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The Type Strain of Bifidobacterium indicum Scardovi and Trovatelli 1969 (Approved Lists 1980) is ATCC 25912, not DSM 20214, and Rejection to Reclassify Bifidobacterium coryneforme as Bifidobacterium indicum

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Abstract

In 2018, Nouioui et al. proposed that Bifidobacterium coryneforme was a later synonym of Bifidobacterium indicum on the basis of the digital DNA-DNA hybridization (dDDH) value (85.0%) between B. coryneforme LMG 18911T and B. indicum LMG 11587T. However, in the study of Scardovi et al. (1970), the type strains of B. indicum and B. coryneforme only exhibited 60% DNA-DNA hybridization value. In the present study, the genomes of B. coryneforme CGMCC 1.2279T, B. coryneforme JCM 5819T, B. indicum JCM 1302T, B. indicum CGMCC 1.2275T, B. indicum DSM 20214T, B. indicum LMG 27437T, B. indicum ATCC 25912T, B. indicum KCTC 3230T, B. indicum CCUG 34985T, were sequenced, and the taxonomic relationship between B. coryneforme and B. indicum was re-evaluated. On the basis of the results presented here, (i) ATCC 25912 and DSM 20214 deposited by Vittorio Scardovi are two different strains; (ii) the type strain of B. indicum is ATCC 25912T (= JCM 1302T = LMG 27437T = CGMCC 1.2275T = KCTC 3230T), and not DSM 20214 (= BCRC 14674 = CCUG 34985 = LMG 11587); (iii) B. coryneforme and B. indicum represent two different species of the genus Bifidobacterium; (iv) strain DSM 20214 (= BCRC 14674 = CCUG 34985 = LMG 11587) belongs to B. coryneforme.

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Fig. 1

Abbreviations

ANI:

Average nucleotide identity

dDDH:

Digital DNA–DNA hybridization

mMRS:

Modified de Man–Rogosa–Sharpe

GBDP:

Genome BLAST distance phylogeny

TYGS:

Type (strain) genome server

References

  1. Scardovi V, Trovatelli LD (1969) New species of bifidobacteria from Apis mellifica L. and Apis indica F. A contribution to the taxonomy and biochemistry of the genus Bifidobacterium. Zentralblatt für Bakteriologie, Parasitenkunde. Infektionskrankheiten und Hygiene Abteilung II 123:64–88

    CAS  Google Scholar 

  2. Skerman VBD, McGowan V, Sneath PHA (1980) Approved lists of bacterial names. Int J Syst Bacteriol 30:225–420. https://doi.org/10.1099/00207713-30-1-225

    Article  Google Scholar 

  3. Biavati B, Scardovi V, Moore WEC (1982) Electrophoretic patterns of proteins in the genus Bifidobacterium and proposal of four new species. Int J Syst Bacteriol 32:358–373. https://doi.org/10.1099/00207713-32-3-358

    Article  CAS  Google Scholar 

  4. Scardovi V, Zani G, Trovatelli LD (1970) Deoxyribonucleic acid homology among the species of the genus Bifidobacterium isolated from animals. Arch Mikrobiol 72:318–325. https://doi.org/10.1007/BF00409030

    Article  CAS  PubMed  Google Scholar 

  5. Li TT, Zhang HX, Gu CT (2022) Bifidobacterium mizhiense sp. nov., isolated from the gut of honeybee (Apis mellifera). Int J Syst Evol Microbiol 72:005390. https://doi.org/10.1099/ijsem.0.005390

    Article  Google Scholar 

  6. Lugli GA, Calvete-Torre I, Alessandri G, Milani C, Turroni F et al (2021) Phylogenetic classification of ten novel species belonging to the genus Bifidobacterium comprising B. phasiani sp. nov., B. pongonis sp. nov., B. saguinibicoloris sp. nov., B. colobi sp. nov., B. simiiventris sp. nov., B. santillanense sp. nov., B. miconis sp. nov., B. amazonense sp. nov., B. pluvialisilvae sp. nov., and B. miconisargentati sp. nov. Appl Microbiol 44:126273. https://doi.org/10.1016/j.syapm.2021.126273

    Article  CAS  Google Scholar 

  7. Nouioui I, Carro L, Garcia-Lopez M, Meier-Kolthoff JP, Woyke T et al (2018) Genome-based taxonomic classification of the phylum Actinobacteria. Front Microbiol 9:2007. https://doi.org/10.3389/fmicb.2018.02007

