Name: Maribacter sedimenticola DSM 19840
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5604

Type strain:

Species: Maribacter sedimenticola

Variant: Isotype of BacDive ID 132751

Culture col. no.: DSM 19840, CCUG 47098, KCTC 12966, KMM 3903, CIP 108493

Strain history: CIP <- 2004, CCUG <- 2002, KMM

NCBI tax ID(s): 228956 (species)

SI-ID 99593

KCTC 12966, CCUG 47098, CIP 108493, DSM 16470, DSM 19840

Other strains from Maribacter sedimenticola

M. sedimenticola DSM 16470, CCUG 47098, KCTC 12966, ... (type strain)

Section

Maribacter sedimenticola DSM 19840 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from bottom sediment sample.

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	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacteroidota*
	Class	*Flavobacteriia*
	Order	*Flavobacteriales*
	Family	*Flavobacteriaceae*
	Genus	*Maribacter*
	Species	**Maribacter sedimenticola**
	Full Scientific Name (LPSN)	Maribacter sedimenticola Nedashkovskaya et al. 2004

Information on morphological and physiological properties Morphology

[Ref.: #30026]	Gram stain	negative
[Ref.: #122532]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.938

[Ref.: #30026]	Cell length	6 µm

[Ref.: #30026]	Cell width	0.6 µm

[Ref.: #30026]	Cell shape	rod-shaped
[Ref.: #122532]	Cell shape	rod-shaped

[Ref.: #30026]	Motility	no
[Ref.: #122532]	Motility	no

[Ref.: #30026]	Pigment production	yes
[Ref.: #122532]	Pigment production	no
[Ref.: #122532]	Pigment name	Flexirubin

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8273]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #8273]

Culture medium growth

[Ref.: #8273]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8273]

Culture medium composition

expand / minimize

[Ref.: #37439]

Culture medium

Marine agar (MA)

[Ref.: #37439]

Culture medium growth

[Ref.: #37439]

Culture medium composition

expand / minimize

[Ref.: #122532]

Culture medium

CIP Medium 13

[Ref.: #122532]

Culture medium growth

[Ref.: #122532]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #8273]		growth	25 °C
[Ref.: #30026]		growth	4.0-33 °C
[Ref.: #30026]		optimum	23 °C
[Ref.: #37439]		growth	30 °C
[Ref.: #122532]		growth	5-30 °C
[Ref.: #122532]	no	growth	37 °C
[Ref.: #122532]	no	growth	41 °C
[Ref.: #122532]	no	growth	45 °C

[Ref.: #8273]	Temperature range	mesophilic
[Ref.: #30026]	Temperature range	psychrophilic
[Ref.: #37439]	Temperature range	mesophilic
[Ref.: #122532]	Temperature range	mesophilic
[Ref.: #122532]	Temperature range	thermophilic

	pH	Kind of pH		pH
[Ref.: #30026]			optimum	8
[Ref.: #30026]			growth	5.5-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30026]

Oxygen tolerance

aerobe

[Ref.: #30026]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.974

	Salt	Tested relation		Salt conc.
[Ref.: #30026]	NaCl		growth	1.0-6.0	%
[Ref.: #30026]	NaCl		optimum	3.5	%
[Ref.: #122532]	NaCl	no	growth	0	%
[Ref.: #122532]	NaCl	no	growth	2	%
[Ref.: #122532]	NaCl	no	growth	4	%
[Ref.: #122532]	NaCl	no	growth	6	%
[Ref.: #122532]	NaCl	no	growth	8	%
[Ref.: #122532]	NaCl	no	growth	10	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30026]	arabinose ChEBI	+	carbon source
[Ref.: #122532]	esculin ChEBI	+	hydrolysis
[Ref.: #122532]	hippurate ChEBI	-	hydrolysis
[Ref.: #122532]	malonate ChEBI	-	assimilation
[Ref.: #122532]	nitrate ChEBI	-	reduction
[Ref.: #122532]	nitrite ChEBI	-	reduction
[Ref.: #30026]	tween 40 ChEBI	+	carbon source
[Ref.: #30026]	tween 80 ChEBI	+	carbon source

