Croceibacterium xixiisoli (CGMCC 1.12804, NBRC 110413, S36)

Name: Croceibacterium xixiisoli (CGMCC 1.12804, NBRC 110413, S36)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 140743

Type strain

Strain Designation S36

Culture col. no. CGMCC 1.12804 NBRC 110413 S36

NCBI tax ID(s) 1476466

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Croceibacterium xixiisoli S36 is an aerobe, Gram-negative, coccus-shaped bacterium that forms circular colonies and was isolated from soil of the Xixi wetland.

Gram-negative coccus-shaped colony-forming aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 133796

NBRC 110413

@ref 20215

Last LPSN update 2026-05-29 08:39:47

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Erythrobacteraceae

Genus Croceibacterium

Species Croceibacterium xixiisoli

Full scientific name Croceibacterium xixiisoli (Yuan et al. 2017) Xu et al. 2020

Synonyms (1)

Altererythrobacter xixiisoli

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell shape	Motility	Confidence
43520	negative	0.4-0.5 µm	coccus-shaped
125438	negative				96.328

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
43520	1-2 mm	yellow, opaque	circular	5 days	Luria Bertani agar

Culture and growth conditions

Culture medium

@ref	Name	Growth
43520	LB (Luria-Bertani) MEDIUM

Culture temp

@ref	Growth	Type	Temperature (°C)
43520	positive	growth	10-37
43520	positive	optimum	32

Culture pH

@ref	Ability	Type	PH	PH range
43520	positive	optimum	7
43520	positive	growth	5-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
43520	aerobe
125439	obligate aerobe	98.062

Spore formation

@ref	Spore formation	Confidence
125439		97.853

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43520	NaCl	positive	growth	0.5-3 %(w/v)
43520	NaCl	positive	optimum	1 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43520	16651 ChEBI	(S)-lactate	-	carbon source
43520	64552 ChEBI	2-hydroxybutyrate	+	carbon source
43520	16763 ChEBI	2-oxobutanoate	-	carbon source
43520	30916 ChEBI	2-oxoglutarate	-	carbon source
43520	73918 ChEBI	3-O-methyl-D-glucose	-	carbon source
43520	18101 ChEBI	4-hydroxyphenylacetic acid	-	carbon source
43520	30089 ChEBI	acetate	-	carbon source
43520	13705 ChEBI	acetoacetate	-	carbon source
43520	17925 ChEBI	alpha-D-glucose	+	carbon source
43520	8295 ChEBI	beta-hydroxybutyrate	-	carbon source
43520	73706 ChEBI	bromosuccinate	-	carbon source
43520	17057 ChEBI	cellobiose	-	carbon source
43520	16947 ChEBI	citrate	-	carbon source
43520	18333 ChEBI	D-arabitol	-	carbon source
43520	29990 ChEBI	D-aspartate	-	carbon source
43520	15824 ChEBI	D-fructose	-	carbon source
43520	78697 ChEBI	D-fructose 6-phosphate	-	carbon source
43520	28847 ChEBI	D-fucose	-	carbon source
43520	15895 ChEBI	D-galactonic acid lactone	-	carbon source
43520	12936 ChEBI	D-galactose	-	carbon source
43520	18024 ChEBI	D-galacturonic acid	-	carbon source
43520	8391 ChEBI	D-gluconate	-	carbon source
43520	14314 ChEBI	D-glucose 6-phosphate	-	carbon source
43520	15748 ChEBI	D-glucuronate	-	carbon source
43520	15588 ChEBI	D-malate	-	carbon source
43520	16899 ChEBI	D-mannitol	-	carbon source
43520	16024 ChEBI	D-mannose	+	carbon source
43520	33801 ChEBI	D-saccharate	-	carbon source
43520	16523 ChEBI	D-serine	-	carbon source
43520	17924 ChEBI	D-sorbitol	-	carbon source
43520	23652 ChEBI	dextrin	-	carbon source
43520	4853 ChEBI	esculin	+	hydrolysis
43520	15740 ChEBI	formate	-	carbon source
43520	16537 ChEBI	galactarate	-	carbon source
43520	16865 ChEBI	gamma-aminobutyric acid	-	carbon source
43520	5291 ChEBI	gelatin	-	carbon source
43520	5291 ChEBI	gelatin	-	hydrolysis
43520	28066 ChEBI	gentiobiose	-	carbon source
43520	17234 ChEBI	glucose	-	fermentation
43520	32323 ChEBI	glucuronamide	-	carbon source
43520	17754 ChEBI	glycerol	-	carbon source
43520	70744 ChEBI	glycine-proline	-	carbon source
43520	17596 ChEBI	inosine	-	carbon source
43520	16977 ChEBI	L-alanine	-	carbon source
43520	16467 ChEBI	L-arginine	-	carbon source
43520	29991 ChEBI	L-aspartate	-	carbon source
43520	18287 ChEBI	L-fucose	-	carbon source
43520	29985 ChEBI	L-glutamate	-	carbon source
43520	15971 ChEBI	L-histidine	-	carbon source
43520	15589 ChEBI	L-malate	-	carbon source
43520	18183 ChEBI	L-pyroglutamic acid	-	carbon source
43520	62345 ChEBI	L-rhamnose	-	carbon source
43520	17115 ChEBI	L-serine	-	carbon source
43520	17716 ChEBI	lactose	-	carbon source
43520	17306 ChEBI	maltose	-	carbon source
43520	28053 ChEBI	melibiose	+	carbon source
43520	74611 ChEBI	methyl (R)-lactate	-	carbon source
43520	37657 ChEBI	methyl D-glucoside	-	carbon source
43520	51850 ChEBI	methyl pyruvate	-	carbon source
43520	17268 ChEBI	myo-inositol	-	carbon source
43520	63154 ChEBI	N-acetyl-beta-D-mannosamine	-	carbon source
43520	28037 ChEBI	N-acetylgalactosamine	-	carbon source
43520	506227 ChEBI	N-acetylglucosamine	-	carbon source
43520	35418 ChEBI	n-acetylneuraminate	-	carbon source
43520	17632 ChEBI	nitrate	+	reduction
43520	17309 ChEBI	pectin	-	carbon source
43520	17272 ChEBI	propionate	-	carbon source
43520	26490 ChEBI	quinate	-	carbon source
43520	16634 ChEBI	raffinose	+	carbon source
43520	17814 ChEBI	salicin	-	carbon source
43520	17164 ChEBI	stachyose	-	carbon source
43520	28017 ChEBI	starch	-	hydrolysis
43520	17992 ChEBI	sucrose	-	carbon source
43520	27082 ChEBI	trehalose	-	carbon source
43520	32528 ChEBI	turanose	-	carbon source
43520	53423 ChEBI	tween 40	-	carbon source
43520	16199 ChEBI	urea	-	hydrolysis

