journal of Systematic and Evolutionary Microbiology, 63, 4350–4353. 10.1099/ijs.0.054957-0 PubMed DOI

Librado, P. , & Rozas, J. (2009). DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25, 1451–1452. 10.1093/bioinformatics/btp187 PubMed DOI

Lugli, G. A. , Milani, C. , Turroni, F. , Duranti, S. , Ferrario, C. , Viappiani, A. , … Ventura, M. (2014). Investigation of the evolutionary development of the genus Bifidobacterium by comparative genomics. Applied and Environmental Microbiology, 80, 6383–6394. 10.1128/AEM.02004-14 PubMed DOI PMC

Lugli, G. A. , Milani, C. , Turroni, F. , Duranti, S. , Mancabelli, L. , Mangifesta, M. , … Ventura, M. (2017). Comparative genomic and phylogenomic analyses of the Bifidobacteriaceae family. BMC Genomics, 18, 568 10.1186/s12864-017-3955-4 PubMed DOI PMC

Mahlen, S. D. , & Clarridge, J. E. (2009). Site and clinical significance of Alloscardovia omnicolens and Bifidobacterium species isolated in the clinical laboratory. Journal of Clinical Microbiology, 47, 3289–3293. 10.1128/JCM.00555-09 PubMed DOI PMC

Martin, D. P. , Lemey, P. , Lott, M. , Moulton, V. , Posada, D. , & Lefeuvre, P. (2010). RDP3: A flexible and fast computer program for analyzing recombination. Bioinformatics, 26, 2462–2463. 10.1093/bioinformatics/btq467 PubMed DOI PMC

Martin, D. , & Rybicki, E. (2000). RDP: Detection of recombination amongst aligned sequences. Bioinformatics, 16, 562–563. 10.1093/bioinformatics/16.6.562 PubMed DOI

Mattarelli, P. , Holzapfel, W. , Franz, C. M. , Endo, A. , Felis, G. E. , Hammes, W. , … Dellaglio, F. (2014). Recommended minimal standards for description of new taxa of the genera Bifidobacterium, Lactobacillus and related genera. International Journal of Systematic and Evolutionary Microbiology, 64, 1434–1451. 10.1099/ijs.0.060046-0 PubMed DOI

Milani, C. , Lugli, G. A. , Duranti, S. , Turroni, F. , Bottacini, F. , Mangifesta, M. , … Ventura, M. (2014). Genomic encyclopedia of type strains of the genus Bifidobacterium . Applied and Environmental Microbiology, 80, 6290–6302. 10.1128/AEM.02308-14 PubMed DOI PMC

Milani, C. , Turroni, F. , Duranti, S. , Lugli, G. A. , Mancabelli, L. , Ferrario, C. , … Ventura, M. (2015). Genomics of the genus Bifidobacterium reveals species‐specific adaptation to the glycan‐rich gut environment. Applied and Environmental Microbiology, 82, 980–991. PubMed PMC

Naushad, H. S. , & Gupta, R. S. (2013). Phylogenomics and molecular signatures for species from the plant pathogen‐containing order xanthomonadales. PLoS ONE, 8, e55216 10.1371/journal.pone.0055216 PubMed DOI PMC

Nuñez, H. , Loyola, D. , Cárdenas, J. P. , Holmes, D. S. , Johnson, D. B. , & Quatrini, R. (2014). Multi locus sequence typing scheme for Acidithiobacillus caldus strain evaluation and differentiation. Research in Microbiology, 165, 735–742. 10.1016/j.resmic.2014.07.014 PubMed DOI

O'Callaghan, A. , & van Sinderen, D. (2016). Bifidobacteria and their role as members of the human gut microbiota. Frontiers in Microbiology, 7, 925. PubMed PMC

Pechar, R. , Killer, J. , Mekadim, C. , Geigerová, M. , & Rada, V. (2017a). Classification of culturable bifidobacterial population from colonic samples of wild pigs (Sus scrofa) based on three molecular genetic methods. Current Microbiology, 74, 1324–1331. 10.1007/s00284-017-1320-0 PubMed DOI