    Article  PubMed  PubMed Central  Google Scholar 

  8. Gu CT, Li CY, Yang LJ, Huo GC (2013) Lactobacillus heilongjiangensis sp. nov., isolated from Chinese pickle. Int J Syst Evol Microbiol 63:4094–4099. https://doi.org/10.1099/ijs.0.053355-0

    Article  CAS  PubMed  Google Scholar 

  9. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. https://doi.org/10.1089/cmb.2012.0021

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW (2015) CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25:1043–1055. https://doi.org/10.1101/gr.186072.114

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Alanjary M, Steinke K, Ziemert N (2019) AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential. Nucleic Acids Res 47(W1):W276–W282. https://doi.org/10.1093/nar/gkz282

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Na SI, Kim YO, Yoon SH, Ha SM, Baek I, Chun J (2018) UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 56:280–285. https://doi.org/10.1007/s12275-018-8014-6

    Article  CAS  PubMed  Google Scholar 

  13. Kim J, Na SI, Kim D, Chun J (2021) UBCG2: Up-to-date bacterial core genes and pipeline for phylogenomic analysis. J Microbiol 59:609–615. https://doi.org/10.1007/s12275-021-1231-4

    Article  CAS  PubMed  Google Scholar 

  14. Trifinopoulos J, Nguyen LT, von Haeseler A, Minh BQ (2016) W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Res 44:W232–W235. https://doi.org/10.1093/nar/gkw256

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Olson RD, Assaf R, Brettin T, Conrad N, Cucinell C, Davis JJ, Dempsey DM, Dickerman A, Dietrich EM, Kenyon RW, Kuscuoglu M, Lefkowitz EJ, Lu J, Machi D, Macken C, Mao C, Niewiadomska A, Nguyen M, Olsen GJ, Overbeek JC, Parrello B, Parrello V, Porter JS, Pusch GD, Shukla M, Singh I, Stewart L, Tan G, Thomas C, VanOeffelen M, Vonstein V, Wallace ZS, Warren AS, Wattam AR, Xia F, Yoo H, Zhang Y, Zmasek CM, Scheuermann RH, Stevens RL (2023) Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR. Nucleic Acids Res 51:D678–D689. https://doi.org/10.1093/nar/gkac1003

    Article  CAS  PubMed  Google Scholar 

  16. Meier-Kolthoff JP, Göker M (2019) TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 10:2182. https://doi.org/10.1038/s41467-019-10210-3

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Lee I, Ouk Kim Y, Park SC, Chun J (2016) OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66:1100–1103. https://doi.org/10.1099/ijsem.0.000760

    Article  CAS  PubMed  Google Scholar 

  18. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J (2017) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110:1281–1286. https://doi.org/10.1007/s10482-017-0844-4

    Article  CAS  PubMed  Google Scholar 

  19. Auch AF, von Jan M, Klenk H-P, Göker M (2010) Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2:117–134. https://doi.org/10.4056/sigs.531120

    Article  PubMed  PubMed Central  Google Scholar 

  20. Sakata S, Ryu CS, Kitahara M, Sakamoto M, Hayashi H et al (2006) Characterization of the genus Bifidobacterium by automated ribotyping and 16S rRNA gene sequences. Microbiol Immunol 50:1–10. https://doi.org/10.1111/j.1348-0421.2006.tb03762.x

    Article  CAS  PubMed  Google Scholar 

  21. Miyake T, Watanabe K, Watanabe T, Oyaizu H (1998) Phylogenetic analysis of the genus Bifidobacterium and related genera based on 16S rDNA sequences. Microbiol Immunol 42:661–667. https://doi.org/10.1111/j.1348-0421.1998.tb02337.x

    Article  CAS  PubMed  Google Scholar 

  22. Jian W, Zhu L, Dong X (2001) New approach to phylogenetic analysis of the genus Bifidobacterium based on partial HSP60 gene sequences. Int J Syst Evol Microbiol 51:1633–1638. https://doi.org/10.1099/00207713-51-5-1633

    Article  CAS  PubMed  Google Scholar 

  23. Kim BJ, Kim HY, Yun YJ, Kim BJ, Kook YH (2010) Differentiation of Bifidobacterium species using partial RNA polymerase β-subunit (rpoB) gene sequences. Int J Syst Evol Microbiol 60:2697–2704. https://doi.org/10.1099/ijs.0.020339-0

    Article  PubMed  Google Scholar 

  24. Berthoud H, Chavagnat F, Haueter M, Casey MG (2005) Comparison of partial gene sequences encoding a phosphoketolase for the identification of bifidobacteria. LWT-Food Sci Technol 38:101–105. https://doi.org/10.1016/j.lwt.2004.05.002

