Archive BacDiveID:10.13145/bacdive14145.20230509.8.1

Strain identifier

BacDive ID: 14145

Type strain:

Species: Novosphingobium rosa

Strain Designation: 68, R135

Strain history: CIP <- 2012, DSMZ <- NCPPB <- A. Kerr: strain 68 <- IPPB: strain TRI106 <- D. Munnecke: strain R135

NCBI tax ID(s): 1219053 (strain), 76978 (species)

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

General

@ref: 3091

BacDive-ID: 14145

DSM-Number: 7285

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

description: Novosphingobium rosa 68 is a mesophilic, Gram-negative bacterium that was isolated from rose.

NCBI tax id

NCBI tax id	Matching level
76978	species
1219053	strain

strain history

@ref	history
3091	<- NCPPB <- A. Kerr, 68 <- IPPB, TRI106 <- D. Munnecke, R135
67770	DSM 7285 <-- NCPPB 2661 <-- A. Kerr; 68 <-- IPPB; TRI106 <-- D. Munnecke; R135.
122249	CIP <- 2012, DSMZ <- NCPPB <- A. Kerr: strain 68 <- IPPB: strain TRI106 <- D. Munnecke: strain R135

doi: 10.13145/bacdive14145.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Alphaproteobacteria
order: Sphingomonadales
family: Erythrobacteraceae
genus: Novosphingobium
species: Novosphingobium rosa
full scientific name: Novosphingobium rosa corrig. (Takeuchi et al. 1995) Takeuchi et al. 2001
synonyms
@ref synonym
20215 Novosphingobium roseae
20215 Sphingomonas rosa

@ref	synonym
20215	Novosphingobium roseae
20215	Sphingomonas rosa

@ref: 3091

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Erythrobacteraceae

genus: Novosphingobium

species: Novosphingobium rosa

full scientific name: Novosphingobium rosa (Takeuchi et al. 1995) Takeuchi et al. 2001

strain designation: 68, R135

type strain: yes

Morphology

cell morphology

@ref	gram stain	confidence	cell shape	motility
69480	negative	99.92
122249	negative		rod-shaped	no

Culture and growth conditions

culture medium

@ref	name	growth	link	composition
3091	NUTRIENT AGAR (DSMZ Medium 1)	yes	https://mediadive.dsmz.de/medium/1	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
34735	MEDIUM 328- for nutrient agar	yes		Distilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
40124	MEDIUM 72- for trypto casein soja agar	yes		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122249	CIP Medium 328	yes	https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@ref	growth	type	temperature	range
3091	positive	growth	28	mesophilic
34735	positive	growth	25	mesophilic
40124	positive	growth	30	mesophilic
67770	positive	growth	28	mesophilic

Physiology and metabolism

spore formation

@ref	spore formation	confidence
69481	no	99
69480	no	99.973

observation

@ref: 67770
observation: quinones: Q-10

Isolation, sampling and environmental information

isolation

@ref	sample type	host species
3091	rose
61576	Hairy root of Rosa sp.
67770	Hairy root of Rosa sp.	Rosa sp.
122249	Rose, Agrobacterium rhizogenes

isolation source categories

Cat1: #Host Body-Site
Cat2: #Plant
Cat3: #Flower

taxonmaps

@ref: 69479
File name: preview.99_494.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_323;97_359;98_406;99_494&stattab=map
Last taxonomy: Novosphingobium rosa subclade
16S sequence: AB680810
Sequence Identity:
Total samples: 2335
soil counts: 755
aquatic counts: 747
animal counts: 326
plant counts: 507

Safety information

risk assessment

@ref	biosafety level	biosafety level comment
3091	1	Risk group (German classification)
122249	1	Risk group (French classification)

Sequence information

16S sequences

@ref	description	accession	length	database	NCBI tax ID
20218	Novosphingobium rosa 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence	GQ907185	661	ena	76978
20218	Novosphingobium rosa gene for 16S rRNA, partial sequence, strain: NBRC 15208	AB680810	1414	ena	76978
67770	Novosphingobium rosa gene for, partial sequence, strain: IAM 14222	D13945	1369	ena	76978

