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Environmental Microbiology and Biotechnology (EMB) | Microbial Ecology and Taxonomy
Synonymy of Micropolyspora internatus and Saccharomonospora viridis and Emended Description of Saccharomonospora viridis
1BK21PLUS Program in Embodiment: Health-Society Interaction, Department of Public Health Sciences, Graduate School, Korea University, Seoul 02841, Republic of Korea, 2Chunlab, Inc., Seoul 08826, Republic of Korea, 3School of Biosystem and Biomedical Science, Korea University, Seoul 02841, Republic of Korea
Received: October 12, 2016; Accepted: October 28, 2016
J. Microbiol. Biotechnol. 2017; 27(1): 149-154
Published January 28, 2017 https://doi.org/10.4014/jmb.1610.10033
Copyright © The Korean Society for Microbiology and Biotechnology.
Abstract
Transfer of Micropolyspora internatus into the genus Saccharomonospora as “Saccharomonospora
internatus comb. nov.” was proposed by Kurup and Greiner-Mai, but the nomenclatural
change has not been validly published. Although the inclusion of M. internatus in the genus
Saccharomonospora has not being established, the synonymy of “Saccharomonospora internatus”
and S. viridis was proposed by Greiner-Mai. A number of recent publications regarded
M. internatus as a synonym of S. viridis, but the name M. internatus is still used in some cases
instead of S. viridis. This is because of the complicated history of M. internatus and S. viridis,
but it is different from the generally accepted view of prokaryotic taxonomy. To clearly verify
the synonymy of M. internatus and S. viridis, a literature review and experimental verification
were conducted in this study. Based on the genomic and phenotypic characteristics obtained
in this study, the synonymy of the two species was obvious. The emended description of
S. viridis is given.
Keywords
Micropolyspora internatus, Saccharomonospora viridis, whole genome sequencing
References
- Nonomura H, Ohara Y. 1971. Distribution of actinomycetes in soil. 10 new genus and species of monosporic actinomycetes. J. Ferment. Technol. 49: 895-903.
- Lechevalier MP, Lechevalier H. 1970. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int. J. Syst. Bacteriol. 20: 435-443.
- Schuurmans DM, Olson BH, San Clemente CL. 1956. Production and isolation of thermoviridin, an antibiotic produced by Thermoactinomyces viridis n. sp. Appl. Microbiol. 4: 61-66.
- Skerman VBD, Mcgowan V, Sneath PHA. 1980. Approved lists of bacterial names. Int. J. Syst. Bacteriol. 30: 225-420.
- Lechevalier H, Solotorovsky M, McDurmont CI. 1961. A new genus of actinomycetales - Micropolyspora gen. nov. J. Gen. Microbiol. 26: 11-18.
- Zhukova RA, Tsyganov VA, Morozov VM. 1968. A new species of Micropolyspora: Micropolyspora angiospora sp. nov. Mikrobiologiya 37: 724-728.
- Cross T, Maciver AM, Lacey J. 1968. Thermophilic actinomycetes in mouldy hay - Micropolyspora faeni sp. nov. J. Gen. Microbiol. 50: 351-359.
- Agre NS, Guzeva LN, Dorokhova LA. 1974. New species of genus Micropolyspora - Micropolyspora internatus. Microbiology 43: 577-583.
- Krasil’nikov NA, Agre NS. 1964. On two new species of Thermopolyspora. Hind. Antibiot. Bull. 6: 97-107.
- Prauser H, Momirova S. 1970. Phage sensitivity, cell wall composition and taxonomy of a thermophilic actinomycete. Z. Allg. Mikrobiol. 10: 219-222.
- Kurup VP. 1981. Taxonomic study of some members of Micropolyspora and Saccharomonospora. Microbiologica 4: 249-259.
- Korn-Wendisch F, Kempf A, Grund E, Kroppenstedt RM, Kutzner HJ. 1989. Transfer of Faenia rectivirgula Kurup and Agre 1983 to the genus Saccharopolyspora Lacey and Goodfellow 1975, elevation of Saccharopolyspora hirsuta subsp. taberi Labeda 1987 to species level, and emended description of the genus Saccharopolyspora. Int. J. Syst. Bacteriol. 39: 430-441.
- Zhang ZS, Wang Y, Ruan JS. 1998. Reclassification of Thermomonospora and Microtetraspora. Int. J. Syst. Bacteriol. 48: 411-422.
- Greiner-Mai E, Kroppenstedt RM, Korn-Wendisch F, Kutzner HJ. 1987. Morphological and biochemicalcharacterization and emended descriptions of thermophilic actinomycetes species. Syst. Appl. Microbiol. 9: 97-109.
- Greiner-Mai E, Korn-Wendisch F, Kutzner HJ. 1988. Taxonomic revision of the genus Saccharomonospora and description of Saccharomonospora glauca sp. nov. Int. J. Syst. Bacteriol. 38:398-405.
- Wayne L, Brenner D, Colwell R, Grimont P, Kandler O, Krichevsky M, et al. 1987. Report of the Ad Hoc Committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 37: 463-464.