Antibiotic resistance

@ref	ChEBI	Metabolite	Resistance conc.	Sensitivity conc.
43520	2676	amoxicillin	10 µg (disc)
43520	28971	ampicillin		10 µg (disc)
43520	28669	bacitracin		0.04 Unit (disc)
43520	3393	carbenicillin	100 µg (disc)
43520	204928	cefotaxime	30 µg (disc)
43520	209807	cefoxitin	30 µg (disc)
43520	17698	chloramphenicol	30 µg (disc)
43520	48923	erythromycin		15 µg (disc)
43520	6104	kanamycin	30 µg (disc)
43520	25105	macrolide antibiotic		300 µg (disc)
43520	7507	neomycin	30 µg (disc)
43520	28368	novobiocin	30 µg (disc)
43520	7660	nystatin		100 µg (disc)
43520	17334	penicillin		10 Unit (disc)
43520	59062	polymyxin		300 Unit (disc)
43520	28077	rifampicin	5 µg (disc)
43520	17076	streptomycin	10 µg (disc)
43520	27902	tetracycline	30 µg (disc)
43520	28864	tobramycin	10 µg (disc)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
43520	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
43520	acid phosphatase	-	3.1.3.2
43520	alkaline phosphatase	-	3.1.3.1
43520	alpha-chymotrypsin	-	3.4.21.1
43520	alpha-galactosidase	+	3.2.1.22
43520	alpha-glucosidase	-	3.2.1.20
43520	alpha-mannosidase	+	3.2.1.24
43520	arginine dihydrolase	-	3.5.3.6
43520	beta-D-fucosidase	+	3.2.1.38
43520	beta-galactosidase	+	3.2.1.23
43520	beta-glucosidase	-	3.2.1.21
43520	beta-glucuronidase	-	3.2.1.31
43520	catalase	+	1.11.1.6
43520	cystine arylamidase	+	3.4.11.3
43520	cytochrome oxidase	+	1.9.3.1
43520	esterase (C 4)	-
43520	esterase Lipase (C 8)	-
43520	leucine arylamidase	-	3.4.11.1
43520	lipase (C 14)	+
43520	N-acetyl-beta-glucosaminidase	+	3.2.1.52
43520	naphthol-AS-BI-phosphohydrolase	-
43520	trypsin	+	3.4.21.4
43520	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@ref

43520

Fatty acid	Percentage
C17:0 anteiso	22.6
C16:0 iso	22.2
C15:0 iso	14.2
C15:0 anteiso	6
C17:0 iso	5.9
C18:1ω9c	5.3

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Wetland (Swamp)
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
43520	soil of the Xixi wetland	Hangzhou	China	CHN	Asia	30.265	120.045 30.265/120.045

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM982730v1 assembly for Croceibacterium xixiisoli S36	scaffold	GCA_009827305	1476466.3	2915124296	1476466	69.12
124043	ASM4265122v1 assembly for Croceibacterium xixiisoli CGMCC 1.12804	scaffold	GCA_042651225			1476466	51.02

16S sequences

@ref	Description	Accession	Database
43520	Croceibacterium xixiisoli 16S ribosomal RNA gene, partial sequence	KJ150597

GC content

@ref	GC-content (mol%)	Method
43520	62.7	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: ASM982730v1 assembly for Croceibacterium xixiisoli S36
NCBI: GCA_009827305

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	negative	70.94	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.06	no
125439	motility	BacteriaNetⓘ	yes	58.48	no
125439	spore_formation	BacteriaNetⓘ	no	97.85	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Croceibacterium xixiisoli S36
NCBI: GCA_009827305.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.33	yes
125438	anaerobic	anaerobicⓘ	no	95.77	yes
125438	aerobic	aerobicⓘ	yes	86.76	yes
125438	spore-forming	spore-formingⓘ	no	85.55	no
125438	thermophilic	thermophileⓘ	no	98.34	yes
125438	flagellated	motile2+ⓘ	yes	59.33	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 )
#43520	Nate Yuan, Yanhua Zeng, Hao Feng, Zhiliang Yu, Yili Huang: Altererythrobacter xixiisoli sp. nov., isolated from wetland soil. IJSEM 67: 3655 - 3659 2017 ( DOI 10.1099/ijsem.0.002198 , PubMed 28879849 )
#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) .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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