Name: Chryseobacterium formosense CC-H3-2
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 5679

Type strain:

Species: Chryseobacterium formosense

Strain Designation: CC-H3-2

Culture col. no.: DSM 17452, CCUG 49271, CIP 108367, KCTC 12435

Strain history: CIP <- 2004, P. Kämpfer, Giessen, Germany: strain CC-H3-2

NCBI tax ID(s): 236814 (species)

SI-ID 135107

CCUG 49271, CIP 108367, KCTC 12435, DSM 17452, BCRC 17514, CCRC 17514, LMG 24722

Special Collections

Section

When using BacDive for research please cite our paper

Chryseobacterium formosense CC-H3-2 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from rhizosphere of Lactuca sativa L. .

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Bacteroidota*
	Class	*Flavobacteriia*
	Order	*Flavobacteriales*
	Family	*Weeksellaceae*
	Genus	*Chryseobacterium*
	Species	**Chryseobacterium formosense**
	Full Scientific Name (LPSN)	Chryseobacterium formosense Young et al. 2005

Information on morphological and physiological properties Morphology

[Ref.: #119426]	Gram stain	negative
[Ref.: #125438]	Gram stain	negative Confidence in %97.455
[Ref.: #125439]	Gram stain	negative Confidence in %99.8

[Ref.: #119426]	Cell shape	rod-shaped

[Ref.: #119426]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6992]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #6992]

Culture medium growth

[Ref.: #6992]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6992]

Culture medium composition

expand / minimize

[Ref.: #38272]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #38272]

Culture medium growth

[Ref.: #38272]

Culture medium composition

expand / minimize

[Ref.: #119426]

Culture medium

CIP Medium 72

[Ref.: #119426]

Culture medium growth

[Ref.: #119426]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #6992]		growth	28 °C
[Ref.: #38272]		growth	30 °C
[Ref.: #58489]		growth	30-37 °C
[Ref.: #119426]		growth	15-30 °C
[Ref.: #119426]	negative	growth	5 °C
[Ref.: #119426]	negative	growth	37 °C
[Ref.: #119426]	negative	growth	41 °C
[Ref.: #119426]	negative	growth	45 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #58489]	Oxygen tolerance	aerobe
[Ref.: #119426]	Oxygen tolerance	obligate aerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %97.8

[Ref.: #125439]

Ability of spore formation

no Confidence in %97.8

	Salt	Tested relation		Salt conc.
[Ref.: #119426]	NaCl		growth	0-2	%
[Ref.: #119426]	NaCl	no	growth	4	%
[Ref.: #119426]	NaCl	no	growth	6	%
[Ref.: #119426]	NaCl	no	growth	8	%
[Ref.: #119426]	NaCl	no	growth	10	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #119426]	esculin ChEBI	+	hydrolysis
[Ref.: #119426]	hippurate ChEBI	-	hydrolysis
[Ref.: #119426]	malonate ChEBI	-	assimilation
[Ref.: #119426]	nitrate ChEBI	-	builds gas from
[Ref.: #119426]	nitrate ChEBI	-	reduction
[Ref.: #119426]	nitrate ChEBI	-	respiration
[Ref.: #119426]	nitrite ChEBI	-	builds gas from
[Ref.: #119426]	nitrite ChEBI	-	reduction

	Antibiotica	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #119426]		0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)	yes	no