Pechar, R. , Killer, J. , Salmonová, H. , Geigerová, M. , Švejstil, R. , Švec, P. , … Benada, O. (2017b). Bifidobacterium apri sp. nov., a thermophilic actinobacterium isolated from the digestive tract of wild pigs (Sus scrofa). International Journal of Systematic and Evolutionary Microbiology, 67, 2349–2356. PubMed

Pechar, R. , Killer, J. , Švejstil, R. , Salmonová, H. , Geigerová, M. , Bunešová, V. , … Benada, O. (2017c). Galliscardovia ingluviei gen. nov., sp. nov., a thermophilic bacterium of the family Bifidobacteriaceae isolated from the crop of a laying hen (Gallus gallus f. domestica). International Journal of Systematic and Evolutionary Microbiology, 67, 2403–2411. PubMed

Rada, V. , & Petr, J. (2000). A new selective medium for the isolation of glucose non‐fermenting bifidobacteria from hen caeca. Journal of Microbiological Methods, 43, 127–132. 10.1016/S0167-7012(00)00205-0 PubMed DOI

Roux, S. , Enault, F. , Bronner, G. , & Debroas, D. (2011). Comparison of 16S rRNA and protein‐coding genes as molecular markers for assessing microbial diversity (Bacteria and Archaea) in ecosystems. FEMS Microbiology Ecology, 78, 617–628. 10.1111/j.1574-6941.2011.01190.x PubMed DOI

Rudenko, N. , Golovchenko, M. , Belfiore, N. M. , Grubhoffer, L. , & Oliver, J. H. Jr (2014). Divergence of Borrelia burgdorferi sensu lato spirochetes could be driven by the host: Diversity of Borrelia strains isolated from ticks feeding on a single bird. Parasites and Vectors, 7, 4 10.1186/1756-3305-7-4 PubMed DOI PMC

Sarmiento‐Rubiano, L. A. , Berger, B. , Moine, D. , Zúñiga, M. , Pérez‐Martínez, G. , & Yebra, M. J. (2010). Characterization of a novel Lactobacillus species closely related to Lactobacillus johnsonii using a combination of molecular and comparative genomics methods. BMC Genomics, 11, 504 10.1186/1471-2164-11-504 PubMed DOI PMC

Satokari, R. M. , Vaughan, E. E. , Akkermans, A. D. , Saarela, M. , & de Vos, W. M. (2001). Bifidobacterial diversity in human feces detected by genus‐specific PCR and denaturing gradient gel electrophoresis. Applied and Environmental Microbiology, 67, 504–513. 10.1128/AEM.67.2.504-513.2001 PubMed DOI PMC

Scardovi, V. (1986). Genus Bifidobacterium In Sneath P. H. A., Mair N. S., Sharp M. E. & Holt J. G. (Eds.), Bergey′s manual of systematic bacteriology (p. 1423). Baltimore: Williams & Wilkins.

Scardovi, V. , Trovatelli, L. D. , Biavati, B. , & Zani, G. (1979). Bifidobacterium cuniculi, Bifidobacterium choerinum, Bifidobacterium boum, and Bifidobacterium pseudocatenulatum: Four new species and their deoxyribonucleic acid homlogy relationships. International Journal of Systematic Bacteriology, 29, 291–311. 10.1099/00207713-29-4-291 DOI

Sechovcová, H. , Killer, J. , Pechar, R. , Geigerová, M. , Švejstil, R. , Salmonová, H. , … Benada, O. (2017). Alloscardovia venturai sp. nov., a fructose 6‐phosphate phosphoketolase‐positive species isolated from the oral cavity of a guinea‐pig (Cavia aperea f. porcellus). International Journal of Systematic and Evolutionary Microbiology, 67, 2842–2847. PubMed

Simpson, P. J. , Ross, R. P. , Fitzgerald, G. F. , & Stanton, C. (2004). Bifidobacterium psychraerophilum sp. nov. and Aeriscardovia aeriphila gen. nov., sp. nov., isolated from a porcine caecum. International Journal of Systematic and Evolutionary Microbiology, 54, 401–406. 10.1099/ijs.0.02667-0 PubMed DOI

