Chryseobacterium palustre (DSM 21579, LMG 24685, NBRC 104928)

Name: Chryseobacterium palustre (DSM 21579, LMG 24685, NBRC 104928)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5706

Type strain

Strain Designation 3A10

Culture col. no. DSM 21579 LMG 24685 NBRC 104928 3A10 CIP 110180

NCBI tax ID(s) 1121288 493376

Special Collections DSMZ Literature strains CIP

History <- C. Pires, Escola Superior Biotecnol. (UCP), Porto, Portugal; 3A10 CIP <- 2010, DSMZ <- C. Pires, UCP, Porto, Portugal: strain 3A10

Links

Chryseobacterium palustre 3A10 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from rhizosphere sediment sample from a polluted site.

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

Name and taxonomic classification

SI-ID 358561

LMG 24685,NBRC 104928,DSM 21579,CIP 110180

@ref 20215

Last LPSN update 2026-02-09 11:19:01

Domain Bacteria

Phylum Bacteroidota

Class Flavobacteriia

Order Flavobacteriales

Family Weeksellaceae

Genus Chryseobacterium

Species Chryseobacterium palustre

Full scientific name Chryseobacterium palustre Pires et al. 2010

Synonyms (1)

Kaistella palustris

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29291	negative	1.8 µm	0.6 µm	rod-shaped
121516	negative			rod-shaped
125438					90
125438	negative				98.94
125439	negative				99.9

Pigmentation

29291

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
15821	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
40741	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121516	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
15821	positive	growth	28
29291	positive	growth	10-37
29291	positive	optimum	30
40741	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
29291	positive	optimum	7
29291	positive	growth	06-09	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29291	aerobe
121516	obligate aerobe
125439	obligate aerobe	99.2

Spore formation

@ref	Spore formation	Confidence
125438		92.91
125439		98.5

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29291	NaCl	positive	growth	0-6 %
29291	NaCl	positive	optimum	2.5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29291	17128 ChEBI	adipate	+	carbon source
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
29291	22599 ChEBI	arabinose	+	carbon source
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
68371	17057 ChEBI	cellobiose	-	builds acid from	from API 50CH acid
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	-	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	-	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68371	16988 ChEBI	D-ribose	-	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
29291	4853 ChEBI	esculin	+	hydrolysis
68371	4853 ChEBI	esculin	-	builds acid from	from API 50CH acid
29291	28757 ChEBI	fructose	+	carbon source
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
29291	17234 ChEBI	glucose	+	carbon source
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
29291	28087 ChEBI	glycogen	+	carbon source
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	-	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
29291	17716 ChEBI	lactose	+	carbon source
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
29291	25115 ChEBI	malate	+	carbon source
29291	17306 ChEBI	maltose	+	carbon source
29291	29864 ChEBI	mannitol	+	carbon source
29291	37684 ChEBI	mannose	+	carbon source
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
29291	506227 ChEBI	N-acetylglucosamine	+	carbon source
68371	59640 ChEBI	N-acetylglucosamine	-	builds acid from	from API 50CH acid
121516	17632 ChEBI	nitrate	-	reduction
121516	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
29291	26546 ChEBI	rhamnose	+	carbon source
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	-	builds acid from	from API 50CH acid
29291	30911 ChEBI	sorbitol	+	carbon source
29291	17992 ChEBI	sucrose	+	carbon source
68371	17992 ChEBI	sucrose	-	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	-	builds acid from	from API 50CH acid
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid
29291	18222 ChEBI	xylose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
121516	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
29291	catalase	+	1.11.1.6
121516	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
29291	cytochrome oxidase	+	1.9.3.1
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
29291	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
121516	oxidase	+
68382	trypsin	+	3.4.21.4	from API zym
121516	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
121516	-	+	+	+	+	+	+	+	+	+	+	+	-	-	-	+	-	-	-	-

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
121516	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	+/-	-	+/-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+/-	-	-	-	-	-	-	-	+/-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Contamination	-
#Environmental	#Terrestrial	#Sediment
#Host Body-Site	#Plant	#Rhizosphere

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
15821	rhizosphere sediment sample from a polluted site	Northwest Portugal, Estarreja	Portugal	PRT	Europe
121516	Environment, Rhizosphere sediment, sample from a polluted site	Estarreja	Portugal	PRT	Europe

Taxonmaps

69479

Global distribution of 16S sequence AB682225 (>99% sequence identity) for Chryseobacterium palustre subclade from Microbeatlas

Aquatic Samples	130
Soil Samples	43
Animal Samples	313
Plant Samples	8
Total Samples	494

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15821	1	Risk group (German classification) According to TRBA 466
121516	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	ASM42226v1 assembly for Kaistella palustris DSM 21579	scaffold	GCA_000422265	1121288.4	2523533629	1121288	75.09

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Chryseobacterium palustre gene for 16S rRNA, partial sequence, strain: NBRC 104928	AB682225	1442		493376
15821	Chryseobacterium palustre strain 3A10 16S ribosomal RNA gene, partial sequence	EU360967	1444		1121288

GC content

@ref	GC-content (mol%)	Method
15821	43
15821	42.4
15821	41.5	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Kaistella palustris DSM 21579
NCBI: GCA_000422265

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.50	no
125439	motility	BacteriaNetⓘ	no	83.50	no
125439	gram_stain	BacteriaNetⓘ	negative	99.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Chryseobacterium palustre DSM 21579 DSM 21579
NCBI: GCA_000422265.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.94	no
125438	anaerobic	anaerobicⓘ	no	97.30	yes
125438	aerobic	aerobicⓘ	yes	87.52	no
125438	spore-forming	spore-formingⓘ	no	92.91	no
125438	thermophilic	thermophileⓘ	no	98.87	yes
125438	flagellated	motile2+ⓘ	no	90.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Kaistella flava sp. nov., isolated from Antarctic tundra soil, and emended descriptions of Kaistella yonginensis, Kaistella jeonii, Kaistella antarctica and Kaistella chaponensis.	Peng X, Zhang Y, Lu Y, Zhou X, Wei Z, Sun Y, Kuang C, Lu L, Geng Y, Qin K, Liu J, Peng F	Int J Syst Evol Microbiol	10.1099/ijsem.0.004740	2021
Phylogeny	Chryseobacterium palustre sp. nov. and Chryseobacterium humi sp. nov., isolated from industrially contaminated sediments.	Pires C, Carvalho MF, De Marco P, Magan N, Castro PML	Int J Syst Evol Microbiol	10.1099/ijs.0.010348-0	2009

References

#15821	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21579
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#25707	IJSEM 402 2010 ( DOI 10.1099/ijs.0.010348-0 , PubMed 19651727 )
#29291	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 #25707
#40741	; Curators of the CIP;
#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) .
#68371	Automatically annotated from API 50CH acid .
#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 .
#121516	Collection of Institut Pasteur ; Curators of the CIP; CIP 110180
#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 palustre (DSM 21579, LMG 24685, NBRC 104928)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Enzymes

API zym

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000422265

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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