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.
Journal
Current microbiology
ISSN: 1432-0991
Titre abrégé: Curr Microbiol
Pays: United States
ID NLM: 7808448
Informations de publication
Date de publication:
11 May 2024
11 May 2024
Historique:
received:
27
01
2024
accepted:
21
04
2024
medline:
11
5
2024
pubmed:
11
5
2024
entrez:
11
5
2024
Statut:
epublish
Résumé
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 18911
Identifiants
pubmed: 38733376
doi: 10.1007/s00284-024-03712-x
pii: 10.1007/s00284-024-03712-x
doi:
Substances chimiques
DNA, Bacterial
0
RNA, Ribosomal, 16S
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
168Subventions
Organisme : National Natural Science Foundation of China
ID : no. 31471594
Organisme : "Characteristic Probiotics and New Fermented Food" Team in Northeast Agricultural University
ID : no. 50940912, Harbin, China
Informations de copyright
© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.
Références
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
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
doi: 10.1099/00207713-30-1-225
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
doi: 10.1099/00207713-32-3-358
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
doi: 10.1007/BF00409030
pubmed: 5528914
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
doi: 10.1099/ijsem.0.005390
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
doi: 10.1016/j.syapm.2021.126273
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
doi: 10.3389/fmicb.2018.02007
pubmed: 30186281
pmcid: 6113628
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
doi: 10.1099/ijs.0.053355-0
pubmed: 23728376
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
doi: 10.1089/cmb.2012.0021
pubmed: 22506599
pmcid: 3342519
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
doi: 10.1101/gr.186072.114
pubmed: 25977477
pmcid: 4484387
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
doi: 10.1093/nar/gkz282
pubmed: 30997504
pmcid: 6602446
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
doi: 10.1007/s12275-018-8014-6
pubmed: 29492869
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
doi: 10.1007/s12275-021-1231-4
pubmed: 34052993
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
doi: 10.1093/nar/gkw256
pubmed: 27084950
pmcid: 4987875
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
doi: 10.1093/nar/gkac1003
pubmed: 36350631
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
doi: 10.1038/s41467-019-10210-3
pubmed: 31097708
pmcid: 6522516
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
doi: 10.1099/ijsem.0.000760
pubmed: 26585518
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
doi: 10.1007/s10482-017-0844-4
pubmed: 28204908
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
doi: 10.4056/sigs.531120
pubmed: 21304684
pmcid: 3035253
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
doi: 10.1111/j.1348-0421.2006.tb03762.x
pubmed: 16428867
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
doi: 10.1111/j.1348-0421.1998.tb02337.x
pubmed: 9858460
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
doi: 10.1099/00207713-51-5-1633
pubmed: 11594590
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
doi: 10.1099/ijs.0.020339-0
pubmed: 20061504
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
doi: 10.1016/j.lwt.2004.05.002
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
doi: 10.1099/00207713-46-1-102
pubmed: 8573484
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
doi: 10.1007/s10482-019-01307-2
pubmed: 31368048
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
doi: 10.1007/s12223-019-00716-0
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
doi: 10.1007/s12275-018-8167-3
pubmed: 30267314
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
doi: 10.1099/ijs.0.64233-0
pubmed: 17158978
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
doi: 10.1007/s00284-008-9202-0
pubmed: 18663527
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
doi: 10.1128/AEM.70.10.6197-6209.2004
pubmed: 15466567
pmcid: 522111
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
doi: 10.1111/1574-6941.12410
pubmed: 25117972
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
doi: 10.1099/ijsem.0.002516
pubmed: 29292687
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
doi: 10.1099/ijs.0.64483-0
pubmed: 17220447
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
doi: 10.1073/pnas.0906412106
pubmed: 19855009
pmcid: 2776425
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
doi: 10.1099/00207713-44-4-846