Sun, Z. , Zhang, W. , Guo, C. , Yang, X. , Liu, W. , Wu, Y. , … Zhang, H. (2015). Comparative genomic analysis of 45 type strains of the genus Bifidobacterium: A snapshot of its genetic diversity and evolution. PLoS ONE, 10, e0117912 10.1371/journal.pone.0117912 PubMed DOI PMC

Tamura, K. , Peterson, D. , Peterson, N. , Stecher, G. , Nei, M. , & Kumar, S. (2011). MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28, 2731–2739. 10.1093/molbev/msr121 PubMed DOI PMC

Tanner, A. C. , Mathney, J. M. , Kent, R. L. , Chalmers, N. I. , Hughes, C. V. , Loo, C. Y. , … Dewhirst, F. E. (2011). Cultivable anaerobic microbiota of severe early childhood caries. Journal of Clinical Microbiology, 49, 1464–1474. 10.1128/JCM.02427-10 PubMed DOI PMC

Tomasini, N. , Lauthier, J. J. , Llewellyn, M. S. , & Diosque, P. (2013). MLSTest: Novel software for multi‐locus sequence data analysis in eukaryotic organisms. Infection, Genetics and Evolution, 20, 188–196. 10.1016/j.meegid.2013.08.029 PubMed DOI

Untergasser, A. , Cutcutache, I. , Koressaar, T. , Ye, J. , Faircloth, B. C. , Remm, M. , & Rozen, S. G. (2012). Primer3‐new capabilities and interfaces. Nucleic Acids Research, 40, e115 10.1093/nar/gks596 PubMed DOI PMC

Valdez, R. M. , Dos Santos, V. R. , Caiaffa, K. S. , Danelon, M. , Arthur, R. A. , Negrini, T. C. , … Duque, C. (2016). Comparative in vitro investigation of the cariogenic potential of bifidobacteria. Archives of Oral Biology, 71, 97–103. 10.1016/j.archoralbio.2016.07.005 PubMed DOI

Ventura, M. , Canchaya, C. , Del Casale, A. , Dellaglio, F. , Neviani, E. , Fitzgerald, G. F. , & van Sinderen, D. (2006). Analysis of bifidobacterial evolution using a multilocus approach. International Journal of Systematic and Evolutionary Microbiology, 56, 2783–2792. 10.1099/ijs.0.64233-0 PubMed DOI

Větrovský, T. , & Baldrian, P. (2013). The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses. PLoS ONE, 8, e57923 10.1371/journal.pone.0057923 PubMed DOI PMC

Weber, E. , Reynaud, Q. , Suy, F. , Gagneux‐Brunon, A. , Carricajo, A. , Guillot, A. , & Botelho‐Nevers, E. (2015). Bifidobacterium species bacteremia: Risk factors in adults and infants. Clinical Infectious Diseases, 61, 482–484. 10.1093/cid/civ347 PubMed DOI

Wu, D. , Jospin, G. , & Eisen, J. A. (2013). Systematic identification of gene families for use as “markers” for phylogenetic and phylogeny‐driven ecological studies of bacteria and archaea and their major subgroups. PLoS ONE, 8, e77033 10.1371/journal.pone.0077033 PubMed DOI PMC

Yoon, S. H. , Ha, S. M. , Kwon, S. , Lim, J. , Kim, Y. , Seo, H. , & Chun, J. (2017). Introducing EzBioCloud: A taxonomically united database of 16S rRNA gene sequences and whole‐genome assemblies. International Journal of Systematic and Evolutionary Microbiology, 67, 1613–1617. PubMed PMC

Zhang, G. , Gao, B. , Adeolu, M. , Khadka, B. , & Gupta, R. S. (2016). Phylogenomic analyses and comparative studies on genomes of the bifidobacteriales: Identification of molecular signatures specific for the order bifidobacteriales and its different subclades. Frontiers in Microbiology, 7, 978. PubMed PMC

The bifidobacterial distribution in the microbiome of captive primates reflects parvorder and feed specialization of the host

Glutamine synthetase type I (glnAI) represents a rewarding molecular marker in the classification of bifidobacteria and related genera

Fragment of the aspartyl-tRNA synthetase applicable as a shared classification and phylogenetic marker in particular representatives of the order Lactobacillales

The threonine-tRNA ligase gene region is applicable in classification, typing, and phylogenetic analysis of bifidobacteria

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