Chryseobacterium gambrini (DSM 18014, CCUG 52549, 5-1St1a)

Name: Chryseobacterium gambrini (DSM 18014, CCUG 52549, 5-1St1a)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5698

Type strain

Strain Designation 5-1St1a

Culture col. no. DSM 18014 CCUG 52549 5-1St1a CIP 110172

NCBI tax ID(s) 373672

Special Collections DSMZ CCUG Literature strains CIP

Links

Chryseobacterium gambrini 5-1St1a is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from steel surface of a beer-bottling plant.

Gram-negative rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 323954

CCUG 52549,DSM 18014,LMG 25632,CIP 110172

@ref 20215

Last LPSN update 2025-12-16 09:48:08

Domain Pseudomonadati

Phylum Bacteroidota

Class Flavobacteriia

Order Flavobacteriales

Family Weeksellaceae

Genus Chryseobacterium

Species Chryseobacterium gambrini

Full scientific name Chryseobacterium gambrini Herzog et al. 2008

BacDive ID	Other strains from **Chryseobacterium gambrini** (2)	Type strain
170948	C. gambrini 167-84, CIP 100738
172827	C. gambrini CIP 109992

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape
32348	negative	3.6 µm	1.1 µm	rod-shaped
119526	negative			rod-shaped
125438
125438	negative
125439	negative

Pigmentation

32348

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7333	TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)	Medium recipe at MediaDive	Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water
33351	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119526	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
7333	positive	growth	28	mesophilic
32348	positive	growth	25-42
33351	positive	growth	30	mesophilic
59592	positive	growth	30-37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
32348	aerobe
59592	aerobe
119526	obligate aerobe
125438	aerobe
125439	obligate aerobe

Spore formation

@ref	Spore formation
32348
125439

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32348	NaCl	positive	growth	<1 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32348	17128 ChEBI	adipate	+	carbon source
32348	22599 ChEBI	arabinose	+	carbon source
32348	4853 ChEBI	esculin	+	hydrolysis
32348	17234 ChEBI	glucose	+	carbon source
32348	17306 ChEBI	maltose	+	carbon source
32348	37684 ChEBI	mannose	+	carbon source
119526	17632 ChEBI	nitrate	-	reduction
119526	16301 ChEBI	nitrite	-	reduction
32348	18401 ChEBI	phenylacetate	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
119526	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
32348	catalase	+	1.11.1.6
119526	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
32348	cytochrome oxidase	+	1.9.3.1
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
32348	gelatinase	+
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
119526	oxidase	+
68382	trypsin	+	3.4.21.4	from API zym
119526	urease	-	3.5.1.5
68382	valine arylamidase	+		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
119526	-	+	+	+	-	+	+	+	+	-	+	+	-	-	-	+	+	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Food production	#Bottled, canned, packed food
#Engineered	#Food production	#Fermented
#Engineered	#Industrial	#Engineered product
#Engineered	#Industrial	#Plant (Factory)
#Engineered	#Food production	#Beverage

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
7333	steel surface of a beer-bottling plant	Germany	DEU	Europe
59592	Steel surface of a beer-bottling plant	Germany	DEU	Europe
119526	Steel surface of a beer-bottling plant	Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence AM232810 (>99% sequence identity) for Chryseobacterium from Microbeatlas

Aquatic Samples	1137
Soil Samples	371
Animal Samples	977
Plant Samples	604
Total Samples	3089

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7333	1	Risk group (German classification) According to TRBA 466
119526	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	IMG-taxon 2681813561 annotated assembly for Chryseobacterium gambrini DSM 18014	contig	GCA_900156825	373672.4	2681813561	373672	69.05

Genome browser: GCA_900156825

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7333	Chryseobacterium gambrini partial 16S rRNA gene, type strain 5-1St1aT	AM232810	1403		373672

GC content

32348

GC-content (mol%)37.8

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Chryseobacterium gambrini DSM 18014
NCBI: GCA_900156825

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.40	no
125439	motility	BacteriaNetⓘ	no	79.90	no
125439	gram_stain	BacteriaNetⓘ	negative	99.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	94.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Chryseobacterium gambrini strain DSM 18014
PATRIC: 373672.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.44	yes
125438	anaerobic	anaerobicⓘ	no	96.80	yes
125438	spore-forming	spore-formingⓘ	no	89.16	no
125438	aerobic	aerobicⓘ	yes	90.08	yes
125438	thermophilic	thermophileⓘ	no	96.64	no
125438	flagellated	motile2+ⓘ	no	90.50	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genome analysis deciphered Chryseobacterium indicum is a distinct species associated with freshwater pufferfish.	Victor MP, Kujur RRA, Das L, Das SK.	Infect Genet Evol	10.1016/j.meegid.2024.105561	2024
	Phylogenetic insights into the diversity of Chryseobacterium species.	Siddaramappa S, Narjala A, Viswanathan V, Maliye C, Lakshminarayanan R.	Access Microbiol	10.1099/acmi.0.000019	2019
Metabolism	Prokaryotic viperins produce diverse antiviral molecules.	Bernheim A, Millman A, Ofir G, Meitav G, Avraham C, Avraham C, Shomar H, Rosenberg MM, Tal N, Melamed S, Amitai G, Sorek R.	Nature	10.1038/s41586-020-2762-2	2021
Genetics	Marnyiella aurantia, gen. nov., sp. nov., a novel bacterial species of the family Weeksellaceae that could produce flexirubin type pigments.	Zhao L, Yang C, Chen M, Zhang J, Kong M, Dong L, Gong J, Yang J, Pu J, Lu S, Jin D, Liu L, Wang S, Xu J.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006020	2023
	Draft Genome Sequence of Chryseobacterium mucoviscidosis sp. nov. Strain VT16-26, Isolated from the Bronchoalveolar Lavage Fluid of a Patient with Cystic Fibrosis.	Tetz G, Tetz V.	Genome Announc	10.1128/genomea.01473-17	2018
Phylogeny	Chryseobacterium ureilyticum sp. nov., Chryseobacterium gambrini sp. nov., Chryseobacterium pallidum sp. nov. and Chryseobacterium molle sp. nov., isolated from beer-bottling plants.	Herzog P, Winkler I, Wolking D, Kampfer P, Lipski A	Int J Syst Evol Microbiol	10.1099/ijs.0.65362-0	2008

References

#7333	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18014
#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 )
#32348	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28579 (see below)
#33351	; Curators of the CIP;
#59592	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 52549
#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) .
#68382	Automatically annotated from API zym .
#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 .
#119526	Collection of Institut Pasteur ; Curators of the CIP; CIP 110172
#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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Chryseobacterium gambrini (DSM 18014, CCUG 52549, 5-1St1a)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900156825

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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