Archive BacDiveID:10.13145/bacdive23448.20230509.8.1

Strain identifier

BacDive ID: 23448

Type strain:

Species: Luminiphilus syltensis

Strain Designation: Ivo14, Nor5-1B

Strain history: DSM 22749 <-- R. Amann NOR5-1B <-- I. Kosadinov Ivo14.

NCBI tax ID(s): 1341119 (species)

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

General

@ref: 19327

BacDive-ID: 23448

DSM-Number: 22749

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Luminiphilus syltensis Ivo14 is a mesophilic bacterium that was isolated from oxic sediment layer.

NCBI tax id

NCBI tax id: 1341119
Matching level: species

strain history

@ref	history
19327	<- B. Fuchs, Max-Planck-Inst. Marine Microbiology, Bremen, Germany; Ivo14 <- J. Harder and I. Kostadinov {2007}
67770	DSM 22749 <-- R. Amann NOR5-1B <-- I. Kosadinov Ivo14.

doi: 10.13145/bacdive23448.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Gammaproteobacteria
order: Cellvibrionales
family: Halieaceae
genus: Luminiphilus
species: Luminiphilus syltensis
full scientific name: Luminiphilus syltensis Spring et al. 2013

@ref: 19327

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Halieaceae, not assigned to order

family: Halieaceae

genus: Luminiphilus

species: Luminiphilus syltensis

full scientific name: Luminiphilus syltensis Spring et al. 2013

strain designation: Ivo14, Nor5-1B

type strain: yes

Morphology

colony morphology

@ref: 19327
incubation period: 2-3 days

Culture and growth conditions

culture medium

@ref: 19327
name: CONGREGIBACTER (SYPHC) MEDIUM (DSMZ Medium 1115)
growth: yes
link: https://mediadive.dsmz.de/medium/1115
composition: Name: CONGREGIBACTER (SYPHC) MEDIUM (DSMZ Medium 1115) Composition: Sea Salt 34.965 g/l HEPES 2.4975 g/l Na-pyruvate 1.0989 g/l Yeast extract 0.999001 g/l NH4Cl 0.0999001 g/l KH2PO4 0.04995 g/l L-Cysteine HCl x H2O 0.03996 g/l L-Histidine 0.03996 g/l MgSO4 x 7 H2O 0.02997 g/l NaCl 0.00999001 g/l MnSO4 x H2O 0.00499501 g/l (NH4)2Ni(SO4)2 x 6 H2O 0.0027972 g/l CoCl2 x 6 H2O 0.0017982 g/l ZnSO4 x 7 H2O 0.0017982 g/l CaCl2 x 2 H2O 0.000999001 g/l FeSO4 x 7 H2O 0.000999001 g/l AlK(SO4)2 x 12 H2O 0.00017982 g/l Pyridoxine hydrochloride 0.00014985 g/l CuSO4 x 5 H2O 9.99001e-05 g/l H3BO3 9.99001e-05 g/l Nicotinic acid 9.99001e-05 g/l Thiamine-HCl x 2 H2O 9.99001e-05 g/l Na2SeO4 9.99001e-05 g/l Na2WO4 x 2 H2O 9.99001e-05 g/l Na2MoO4 x 2 H2O 9.99001e-05 g/l Calcium pantothenate 4.995e-05 g/l Vitamin B12 4.995e-05 g/l p-Aminobenzoic acid 3.996e-05 g/l D-(+)-biotin 9.99001e-06 g/l Distilled water

culture temp

@ref	growth	type	temperature	range
19327	positive	growth	28	mesophilic
67770	positive	growth	25	mesophilic

Physiology and metabolism

observation

@ref: 67770
observation: quinones: Q-8

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
19327	oxic sediment layer	Sylt island	Germany	DEU	Europe
67770	Top oxic layer of a muddy littoral sediment close to the island of Sylt	North Sea	Germany	DEU	Europe

isolation source categories

Cat1: #Environmental
Cat2: #Aquatic
Cat3: #Sediment

taxonmaps

@ref: 69479
File name: preview.99_5223.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_305;96_2538;97_3101;98_3894;99_5223&stattab=map
Last taxonomy: Luminiphilus syltensis subclade
16S sequence: EU672849
Sequence Identity:
Total samples: 2301
soil counts: 85
aquatic counts: 2103
animal counts: 105
plant counts: 8

Safety information

risk assessment

@ref: 19327
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref	description	accession	length	database	NCBI tax ID
19327	Luminiphilus syltensis NOR5-1B 16S ribosomal RNA gene, partial sequence	EU672849	1492	ena	565045
67770	Luminiphilus syltensis NOR5-1B ctg_1109846220905, whole genome shotgun sequence	ACCY01000005	148281	ena	565045

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Luminiphilus syltensis NOR5-1B	565045.6	wgs	patric	565045
66792	Luminiphilus syltensis NOR5-1B	647533250	draft	img	565045
67770	Luminiphilus syltensis NOR5-1B	GCA_000158175	scaffold	ncbi	565045

GC content

@ref	GC-content	method
19327	57	sequence analysis
67770	56.7	genome sequence analysis

Genome-based predictions

predictions

trait	prediction	confidence	training_data
gram-positive	no	98.702	no
anaerobic	no	98.616	no
halophile	yes	75.869	no
spore-forming	no	97.821	no
glucose-util	yes	57.667	no
thermophile	no	98.421	yes
flagellated	no	95.649	no
motile	no	81.073	no
aerobic	yes	89.142	no
glucose-ferment	no	92.66	no

External links

@ref: 19327

culture collection no.: DSM 22749, JCM 17770

straininfo link

@ref: 87600
straininfo: 403108

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Metabolism	23705861	Mixotrophic growth of bacteriochlorophyll a-containing members of the OM60/NOR5 clade of marine gammaproteobacteria is carbon-starvation independent and correlates with the type of carbon source and oxygen availability.	Spring S, Riedel T	BMC Microbiol	10.1186/1471-2180-13-117	2013	Aquatic Organisms/chemistry/growth & development/metabolism, Bacteriochlorophyll A/analysis, Carbon/metabolism, Energy Metabolism, Gammaproteobacteria/chemistry/growth & development/metabolism, Gene Expression Regulation, Bacterial, Light, Oxidation-Reduction, Oxygen/*metabolism, Photosynthesis
Phylogeny	23705883	Taxonomy and evolution of bacteriochlorophyll a-containing members of the OM60/NOR5 clade of marine gammaproteobacteria: description of Luminiphilus syltensis gen. nov., sp. nov., reclassification of Haliea rubra as Pseudohaliea rubra gen. nov., comb. nov., and emendation of Chromatocurvus halotolerans.	Spring S, Riedel T, Sproer C, Yan S, Harder J, Fuchs BM	BMC Microbiol	10.1186/1471-2180-13-118	2013	Aerobiosis, Aquatic Organisms/chemistry/classification/genetics/isolation & purification, Bacteriochlorophyll A/analysis, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Gammaproteobacteria/chemistry/classification/genetics/isolation & purification, Genetic Variation, Germany, Metabolic Networks and Pathways/genetics, Molecular Sequence Data, North Sea, Photosynthesis, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA	Enzymology

Reference

@id	authors	catalogue	doi/url	title
19327	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22749)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-22749
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)
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
87600	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID403108.1	StrainInfo: A central database for resolving microbial strain identifiers