Research Article
Free
- Xin Liu1,†, Lingling Wang1,†, Meilin Han1, Qian-hui Xue1,2, Gui-shan Zhang3, Junlian Gao1and Xiaohong sun1
View AffiliationsHide Affiliations
Affiliations:
1Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, PR China
2School of Materials Science and Engineering, Beijing Institute of Technology, Beijing 100081, PR China
3Key Laboratory of Microbial Resources Collection and Preservation, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
*Correspondence: Junlian Gao, [emailprotected] *Correspondence: Xiaohong sun, [emailprotected]
† These authors contributed equally to this work
- Published:10 March 2020https://doi.org/10.1099/ijsem.0.003673
Abstract
A facultatively anaerobic, Gram-stain-positive, spore-forming Bacillus strain, 17-SMS-01T, isolated from spent mushroom substrate in the Fangshan District, Beijing, PR China, was initially identified as a Bacillus cereus group species based on 16S rRNA gene sequences. Strain 17-SMS-01T had the highest sequence similarities to Bacillus wiedmannii FSL W8-0169T (99.9 %), Bacillus albus N35-10-2T (99.9 %), Bacillus luti TD41T (99.9 %) and Bacillus proteolyticus TD42T (99.9 %). However, the average nucleotide identity (ANI) and digital DNA–DNA hybridization (DDH) values between strain 17-SMS-01T and the most closely related species were less than the previously proposed cut-off values of 96 % (ANI) and 70 % (DDH) for differentiating species within the genus, suggesting that this strain represents a novel Bacillus group species. The fatty acid profile of strain 17-SMS-01T, which showed a predominance of iso-C15 : 0 and anteiso-C15 : 0, supported the allocation of the strain to the genus Bacillus. The predominant menaquinone was MK-7 (100%). The major polar lipids were diphosphatidylglycerol, phosphatidyl ethanolamine, phosphatidyl glycerol, an unidentified aminophospholiped and unidentified lipids. The DNA G+C content of the novel strain was 35.0 mol%. The results of physiological and biochemical tests also allowed the phenotypic differentiation of strain 17-SMS-01T from the most closely related recognized species. On the basis of the phylogenetic and phenotypic evidence, strain 17-SMS-01T represents a novel Bacillus species, for which the name Bacillus fungorum sp. nov. is proposed. Type strain of the novel species is 17-SMS-01T (=MCCC 1K03483T=KCTC 33949T).
- Received:
- Accepted:
- Published Online:
Keyword(s):Bacillus fungorum sp. nov., new taxaand spent mushroom substrate
Funding
This study was supported by the:
- Beijing Innovation Consortium of Agriculture Research System(AwardBAIC05-2016)
- Principle Award Recipient: xiaohong sun
© 2020 The Authors
Article metrics loading...
/content/journal/ijsem/10.1099/ijsem.0.003673
2020-03-10
2024-04-10
Full text loading...
/deliver/fulltext/ijsem/70/3/1457.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003673&mimeType=html&fmt=ahah
References
Logan NA, Berge O, Bishop AH, Busse H-J, De Vos P et al. Proposed minimal standards for describing new taxa of aerobic. endospore-forming bacteria 2009; 59:2114–2121
[Google Scholar]Sneath PHA, Mair NS, Sharpe ME, Holt JG. Bergey's Manual of Systematic Bacteriology 2 1986
[Google Scholar]Okinaka RT, Keim P. The Phylogeny of Bacillus Cereus Sensu Lato. The Bacterial Spore: from Molecules to Systems 4 American Society of Microbiology; 2016 [View Article]
[Google Scholar]Bazinet A. Pan-genome and phylogeny of Bacillus cereus sensu lato. journal article; 2017; 17176
Nakamura LK. Bacillus pseudomycoides sp. nov. Int J Syst Bacteriol 1998; 48:1031–1035 [View Article]
[Google Scholar]Lechner S, Mayr R, Francis KP, Prüss BM, Kaplan T et al. Bacillus weihenstephanensis sp. nov. is a new psychrotolerant species of the Bacillus cereus group. Int J Syst Bacteriol 1998; 48:1373–1382 [View Article]
[Google Scholar]Nakamura LK, Jackson MA. Clarification of the Taxonomy of Bacillus mycoides. Int J Syst Bacteriol 1995; 45:46–49 [View Article]
[Google Scholar]Smith NR, Gordon RE, Clark FE. Aerobic sporeforming bacteria: US government printing office; 1952
Somerville HJ, Jones ML. Dna competition studies within the Bacillus cereus group of bacilli. J Gen Microbiol 1972; 73:257–265 [View Article]
[Google Scholar]Nakamura LK. Dna relatedness among Bacillus thuringiensis serovars. Int J Syst Bacteriol 1994; 44:125–129 [View Article]
[Google Scholar]Logan NA, Carman JA, Melling J, Berkeley RC. Identification of Bacillus anthracis by API tests. J Med Microbiol 1985; 20:75–85 [View Article]
