Croceibacterium atlanticum (DSM 100738, CGMCC 1.12411, JCM 18865)

Name: Croceibacterium atlanticum (DSM 100738, CGMCC 1.12411, JCM 18865)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 131265

Type strain

Strain Designation 26DY36

Culture col. no. DSM 100738 CGMCC 1.12411 JCM 18865 26DY36

NCBI tax ID(s) 1267766

Special Collections DSMZ JCM

History DSMZ <- Y.-H. Wu, Second Inst. Oceanography, State Oceanic Admin., Hangzhou, China; CGMCC 1.12411 JCM <-- Y.-H. Wu 26DY36.

Links

Croceibacterium atlanticum 26DY36 is a bacterium that was isolated from North Atlantic Rise.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 407893

JCM 18865,DSM 100738

@ref 20215

Last LPSN update 2026-05-29 08:37:34

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Erythrobacteraceae

Genus Croceibacterium

Species Croceibacterium atlanticum

Full scientific name Croceibacterium atlanticum (Wu et al. 2014) Xu et al. 2020

Synonyms (1)

Altererythrobacter atlanticus

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	97.828
125439	negative	99.139

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
22492	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)		Medium recipe at MediaDive	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 (°C)
22492	positive	growth	28
67770	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	95.265

Spore formation

@ref	Spore formation	Confidence
125439		99.558

Observation

67770

Observationquinones: Q-10

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	suberin monomers biosynthesis	100	2 of 2
66794	gluconeogenesis	100	8 of 8
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	butanoate fermentation	100	4 of 4
66794	denitrification	100	2 of 2
66794	quinate degradation	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	glycine betaine biosynthesis	100	5 of 5
66794	resorcinol degradation	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	ethanol fermentation	100	2 of 2
66794	Entner Doudoroff pathway	100	10 of 10
66794	cardiolipin biosynthesis	100	7 of 7
66794	palmitate biosynthesis	100	22 of 22
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	ppGpp biosynthesis	100	4 of 4
66794	taurine degradation	100	1 of 1
66794	methylglyoxal degradation	100	5 of 5
66794	formaldehyde oxidation	100	3 of 3
66794	phenylalanine metabolism	92.31	12 of 13
66794	threonine metabolism	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	leucine metabolism	84.62	11 of 13
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	peptidoglycan biosynthesis	80	12 of 15
66794	propionate fermentation	80	8 of 10
66794	3-phenylpropionate degradation	80	12 of 15
66794	glycogen metabolism	80	4 of 5
66794	gallate degradation	80	4 of 5
66794	citric acid cycle	78.57	11 of 14
66794	heme metabolism	78.57	11 of 14
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	NAD metabolism	77.78	14 of 18
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	sulfopterin metabolism	75	3 of 4
66794	lactate fermentation	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	purine metabolism	74.47	70 of 94
66794	proline metabolism	72.73	8 of 11
66794	d-xylose degradation	72.73	8 of 11
66794	pentose phosphate pathway	72.73	8 of 11
66794	alanine metabolism	72.41	21 of 29
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	propanol degradation	71.43	5 of 7
66794	glutathione metabolism	71.43	10 of 14
66794	methionine metabolism	69.23	18 of 26
66794	pyrimidine metabolism	66.67	30 of 45
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	cyanate degradation	66.67	2 of 3
66794	flavin biosynthesis	66.67	10 of 15
66794	4-hydroxymandelate degradation	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	tryptophan metabolism	65.79	25 of 38
66794	phenol degradation	65	13 of 20
66794	glycolysis	64.71	11 of 17
66794	tyrosine metabolism	64.29	9 of 14
66794	degradation of pentoses	64.29	18 of 28
66794	metabolism of disaccharids	63.64	7 of 11
66794	vitamin B6 metabolism	63.64	7 of 11
66794	arginine metabolism	62.5	15 of 24
66794	degradation of sugar alcohols	62.5	10 of 16
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	sulfate reduction	61.54	8 of 13
66794	cysteine metabolism	61.11	11 of 18
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	cellulose degradation	60	3 of 5
66794	histidine metabolism	58.62	17 of 29
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	non-pathway related	57.89	22 of 38
66794	lysine metabolism	57.14	24 of 42
66794	lipid metabolism	54.84	17 of 31
66794	urea cycle	53.85	7 of 13
66794	ribulose monophosphate pathway	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	biotin biosynthesis	50	2 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	50	4 of 8
66794	glycine metabolism	50	5 of 10
66794	sphingosine metabolism	50	3 of 6
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	pantothenate biosynthesis	50	3 of 6
66794	glycogen biosynthesis	50	2 of 4
66794	toluene degradation	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	ketogluconate metabolism	50	4 of 8
66794	oxidative phosphorylation	47.25	43 of 91
66794	lipid A biosynthesis	44.44	4 of 9
66794	nitrate assimilation	44.44	4 of 9
66794	degradation of hexoses	44.44	8 of 18
66794	polyamine pathway	43.48	10 of 23
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	carotenoid biosynthesis	40.91	9 of 22
66794	3-chlorocatechol degradation	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	degradation of sugar acids	32	8 of 25
66794	ascorbate metabolism	31.82	7 of 22
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	starch degradation	30	3 of 10
66794	myo-inositol biosynthesis	30	3 of 10
66794	coenzyme M biosynthesis	30	3 of 10
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	arachidonic acid metabolism	27.78	5 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	vitamin E metabolism	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	CMP-KDO biosynthesis	25	1 of 4
66794	carnitine metabolism	25	2 of 8

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Country
22492	North Atlantic Rise	Atlantic Ocean
67770	Deep-sea sediment sample collected from the North Atlantic Rise

Taxonmaps

69479

Global distribution of 16S sequence KC018454 (>99% sequence identity) for Altererythrobacter atlanticus subclade from Microbeatlas

Aquatic Samples	364
Soil Samples	342
Animal Samples	264
Plant Samples	26
Total Samples	996

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
22492	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM100816v2 assembly for Croceibacterium atlanticum 26DY36	complete	GCA_001008165	1267766.3	2654587990	1267766	92.56
66792	ASM1419931v1 assembly for Croceibacterium atlanticum DSM 100738	scaffold	GCA_014199315	1267766.10	2828423711	1267766	68.55

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
22492	Altererythrobacter atlanticus strain 26DY36 16S ribosomal RNA gene, partial sequence	KC018454	1444		1267766

GC content

@ref	GC-content (mol%)	Method
67770	61.9	genome sequence analysis
67770	59.4	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM100816v2 assembly for Croceibacterium atlanticum 26DY36
BV-BRC: 1267766.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	negative	99.14	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	95.27	no
125439	motility	BacteriaNetⓘ	yes	40.93	no
125439	spore_formation	BacteriaNetⓘ	no	99.56	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Croceibacterium atlanticum 26DY36
NCBI: GCA_001008165.2

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.83	no
125438	anaerobic	anaerobicⓘ	no	94.72	no
125438	aerobic	aerobicⓘ	yes	83.36	no
125438	spore-forming	spore-formingⓘ	no	88.20	no
125438	thermophilic	thermophileⓘ	no	95.80	yes
125438	flagellated	motile2+ⓘ	yes	66.30	no

Literature

References

#20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#22492	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100738
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: 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: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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.: MicrobeAtlas 1.0 beta .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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