Archive BacDiveID:10.13145/bacdive17492.20230509.8.1

Strain identifier

BacDive ID: 17492

Type strain:

Species: Lysobacter spongiicola

Strain history: M. Uchino <-- L. A. Romanenko KMM 329.

NCBI tax ID(s): 1122188 (strain), 435289 (species)

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

General

@ref: 15912

BacDive-ID: 17492

DSM-Number: 21749

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Lysobacter spongiicola DSM 21749 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sponge .

NCBI tax id

NCBI tax id	Matching level
1122188	strain
435289	species

strain history

@ref	history
15912	<- M. Uchino, Tokyo Univ. of Agriculture; NRIC 0728 <- L. A. Romanenko, Russian Academy of Sciences, Pacific Inst. Bioorganic Chemistry; KMM 329
67770	M. Uchino <-- L. A. Romanenko KMM 329.

doi: 10.13145/bacdive17492.20230509.8.1

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 spongiicola
full scientific name: Lysobacter spongiicola Romanenko et al. 2008

@ref: 15912

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Lysobacteraceae

genus: Lysobacter

species: Lysobacter spongiicola

full scientific name: Lysobacter spongiicola Romanenko et al. 2008

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell length	cell width	cell shape	motility	confidence
32371	negative	1.4 µm	0.55 µm	rod-shaped	yes
69480	negative					99.999

pigmentation

@ref: 32371
production: yes

Culture and growth conditions

culture medium

@ref: 15912
name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
growth: yes
link: https://mediadive.dsmz.de/medium/514
composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@ref	growth	type	temperature	range
15912	positive	growth	28	mesophilic
32371	positive	growth	05-41
32371	positive	optimum	26.5	mesophilic
67770	positive	growth	30	mesophilic

culture pH

@ref	ability	type	pH	PH range
32371	positive	growth	5.5-9.5	alkaliphile
32371	positive	optimum	7.5

Physiology and metabolism

oxygen tolerance

@ref: 32371
oxygen tolerance: aerobe

spore formation

@ref	spore formation	confidence
69481	no	99
69480	no	99.999

halophily

@ref: 32371
salt: NaCl
growth: positive
tested relation: growth
concentration: 0-6 %

metabolite utilization

@ref: 32371
Chebi-ID: 15963
metabolite: ribitol
utilization activity: +
kind of utilization tested: carbon source

enzymes

@ref	value	activity	ec
32371	acid phosphatase	+	3.1.3.2
32371	alkaline phosphatase	+	3.1.3.1
32371	catalase	+	1.11.1.6
32371	gelatinase	+
32371	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

isolation

@ref	sample type	host species	geographic location	country	origin.country	continent
15912	sponge (Pachastrella sp.)	Pachastrella	Philippine Sea at a water depth of 750 m	Philippines	PHL	Asia
67770	Sponge specimen (Pachastrella sp.) collected from the Philippine Sea at a water depth of 750 m	Pachastrella sp.

isolation source categories

Cat1: #Host
Cat2: #Invertebrates (Other)
Cat3: #Porifera (Sponges)

taxonmaps

@ref: 69479
File name: preview.99_5037.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17;96_2460;97_3003;98_3766;99_5037&stattab=map
Last taxonomy: Lysobacter spongiicola subclade
16S sequence: AB299978
Sequence Identity:
Total samples: 682
soil counts: 356
aquatic counts: 161
animal counts: 117
plant counts: 48

Safety information

risk assessment

@ref: 15912
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 15912
description: Lysobacter spongiicola gene for 16S ribosomal RNA, partial sequence, strain: KMM 329
accession: AB299978
length: 1516
database: ena
NCBI tax ID: 435289

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Lysobacter spongiicola DSM 21749 strain DSM 21749	1122188.5	wgs	patric	1122188
66792	Lysobacter spongiicola DSM 21749	2568526003	draft	img	1122188
67770	Lysobacter spongiicola DSM 21749	GCA_900167055	contig	ncbi	1122188

GC content

@ref	GC-content	method
15912	69	thermal denaturation, midpoint method (Tm)
32371	69
67770	69	high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	99	no
motile	yes	81.255	no
flagellated	no	77.96	no
gram-positive	no	98.427	no
anaerobic	no	98.481	no
aerobic	yes	91.075	yes
halophile	no	90.714	no
spore-forming	no	95.549	no
thermophile	no	98.554	no
glucose-util	yes	81.94	no
glucose-ferment	no	93.422	no

External links

@ref: 15912

culture collection no.: DSM 21749, JCM 14760, KMM 329, NRIC 0728, KCTC 23742

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	18218933	Lysobacter spongiicola sp. nov., isolated from a deep-sea sponge.	Romanenko LA, Uchino M, Tanaka N, Frolova GM, Mikhailov VV	Int J Syst Evol Microbiol	10.1099/ijs.0.65391-0	2008	Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, Fatty Acids/analysis, Genes, rRNA, Lysobacter/classification/genetics/isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Porifera/*microbiology, RNA, Ribosomal, 16S/genetics, Seawater, Sequence Analysis, DNA, Species Specificity	Genetics
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	26483081	Lysobacter chengduensis sp. nov. Isolated from the Air of Captive Ailuropoda melanoleuca Enclosures in Chengdu, China.	Wen C, Xi L, She R, Zhao S, Hao Z, Luo L, Liao H, Chen Z, Han G, Cao S, Wu R, Yan Q, Hou R	Curr Microbiol	10.1007/s00284-015-0921-8	2016	Aerobiosis, Air Microbiology, Animals, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Lysobacter/classification/genetics/isolation & purification/physiology, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature, Ursidae/microbiology	Genetics
Phylogeny	36260505	Lysobacter selenitireducens sp. nov., isolated from river sediment.	Mao S, Li S, Guo B, Mu W, Hou X, Liu H, Wei S, Liu A, Kong L, Chen Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.005550	2022	Lysobacter/genetics, RNA, Ribosomal, 16S/genetics, Ubiquinone/chemistry, Phylogeny, Phosphatidylethanolamines/metabolism, Base Composition, Rivers, Sodium Chloride, Cardiolipins, Soil Microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Bacterial Typing Techniques, Sequence Analysis, DNA, Phospholipids/chemistry, Glycolipids/analysis, Amino Acids/metabolism, Nucleotides	Metabolism

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed	journal
15912	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21749)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-21749
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
32371	Barberan A, Caceres Velazquez H, Jones S, Fierer N.		10.1128/mSphere.00237-17	Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information	28599	28776041
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)
66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg		10.1093/nar/gkaa1025	BRENDA, the ELIXIR core data resource in 2021: new developments and updates		33211880	Nucleic Acids Res. 49: D498-D508 2020
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
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