	Metabolite production	Metabolite	Production
[Ref.: #119426]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #119426]		acetoin ChEBI	-
[Ref.: #119426]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #119426]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #119426]	amylase	+
[Ref.: #119426]	beta-galactosidase	+	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	+	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #119426]	caseinase	+	3.4.21.50
[Ref.: #119426]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	+	3.4.11.3	* from API zym
[Ref.: #119426]	DNase	+
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #119426]	gamma-glutamyltransferase	+	2.3.2.2
[Ref.: #119426]	gelatinase	+/-
[Ref.: #119426]	lecithinase	+
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #119426]	lipase	+
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #119426]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #119426]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #119426]	oxidase	+
[Ref.: #119426]	phenylalanine ammonia-lyase	-	4.3.1.24
[Ref.: #119426]	protease	+
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #119426]	tryptophan deaminase	-
[Ref.: #119426]	tween esterase	+
[Ref.: #119426]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #119426]	11121	-	+	+	+	-	+	+	+	+	-	+	+	-	-	-	-	+	-	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #6992]	Sample type/isolated from	rhizosphere of Lactuca sativa L. (garden lettuce)
[Ref.: #6992]	Host species	Lactuca sativa
[Ref.: #6992]	Country	Taiwan, Province of China
[Ref.: #6992]	Country ISO 3 Code	TWN
[Ref.: #6992]	Continent	Asia

[Ref.: #58489]	Sample type/isolated from	Rhizosphere of Lactuca sativa (garden lettuce)
[Ref.: #58489]	Geographic location (country and/or sea, region)	Taichung county,Koshing,R.O.C.
[Ref.: #58489]	Country	Taiwan, Province of China
[Ref.: #58489]	Country ISO 3 Code	TWN
[Ref.: #58489]	Continent	Asia

[Ref.: #119426]	Sample type/isolated from	Environment, Rhizosphere of Lactuca saliva L. (garden lettuce)
[Ref.: #119426]	Country	Taiwan, Province of China
[Ref.: #119426]	Country ISO 3 Code	TWN
[Ref.: #119426]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Rhizosphere

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AY315443 (>99% sequence identity) for Chryseobacterium formosense from Microbeatlas

Aquatic Samples	44
Soil Samples	27
Animal Samples	76
Plant Samples	26
Total Samples	173

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #6992]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #119426]	Biosafety level	1	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #6992]	Chryseobacterium formosense strain CC-H3-2 16S ribosomal RNA gene, partial sequence	AY315443	1455	GenBank ENA	236814 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Chryseobacterium formosense DSM 17452	GCA_900116415	contig	GenBank ENA	236814 tax ID	*
[Ref.: #66792]	Chryseobacterium formosense strain DSM 17452	236814.8	wgs	PATRIC	236814 tax ID	*
[Ref.: #66792]	Chryseobacterium formosense DSM 17452	2684622901	draft	JGI IMG/M	236814 tax ID	*

[Ref.: #6992]

GC-content

34.8 mol%

sequence analysis

Data predicted using genome information as a basis Genome-based predictions

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Chryseobacterium formosense strain DSM 17452 PATRIC: 236814.8
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	97.455	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	96.965	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	87.289	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	88.414	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	97.143	no
[Ref.: #125438]	motile2+	flagellatedⓘ	no	89	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Chryseobacterium formosense DSM 17452 NCBI: GCA_900116415
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	97.8
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	75.6
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	99.8
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	97.8

Availability in culture collections External links

[Ref.: #6992]

Culture collection no.

DSM 17452, CCUG 49271, CIP 108367, KCTC 12435

[Ref.: #75161]

SI-ID 135107

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Chryseobacterium chungangensis sp. nov., a bacterium isolated from soil of sweet gourd garden.	Huq MA	Arch Microbiol	10.1007/s00203-017-1469-8	2017	*
Phylogeny	Chryseobacterium formosense sp. nov., isolated from the rhizosphere of Lactuca sativa L. (garden lettuce).	Young CC, Kampfer P, Shen FT, Lai WA, Arun AB	Int J Syst Evol Microbiol	10.1099/ijs.0.63331-0	2005	*

References

#6992

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17452

#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 )

#38272 ; Curators of the CIP;
#58489 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 49271

#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 .

#75161

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID135107.1 )

#119426 Collection of Institut Pasteur ; Curators of the CIP; CIP 108367

#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 .

* These data were automatically processed and therefore are not curated

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Chryseobacterium formosense strain DSM 17452

Chryseobacterium formosense DSM 17452

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