Lactobacillus paragasseri sp. nov., a sister taxon of Lactobacillus gasseri, based on whole-genome sequence analyses

International Journal of Systematic and Evolutionary Microbiology

Volumn 68, Issue 11, 2018, Pages 3512-3517

  Tanizawa, Yasuhiro ^a   Tada, Ipputa ^b   Kobayashi, Hisami ^c   Endo, Akihito ^d   Maeno, Shintaro ^d   Toyoda, Atsushi ^a   Arita, Masanori ^a,e   Nakamura, Yasukazu ^a   Sakamoto, Mitsuo ^f,g   Ohkuma, Moriya ^f   Tohno, Masanori ^c  

^a NATIONAL INSTITUTE OF GENETICS   (Japan)

^b GRADUATE UNIVERSITY FOR ADVANCED STUDIES   (Japan)

^c FOOD RESEARCH INSTITUTE   (Japan)

^d TOKYO UNIVERSITY OF AGRICULTURE   (Japan)

^e Elements Chemistry Laboratory   (Japan)

^f RIKEN BIORESOURCE CENTER   (Japan)

^g JAPAN AGENCY FOR MEDICAL RESEARCH AND DEVELOPMENT   (Japan)

Author keywords

Lactobacillus gasseri; Lactobacillus paragasseri

Indexed keywords

FATTY ACID; NUCLEOTIDE; PHENYLALANINE TRANSFER RNA LIGASE; RNA POLYMERASE; BACTERIAL DNA; DNA DIRECTED RNA POLYMERASE; RNA 16S; RNA POLYMERASE ALPHA SUBUNIT;

ARTICLE; BACTERIAL STRAIN; CHEMOTAXONOMY; CLADISTICS; COMPUTER MODEL; GENE SEQUENCE; GENOME; LACTOBACILLUS; LACTOBACILLUS GASSERI; LACTOBACILLUS PARAGASSERI; NEW SPECIES; NONHUMAN; PHENOTYPE; PHYLOGENY; PRIORITY JOURNAL; WHOLE GENOME SEQUENCING; BACTERIAL GENOME; BACTERIUM IDENTIFICATION; CHEMISTRY; CLASSIFICATION; DNA SEQUENCE; GENETICS; NUCLEIC ACID HYBRIDIZATION;

BACTERIAL TYPING TECHNIQUES; DNA, BACTERIAL; DNA-DIRECTED RNA POLYMERASES; FATTY ACIDS; GENOME, BACTERIAL; LACTOBACILLUS; LACTOBACILLUS GASSERI; NUCLEIC ACID HYBRIDIZATION; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

EID: 85055818102     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijsem.0.003020     Document Type: Article

References (25)

1. Euźeby JP, Parte JP. List of prokaryotic names with standing in nomenclature. 2018. www.bacterio.net/.
2. Pot B, Felis GE, De Bruyne K, Tsakalidou E, Papadimitriou K et al. The Genus Lactobacillus. In: Holzapfel WH and Wood BJB (editors). Lactic Acid Bacteria: Biodiversity and Taxonomy. Hoboken, NJ: John Wiley & Sons; 2014. pp. 249-353.
3. Lauer E, Kandler O. Lactobacillus gasseri sp. nov., a new species of the subgenus Thermobacterium. Zentralblatt für Bakteriologie: Zentralblatt für Bakteriologie: I. Abt. Originale C.: Allgemeine, angewandte und ökologische Mikrobiologie 1980;1: 75-78.
4. Selle K, Klaenhammer TR. Genomic and phenotypic evidence for probiotic influences of Lactobacillus gasseri on human health. FEMS Microbiol Rev 2013;37: 915-935.
5. Tanizawa Y, Fujisawa T, Kaminuma E, Nakamura Y, Arita M. DFAST and DAGA: web-based integrated genome annotation tools and resources. Biosci Microbiota Food Health 2016;35: 173-184.
6. Tada I, Tanizawa Y, Endo A, Tohno M, Arita M. Revealing the genomic differences between two subgroups in Lactobacillus gasseri. Biosci Microbiota Food Health 2017;36: 155-159.
7. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007;57: 81-91.
8. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009;106: 19126-19131.
9. Naser SM, Dawyndt P, Hoste B, Gevers D, Vandemeulebroecke K et al. Identification of lactobacilli by pheS and rpoA gene sequence analyses. Int J Syst Evol Microbiol 2007;57: 2777-2789.
10. Ramachandran P, Lacher DW, Pfeiler EA, Elkins CA. Development of a tiered multilocus sequence typing scheme for members of the Lactobacillus acidophilus complex. Appl Environ Microbiol 2013; 79: 7220-7228.
11. Weiss JE, Rettger LF. Lactobacillus bifidus. J Bacteriol 1934;28: 501-521.
12. Tohno M, Tanizawa Y, Irisawa T, Masuda T, Sakamoto M et al. Lactobacillus silagincola sp. nov. and Lactobacillus pentosiphilus sp. nov., isolated from silage. Int J Syst Evol Microbiol 2017;67: 3639-3644.
13. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012;62: 716-721.
14. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016;33: 1870-1874.
15. Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y et al. Efficient de novo assembly of highly heterozygous genomes from wholegenome shotgun short reads. Genome Res 2014;24: 1384-1395.
16. Tanizawa Y, Fujisawa T, Nakamura Y. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics 2018;34: 1037-1039.
17. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequencebased species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013;14: 60.
18. Tohno M, Kitahara M, Inoue H, Uegaki R, Irisawa T et al. Weissella oryzae sp. nov., isolated from fermented rice grains. Int J Syst Evol Microbiol 2013;63: 1417-1420.
19. Tohno M, Kitahara M, Uegaki R, Irisawa T, Ohkuma M et al. Lactobacillus hokkaidonensis sp. nov., isolated from subarctic timothy grass (Phleum pratense L.) silage. Int J Syst Evol Microbiol 2013; 63: 2526-2531.
20. Sakamoto M, Suzuki M, Umeda M, Ishikawa I, Benno Y. Reclassification of Bacteroides forsythus (Tanner et al. 1986) as Tannerella forsythensis corrig., gen. nov., comb. nov. Int J Syst Evol Microbiol 2002;52: 841-849.
21. Komagata K, Suzuki K-I. Lipid and cell-wall analysis in bacterial systematics. Method Microbiol 1987;19: 161-207.
22. Minamida K, Ota K, Nishimukai M, Tanaka M, Abe A et al. Asaccharobacter celatus gen. nov., sp. nov., isolated from rat caecum. Int J Syst Evol Microbiol 2008;58: 1238-1240.
23. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 2013;10: 563-569.
24. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 2014;9: e112963.
25. Kawai Y, Saitoh B, Takahashi O, Kitazawa H, Saito T et al. Primary amino acid and DNA sequences of gassericin T, a lactacin F-family bacteriocin produced by Lactobacillus gasseri SBT2055. Biosci Biotechnol Biochem 2000;64: 2201-2208.