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Novosphingobium rosa NBRC 15208	1219053.3	wgs	patric	1219053
66792	Novosphingobium rosa NBRC 15208	2731957706	draft	img	1219053
67770	Novosphingobium rosa NBRC 15208	GCA_001598555	contig	ncbi	1219053

GC content

@ref: 67770
GC-content: 64.7
method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	99	no
motile	yes	69.231	no
gram-positive	no	97.142	no
anaerobic	no	99.049	no
aerobic	yes	92.4	no
halophile	no	92.862	no
spore-forming	no	90.131	no
thermophile	no	97.977	yes
glucose-util	yes	95.427	no
flagellated	no	82.222	no
glucose-ferment	no	90.196	no

External links

@ref: 3091

culture collection no.: DSM 7285, CIP 110407, IAM 14222, IFO 15208, NBRC 15208, NCPPB 2661, CCUG 58055, JCM 10276, HAMBI 2068, ATCC 51837, LMG 17328, JCM 31909, TRI 106, CIP 107362, JCM 10194, JCM 21080, KCTC 2821, NCIMB 13413

straininfo link

@ref	straininfo
83310	13984
83311	410761

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	7537068	Taxonomic study of bacteria isolated from plants: proposal of Sphingomonas rosa sp. nov., Sphingomonas pruni sp. nov., Sphingomonas asaccharolytica sp. nov., and Sphingomonas mali sp. nov.	Takeuchi M, Sakane T, Yanagi M, Yamasato K, Hamana K, Yokota A	Int J Syst Bacteriol	10.1099/00207713-45-2-334	1995	DNA, Bacterial/genetics, Gram-Negative Aerobic Bacteria/chemistry/classification/physiology, Lactose/analogs & derivatives/metabolism, Phylogeny, Plants/microbiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics	Metabolism
Phylogeny	23264506	Novosphingobium aquaticum sp. nov., isolated from the humic-matter-rich bog lake Grosse Fuchskuhle.	Glaeser SP, Bolte K, Busse HJ, Kampfer P, Grossart HP, Glaeser J	Int J Syst Evol Microbiol	10.1099/ijs.0.048280-0	2012	Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Germany, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sphingomonadaceae/classification/genetics/isolation & purification, Ubiquinone/analogs & derivatives/analysis, Water Microbiology, Wetlands	Genetics
Phylogeny	27515386	Novosphingobium lotistagni sp. nov., isolated from a lotus pond.	Ngo HTT, Trinh H, Kim JH, Yang JE, Won KH, Kim JH, Kook M, Yi TH	Int J Syst Evol Microbiol	10.1099/ijsem.0.001418	2016	Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lotus, Nucleic Acid Hybridization, Phospholipids/chemistry, Phylogeny, Ponds/microbiology, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistry	Transcriptome

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
3091	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7285)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-7285
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
20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.		10.1016/j.syapm.2013.11.002	StrainInfo introduces electronic passports for microorganisms.	Syst Appl Microbiol. 37: 42-50 2014	24321274
34735	Curators of the CIP		https://brclims.pasteur.fr/brcWeb/souche/detail/1/8263
40124	Curators of the CIP		https://brclims.pasteur.fr/brcWeb/souche/detail/1/4789
61576	Curators of the CCUG	Culture Collection University of Gothenburg (CCUG) (CCUG 58055)	https://www.ccug.se/strain?id=58055
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)
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
83310	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID13984.1	StrainInfo: A central database for resolving microbial strain identifiers
83311	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID410761.1	StrainInfo: A central database for resolving microbial strain identifiers
122249	Curators of the CIP	Collection of Institut Pasteur (CIP 110407)	https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110407

General

NCBI tax id

strain history

Name and taxonomic classification

LPSN

synonyms

Morphology

cell morphology

Culture and growth conditions

culture medium

culture temp

Physiology and metabolism

spore formation

observation

Isolation, sampling and environmental information

isolation

isolation source categories

taxonmaps

Safety information

risk assessment

Sequence information

16S sequences

Genome sequences

GC content

Genome-based predictions

predictions

External links

straininfo link

literature

Reference