	Metabolite production	Metabolite	Production
[Ref.: #122532]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #122532]		acetoin ChEBI	-
[Ref.: #122532]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[Ref.: #122532]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #30026]	alkaline phosphatase	+	3.1.3.1
[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.: #122532]	amylase	+
[Ref.: #122532]	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.: #122532]	caseinase	+	3.4.21.50
[Ref.: #30026]	catalase	+	1.11.1.6
[Ref.: #122532]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #30026]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68382]	esterase (C 4)	-		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #122532]	gamma-glutamyltransferase	+	2.3.2.2
[Ref.: #30026]	gelatinase	+
[Ref.: #122532]	gelatinase	+/-
[Ref.: #122532]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #122532]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #122532]	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.: #122532]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #122532]	oxidase	-
[Ref.: #122532]	phenylalanine ammonia-lyase	-	4.3.1.24
[Ref.: #122532]	protease	+
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #122532]	tryptophan deaminase	-
[Ref.: #122532]	tween esterase	+
[Ref.: #122532]	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.: #122532]	11225	-	+	-	+	-	+	+	-	-	-	-	+	-	-	-	-	-	+	-	-

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

[Ref.: #8273]	Sample type/isolated from	bottom sediment sample
[Ref.: #8273]	Geographic location (country and/or sea, region)	Sea of Japan, Gulf of Peter the Great
[Ref.: #8273]	Continent	Asia

[Ref.: #122532]	Sample type/isolated from	Environment, Marine bottom sediment
[Ref.: #122532]	Country	Japan
[Ref.: #122532]	Country ISO 3 Code	JPN
[Ref.: #122532]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Sediment

What are isolation sources categories?

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

[Ref.: #8273]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #122532]	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.: #8273]	Bacteroidetes bacterium KMM 3903 16S ribosomal RNA gene, partial sequence	AY271623	1439	ENA	228956 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Maribacter sedimenticola DSM 19840	GCA_900188415	scaffold	GenBank	228956 tax ID	*
[Ref.: #66792]	Maribacter sedimenticola strain DSM 19840	228956.4	wgs	PATRIC	228956 tax ID	*
[Ref.: #66792]	Maribacter sedimenticola DSM 19840	2622736538	draft	JGI IMG/M	228956 tax ID	*

[Ref.: #8273]	GC-content	37.0 mol%
[Ref.: #30026]	GC-content	37.5 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Maribacter sedimenticola DSM 19840 NCBI: GCA_900188415.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Maribacter sedimenticola DSM 19840 NCBI: GCA_900188415.1
[Ref.: #69480]	motile	no	86.169	no
[Ref.: #69480]	flagellated	no	95.57	yes
[Ref.: #69480]	gram-positive	no	96.533	yes
[Ref.: #69480]	anaerobic	no	99.654	no
[Ref.: #69480]	aerobic	yes	95.492	no
[Ref.: #69480]	halophile	no	70.266	no
[Ref.: #69480]	spore-forming	no	96.553	yes
[Ref.: #69480]	thermophile	no	98.675	yes
[Ref.: #69480]	glucose-util	yes	86.493	no
[Ref.: #69480]	glucose-ferment	no	89.789	no

Availability in culture collections External links

[Ref.: #8273]

Culture collection no.

DSM 19840, CCUG 47098, KCTC 12966, KMM 3903, CIP 108493

[Ref.: #75086]

SI-ID 99593

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Maribacter caenipelagi sp. nov., a member of the Flavobacteriaceae isolated from a tidal flat sediment of the Yellow Sea in Korea.	Jung YT, Lee JS, Yoon JH	Antonie Van Leeuwenhoek	10.1007/s10482-014-0243-z	2014	*
Phylogeny	Maribacter gen. nov., a new member of the family Flavobacteriaceae, isolated from marine habitats, containing the species Maribacter sedimenticola sp. nov., Maribacter aquivivus sp. nov., Maribacter orientalis sp. nov. and Maribacter ulvicola sp. nov.	Nedashkovskaya OI, Kim SB, Han SK, Lysenko AM, Rohde M, Rhee MS, Frolova GM, Falsen E, Mikhailov VV, Bae KS	Int J Syst Evol Microbiol	10.1099/ijs.0.02849-0	2004	*

References

#8273

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19840

#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 )

#30026

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 #26390 (see below)

#37439 ; 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) .

#68382

Automatically annotated from API zym .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#75086

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-ID99593.1 )

#122532 Collection of Institut Pasteur ; Curators of the CIP; CIP 108493

#26390

IJSEM 1017 2004 ( DOI 10.1099/ijs.0.02849-0 , PubMed 15280264 )

* These data were automatically processed and therefore are not curated

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