- Yoon JH, Kim SB, Lee ST, Park YH. 1999. DNA-DNA relatedness between Saccharomonospora species: ‘Saccharomonospora caesia’ as a synonym of Saccharomonospora azurea. Int. J. Syst. Bacteriol. 49: 671-673.
- Shriling EB, Gottlieb D. 1996. Methods for characterization of Streptomyces species. Int. J. Syst. Bacteriol. 16: 313-340.
- Shin SK, Kim E, Choi S, Yi H. 2016. Cochleicola gelatinilyticus gen. nov., sp. nov., isolated from a marine gastropod, Reichia luteostoma. J. Microbiol. Biotechnol. 26: 1439-1445.
- Pati A, Sikorski J, Nolan M, Lapidus A, Copeland A, Del Rio TG, et al. 2009. Complete genome sequence of Saccharomonospora viridis type strain (P101T). Stand. Genomic Sci. 1: 141-149.
- Lee I, Kim YO, Park SC, Chun J. 2016. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int. J. Syst. Bacteriol. 66: 1100-1103.
- Jeon YS, Lee K, Park SC, Kim BS, Cho YJ, Ha SM, Chun J. 2014. EzEditor: a versatile sequence alignment editor for both rRNA- and protein-coding genes. Int. J. Syst. Evol. Microbiol. 64: 689-691.
- Sohpal VK, Dey A, Singh A. 2010. MEGA biocentric software for sequence and phylogenetic analysis: a review. Int. J. Bioinform. Res. Appl. 6: 230-240.
- Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
- Felsenstein J. 1993. PHYLIP (phylogenetic inference package) version 3.5c. Department of Genetics, University of Washington.
- Felsenstein J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791.
- Auch AF, von Jan M, Klenk HP, Goker M. 2010. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand. Genomic Sci. 2: 117-134.
- Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM. 2007. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int. J. Syst. Evol. Microbiol. 57: 81-91.
- Kim M, Oh HS, Park SC, 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.
- Konstantinidis KT, Tiedje JM. 2005. Genomic insights that advance the species definition for prokaryotes. Proc. Natl. Acad. Sci. USA 102: 2567-2572.
- Richter M, Rossello-Mora R. 2009. Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. USA 106: 19126-19131.
- Meier-Kolthoff JP, Auch AF, Klenk HP, Goker M. 2013. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14: 60.
- Tindall BJ, Rossello-Mora R, Busse HJ, Ludwig W, Kampfer P. 2010. Notes on the characterization of prokaryote strains for taxonomic purposes. Int. J. Syst. Evol. Microbiol. 60: 249-266.
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Research article
J. Microbiol. Biotechnol. 2017; 27(1): 149-154
Published online January 28, 2017 https://doi.org/10.4014/jmb.1610.10033
Copyright © The Korean Society for Microbiology and Biotechnology.
Synonymy of Micropolyspora internatus and Saccharomonospora viridis and Emended Description of Saccharomonospora viridis
Su-Kyoung Shin 1, Yong-Joon Cho 2 and Hana Yi 1, 3*
1BK21PLUS Program in Embodiment: Health-Society Interaction, Department of Public Health Sciences, Graduate School, Korea University, Seoul 02841, Republic of Korea, 2Chunlab, Inc., Seoul 08826, Republic of Korea, 3School of Biosystem and Biomedical Science, Korea University, Seoul 02841, Republic of Korea
Received: October 12, 2016; Accepted: October 28, 2016
Abstract
Transfer of Micropolyspora internatus into the genus Saccharomonospora as “Saccharomonospora
internatus comb. nov.” was proposed by Kurup and Greiner-Mai, but the nomenclatural
change has not been validly published. Although the inclusion of M. internatus in the genus
Saccharomonospora has not being established, the synonymy of “Saccharomonospora internatus”
and S. viridis was proposed by Greiner-Mai. A number of recent publications regarded
M. internatus as a synonym of S. viridis, but the name M. internatus is still used in some cases
instead of S. viridis. This is because of the complicated history of M. internatus and S. viridis,
but it is different from the generally accepted view of prokaryotic taxonomy. To clearly verify
the synonymy of M. internatus and S. viridis, a literature review and experimental verification
were conducted in this study. Based on the genomic and phenotypic characteristics obtained
in this study, the synonymy of the two species was obvious. The emended description of
S. viridis is given.
Keywords: Micropolyspora internatus, Saccharomonospora viridis, whole genome sequencing
References
- Nonomura H, Ohara Y. 1971. Distribution of actinomycetes in soil. 10 new genus and species of monosporic actinomycetes. J. Ferment. Technol. 49: 895-903.
- Lechevalier MP, Lechevalier H. 1970. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int. J. Syst. Bacteriol. 20: 435-443.
- Schuurmans DM, Olson BH, San Clemente CL. 1956. Production and isolation of thermoviridin, an antibiotic produced by Thermoactinomyces viridis n. sp. Appl. Microbiol. 4: 61-66.
- Skerman VBD, Mcgowan V, Sneath PHA. 1980. Approved lists of bacterial names. Int. J. Syst. Bacteriol. 30: 225-420.
