Archive BacDiveID:10.13145/bacdive17501.20240916.9.1

Strain identifier

BacDive ID: 17501

Type strain:

Species: Lysobacter bugurensis

Strain Designation: ZLD-29

Strain history: <- L Zhang, Northewest A&F Univ., China

NCBI tax ID(s): 543356 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 18149

BacDive-ID: 17501

DSM-Number: 26007

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative

description: Lysobacter bugurensis ZLD-29 is an aerobe, Gram-negative bacterium that was isolated from soil of arid aerea.

NCBI tax id

NCBI tax id: 543356
Matching level: species

strain history

@ref	history
18149	<- KCTC <- C.-X. Fang, Wuhan Univ., China; ZLD-29
67771	<- L Zhang, Northewest A&F Univ., China

doi: 10.13145/bacdive17501.20240916.9.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Gammaproteobacteria
order: Lysobacterales
family: Lysobacteraceae
genus: Lysobacter
species: Lysobacter bugurensis
full scientific name: Lysobacter bugurensis Zhang et al. 2011

@ref: 18149

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Lysobacteraceae

genus: Lysobacter

species: Lysobacter bugurensis

full scientific name: Lysobacter bugurensis Zhang et al. 2011

strain designation: ZLD-29

type strain: yes

Morphology

cell morphology

@ref	gram stain	confidence
67771	negative
69480	negative	98.736

Culture and growth conditions

culture medium

@ref: 18149
name: HALF STRENGTH BACTO MARINE BROTH (DSMZ Medium 514a)
growth: yes
link: https://mediadive.dsmz.de/medium/514a
composition: Name: HALF STRENGTH BACTO MARINE BROTH (DSMZ Medium 514a) Composition: Agar 15.0 g/l NaCl 9.725 g/l MgCl2 2.95 g/l Bacto peptone 2.5 g/l Na2SO4 1.62 g/l CaCl2 0.9 g/l Yeast extract 0.5 g/l KCl 0.275 g/l NaHCO3 0.08 g/l Fe(III) citrate 0.05 g/l KBr 0.04 g/l SrCl2 0.017 g/l H3BO3 0.011 g/l Na2HPO4 0.004 g/l Na-silicate 0.002 g/l NaF 0.0012 g/l (NH4)NO3 0.0008 g/l Distilled water

culture temp

@ref	growth	type	temperature
18149	positive	growth	28
67771	positive	growth	30

Physiology and metabolism

oxygen tolerance

@ref: 67771
oxygen tolerance: aerobe

spore formation

@ref: 69481
spore formation: no
confidence: 100

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent	latitude	longitude
18149	soil of arid aerea	Xinjiang Province	China	CHN	Asia	43.2667	89.2333
67771	From soil	Gobi	China	CHN	Asia

isolation source categories

Cat1: #Environmental
Cat2: #Terrestrial
Cat3: #Soil

taxonmaps

@ref: 69479
File name: preview.99_30395.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17;96_14890;97_18180;98_22616;99_30395&stattab=map
Last taxonomy: Lysobacter bugurensis subclade
16S sequence: EU780693
Sequence Identity:
Total samples: 1035
soil counts: 423
aquatic counts: 90
animal counts: 448
plant counts: 74

Safety information

risk assessment

@ref: 18149
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 18149
description: UNVERIFIED_ORG: Lysobacter bugurensis strain ZLD-29 16S ribosomal RNA gene, partial sequence
accession: EU780693
length: 1453
database: nuccore
NCBI tax ID: 543356

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Lysobacter bugurensis KCTC 23077	GCA_014652095	scaffold	ncbi	543356
66792	Lysobacter bugurensis strain KCTC 23077	543356.4	wgs	patric	543356

GC content

@ref: 18149
GC-content: 68.2
method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@ref	trait	model	description	prediction	confidence	training_data
69481	spore-forming	spore-forming	Ability to form endo- or exospores	no	100	no
69480	gram-positive	gram-positive	Positive reaction to Gram-staining	no	98.736	yes
69480	anaerobic	anaerobic	Ability to grow under anoxygenic conditions (including facultative anaerobes)	no	96.347	yes
69480	aerobic	aerobic	Ability to grow under oxygenic conditions (including facultative aerobes)	yes	79.317	no
69480	spore-forming	spore-forming	Ability to form endo- or exospores	no	88.295	no
69480	thermophilic	thermophile	Ability to grow at temperatures above or equal to 45°C	no	90.947	no
69480	flagellated	motile2+	Ability to perform flagellated movement	yes	51.784	no

External links

@ref: 18149

culture collection no.: DSM 26007, CCTCC AB 207175, KCTC 23077

straininfo link

@ref: 86498
straininfo: 405922

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	20952549	Lysobacter korlensis sp. nov. and Lysobacter bugurensis sp. nov., isolated from soil.	Zhang L, Bai J, Wang Y, Wu GL, Dai J, Fang CX	Int J Syst Evol Microbiol	10.1099/ijs.0.024448-0	2010	Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Locomotion, Lysobacter/classification/genetics/isolation & purification/physiology, Molecular Sequence Data, Phospholipids, Phylogeny, Pigments, Biological/metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Salts/metabolism, Sequence Analysis, DNA, *Soil Microbiology	Genetics
Phylogeny	25500457	Lysobacter mobilis sp. nov., isolated from abandoned lead-zinc ore.	Yang SZ, Feng GD, Zhu HH, Wang YH	Int J Syst Evol Microbiol	10.1099/ijs.0.000026	2014	Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lead, Lysobacter/classification/genetics/isolation & purification, Mining, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry, Zinc	Genetics
Phylogeny	30906954	Lysobacter helvus sp. nov. and Lysobacter xanthus sp. nov., isolated from Soil in South Korea.	Kim I, Choi J, Chhetri G, Seo T	Antonie Van Leeuwenhoek	10.1007/s10482-019-01256-w	2019	Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Lysobacter/classification/genetics/isolation & purification/physiology, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology	Transcriptome

Reference

@id	authors	catalogue	doi/url	title
18149	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26007)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-26007
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67771	Curators of the KCTC		https://kctc.kribb.re.kr/En/Kctc
69479	João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.		https://microbeatlas.org/	MicrobeAtlas 1.0 beta
69480	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481	Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch		10.21203/rs.3.rs-2527258/v1	Predictions based on the model GenomeNet Sporulation v. 1
86498	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID405922.1	StrainInfo: A central database for resolving microbial strain identifiers