[Google Scholar]Guinebretière M-H, Thompson FL, Sorokin A, Normand P, Dawyndt P et al. Ecological diversification in the Bacillus cereus group. Environ Microbiol 2008; 10:851–865 [View Article]
[Google Scholar]Marmur J. A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 1961; 3:208-IN201IN1 [View Article]
[Google Scholar]Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article]
[Google Scholar]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; 2012; 62716–721
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article]
[Google Scholar]Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article]
[Google Scholar]Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article]
[Google Scholar]Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 20:406–416 [View Article]
[Google Scholar]Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article]
[Google Scholar]Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article]
[Google Scholar]Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Gbdp on the Grid: a Genome-Based Approach for Species Delimitation Adjusted for an Automated and Highly Parallel Processing of Large Data Sets. Hochleistungsrechnen in Baden-Württemberg - Ausgewählte Aktivitäten Im Bwgrid 2012 Karlsruhe: KIT Scientific Publishing; 2013
[Google Scholar]Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the AD hoc Committee on reconciliation of approaches to bacterial Systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
[Google Scholar]Logan NA. Bacillus. In De Vos P, Garrity G, Jones D, Krieg NR, Ludwig W. (editors) In Bergey's Manual of Systematic Bacteriology (The Firmicutes) 3, 2nd edn. New York, NY, USA: Springer; 2009 pp 21–128
[Google Scholar]Liao H, Li Y, Zhang M, Lin X, Lai Q et al. Altererythrobacter mangrovi sp. nov.. isolated from mangrove sediment 2017; 67:4851–4856
[Google Scholar]Liu Y, Yao S, Lee Y-J, Cao Y, Zhai L et al. Sphingomonas morindae sp. nov., isolated from noni (Morinda citrifolia L.) branch. Int J Syst Evol Microbiol 2015; 65:2817–2823 [View Article]
[Google Scholar]Collins MD. Isoprenoid quinone analysis in bacterial classification and identification. Chemical Methods in Bacterial Systematics 1985267–285
[Google Scholar]Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
[Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003673
Bacillus fungorum sp. nov., a bacterium isolated from spent mushroom substrate
Int J Syst Evol Microbiol 70, 1457 (2020); https://doi.org/10.1099/ijsem.0.003673
/content/journal/ijsem/10.1099/ijsem.0.003673
/content/journal/ijsem/10.1099/ijsem.0.003673
Data & Media loading...
Supplements
Supplementary material 1
Most citedMost Cited RSS feed
Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies
Seok-Hwan Yoon,Sung-Min Ha,Soonjae Kwon,Jeongmin Lim,Yeseul Kim,Hyungseok SeoandJongsik Chun
DNA–DNA hybridization values and their relationship to whole-genome sequence similarities
Johan Goris,Konstantinos T. Konstantinidis,Joel A. Klappenbach,Tom Coenye,Peter VandammeandJames M. Tiedje
A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae
Jinshui Zheng,Stijn Wittouck,Elisa Salvetti,Charles M.A.P. Franz,Hugh M.B. Harris,Paola Mattarelli,Paul W. O’Toole,Bruno Pot,Peter Vandamme,Jens Walter,Koichi Watanabe,Sander Wuyts,Giovanna E. Felis,Michael G. GänzleandSarah Lebeer
OrthoANI: An improved algorithm and software for calculating average nucleotide identity
Imchang Lee,Yeong Ouk Kim,Sang-Cheol ParkandJongsik Chun
Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes
Jongsik Chun,Aharon Oren,Antonio Ventosa,Henrik Christensen,David Ruiz Arahal,Milton S. da Costa,Alejandro P. Rooney,Hana Yi,Xue-Wei Xu,Sofie De MeyerandMartha E. Trujillo
List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
Aidan C. Parte,Joaquim Sardà Carbasse,Jan P. Meier-Kolthoff,Lorenz C. ReimerandMarkus Göker
Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium
Muriel Derrien,Elaine E. Vaughan,Caroline M. PluggeandWillem M. de Vos
Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes
Mincheol Kim,Hyun-Seok Oh,Sang-Cheol ParkandJongsik Chun
Valid publication of the names of forty-two phyla of prokaryotes
Aharon OrenandGeorge M. Garrity
Taxonomic Note: A Place for DNA-DNA Reassociation and 16S rRNA Sequence Analysis in the Present Species Definition in Bacteriology
E. STACKEBRANDTandB. M. GOEBEL
- More Less