    Article  CAS  Google Scholar 

  25. Leblond-Bourget N, Philippe H, Mangin I, Decaris B (1996) 16S rRNA and 16S to 23S internal transcribed spacer sequence analyses reveal inter- and intraspecific Bifidobacterium phylogeny. Int J Syst Bacteriol 46:102–111. https://doi.org/10.1099/00207713-46-1-102

    Article  CAS  PubMed  Google Scholar 

  26. Mekadim C, Bunešová V, Vlková E, Hroncová Z, Killer J (2019) Genetic marker-based multi-locus sequence analysis for classification, genotyping, and phylogenetics of the family Bifidobacteriaceae as an alternative approach to phylogenomics. Antonie Van Leeuwenhoek 112:1785–1800. https://doi.org/10.1007/s10482-019-01307-2

    Article  CAS  PubMed  Google Scholar 

  27. Killer J, Mekadim C, Bunešová V, Mrázek J, Hroncová Z et al (2020) Glutamine synthetase type I (glnAI) represents a rewarding molecular marker in the classification of bifidobacteria and related genera. Folia Microbiol 65:143–151. https://doi.org/10.1007/s12223-019-00716-0

    Article  CAS  Google Scholar 

  28. Killer J, Mekadim C, Pechar R, Bunešová V, Vlková E (2018) The threonine-tRNA ligase gene region is applicable in classification, typing, and phylogenetic analysis of bifidobacteria. J Microbiol 56:713–721. https://doi.org/10.1007/s12275-018-8167-3

    Article  CAS  PubMed  Google Scholar 

  29. Ventura M, Canchaya C, Casale AD, Dellaglio F, Neviani E et al (2006) Analysis of bifidobacterial evolution using a multilocus approach. Int J Syst Evol Microbiol 56:2783–2792. https://doi.org/10.1099/ijs.0.64233-0

    Article  CAS  PubMed  Google Scholar 

  30. Olofsson TC, Vásquez A (2008) Detection and identification of a novel lactic acid bacterial flora within the honey stomach of the honeybee Apis mellifera. Curr Microbiol 57:356–363. https://doi.org/10.1007/s00284-008-9202-0

    Article  CAS  PubMed  Google Scholar 

  31. Ventura M, Canchaya C, Zink R, Fitzgerald GF, van Sinderen D (2004) Characterization of the groEL and groES loci in Bifidobacterium breve UCC 2003: genetic, transcriptional, and phylogenetic analyses. Appl Environ Microbiol 70:6197–6209. https://doi.org/10.1128/AEM.70.10.6197-6209.2004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Milani C, Lugli GA, Turroni F, Mancabelli L, Duranti S et al (2014) Evaluation of bifidobacterial community composition in the human gut by means of a targeted amplicon sequencing (ITS) protocol. FEMS Microbiol Ecol 90:493–503. https://doi.org/10.1111/1574-6941.12410

    Article  CAS  PubMed  Google Scholar 

  33. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68:461–466. https://doi.org/10.1099/ijsem.0.002516

    Article  CAS  PubMed  Google Scholar 

  34. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al (2007) DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91. https://doi.org/10.1099/ijs.0.64483-0

    Article  CAS  PubMed  Google Scholar 

  35. Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106:19126–19131. https://doi.org/10.1073/pnas.0906412106

    Article  PubMed  PubMed Central  Google Scholar 

  36. Stackebrandt E, Goebel BM (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. https://doi.org/10.1099/00207713-44-4-846

    Article  CAS  Google Scholar 

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Funding

This work was supported by the National Natural Science Foundation of China (No. 31471594) and “Characteristic Probiotics and New Fermented Food” Team in Northeast Agricultural University (No. 50940912, Harbin, China).

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Authors and Affiliations

  1. College of Life Sciences, Northeast Agricultural University, Harbin, 150030, People’s Republic of China

    Cheng-Shan Jiang & Chun Tao Gu

  2. College of Food Science, Northeast Agricultural University, Harbin, 150030, People’s Republic of China

    Chun Yan Li

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  1. Cheng-Shan Jiang
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Contributions

CSJ and CTG conceived and designed the experiments. CSJ performed the experiments. CSJ and CTG analyzed the data. CSJ, CYL and CTG wrote and revised the paper.

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Correspondence to Chun Tao Gu.

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Jiang, CS., Li, C.Y. & Gu, C.T. The Type Strain of Bifidobacterium indicum Scardovi and Trovatelli 1969 (Approved Lists 1980) is ATCC 25912, not DSM 20214, and Rejection to Reclassify Bifidobacterium coryneforme as Bifidobacterium indicum. Curr Microbiol 81, 168 (2024). https://doi.org/10.1007/s00284-024-03712-x

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