- Lechevalier H, Solotorovsky M, McDurmont CI. 1961. A new genus of actinomycetales - Micropolyspora gen. nov. J. Gen. Microbiol. 26: 11-18.
- Zhukova RA, Tsyganov VA, Morozov VM. 1968. A new species of Micropolyspora: Micropolyspora angiospora sp. nov. Mikrobiologiya 37: 724-728.
- Cross T, Maciver AM, Lacey J. 1968. Thermophilic actinomycetes in mouldy hay - Micropolyspora faeni sp. nov. J. Gen. Microbiol. 50: 351-359.
- Agre NS, Guzeva LN, Dorokhova LA. 1974. New species of genus Micropolyspora - Micropolyspora internatus. Microbiology 43: 577-583.
- Krasil’nikov NA, Agre NS. 1964. On two new species of Thermopolyspora. Hind. Antibiot. Bull. 6: 97-107.
- Prauser H, Momirova S. 1970. Phage sensitivity, cell wall composition and taxonomy of a thermophilic actinomycete. Z. Allg. Mikrobiol. 10: 219-222.
- Kurup VP. 1981. Taxonomic study of some members of Micropolyspora and Saccharomonospora. Microbiologica 4: 249-259.
- Korn-Wendisch F, Kempf A, Grund E, Kroppenstedt RM, Kutzner HJ. 1989. Transfer of Faenia rectivirgula Kurup and Agre 1983 to the genus Saccharopolyspora Lacey and Goodfellow 1975, elevation of Saccharopolyspora hirsuta subsp. taberi Labeda 1987 to species level, and emended description of the genus Saccharopolyspora. Int. J. Syst. Bacteriol. 39: 430-441.
- Zhang ZS, Wang Y, Ruan JS. 1998. Reclassification of Thermomonospora and Microtetraspora. Int. J. Syst. Bacteriol. 48: 411-422.
- Greiner-Mai E, Kroppenstedt RM, Korn-Wendisch F, Kutzner HJ. 1987. Morphological and biochemicalcharacterization and emended descriptions of thermophilic actinomycetes species. Syst. Appl. Microbiol. 9: 97-109.
- Greiner-Mai E, Korn-Wendisch F, Kutzner HJ. 1988. Taxonomic revision of the genus Saccharomonospora and description of Saccharomonospora glauca sp. nov. Int. J. Syst. Bacteriol. 38:398-405.
- Wayne L, Brenner D, Colwell R, Grimont P, Kandler O, Krichevsky M, et al. 1987. Report of the Ad Hoc Committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 37: 463-464.
- Yoon JH, Kim SB, Lee ST, Park YH. 1999. DNA-DNA relatedness between Saccharomonospora species: ‘Saccharomonospora caesia’ as a synonym of Saccharomonospora azurea. Int. J. Syst. Bacteriol. 49: 671-673.
- Shriling EB, Gottlieb D. 1996. Methods for characterization of Streptomyces species. Int. J. Syst. Bacteriol. 16: 313-340.
- Shin SK, Kim E, Choi S, Yi H. 2016. Cochleicola gelatinilyticus gen. nov., sp. nov., isolated from a marine gastropod, Reichia luteostoma. J. Microbiol. Biotechnol. 26: 1439-1445.
- Pati A, Sikorski J, Nolan M, Lapidus A, Copeland A, Del Rio TG, et al. 2009. Complete genome sequence of Saccharomonospora viridis type strain (P101T). Stand. Genomic Sci. 1: 141-149.
- Lee I, Kim YO, Park SC, Chun J. 2016. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int. J. Syst. Bacteriol. 66: 1100-1103.
- Jeon YS, Lee K, Park SC, Kim BS, Cho YJ, Ha SM, Chun J. 2014. EzEditor: a versatile sequence alignment editor for both rRNA- and protein-coding genes. Int. J. Syst. Evol. Microbiol. 64: 689-691.
- Sohpal VK, Dey A, Singh A. 2010. MEGA biocentric software for sequence and phylogenetic analysis: a review. Int. J. Bioinform. Res. Appl. 6: 230-240.
- Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
- Felsenstein J. 1993. PHYLIP (phylogenetic inference package) version 3.5c. Department of Genetics, University of Washington.
- Felsenstein J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791.
- Auch AF, von Jan M, Klenk HP, Goker M. 2010. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand. Genomic Sci. 2: 117-134.
- Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM. 2007. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int. J. Syst. Evol. Microbiol. 57: 81-91.
- Kim M, Oh HS, Park SC, 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.
- Konstantinidis KT, Tiedje JM. 2005. Genomic insights that advance the species definition for prokaryotes. Proc. Natl. Acad. Sci. USA 102: 2567-2572.
- Richter M, Rossello-Mora R. 2009. Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. USA 106: 19126-19131.
- Meier-Kolthoff JP, Auch AF, Klenk HP, Goker M. 2013. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14: 60.
- Tindall BJ, Rossello-Mora R, Busse HJ, Ludwig W, Kampfer P. 2010. Notes on the characterization of prokaryote strains for taxonomic purposes. Int. J. Syst. Evol. Microbiol. 60: 249-266.
