Name: Microbacterium sediminicola YM10-847
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 7435

Type strain:

Species: Microbacterium sediminicola

Strain Designation: YM10-847

Culture col. no.: DSM 18905, CIP 109809, JCM 15577, MBIC 08264, MBIC 07778, DSM 18904

Strain history: CIP <- 2008, DSMZ <- H. Kasai <- Y. Matsuo, Heita, Marine Biotech. Inst., Iwate, Japan: strain YM10-847

NCBI tax ID(s): 415210 (species)

Special Collections

Section

Microbacterium sediminicola YM10-847 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from sediment.

Gram-positive
rod-shaped
aerobe
16S sequence
Bacteria

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micrococcales*
	Family	*Microbacteriaceae*
	Genus	*Microbacterium*
	Species	**Microbacterium sediminicola**
	Full Scientific Name (LPSN)	Microbacterium sediminicola Kageyama et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #32148]	Gram stain	positive
[Ref.: #122534]	Gram stain	positive

[Ref.: #32148]	Cell length	1.15 µm

[Ref.: #32148]	Cell width	0.55 µm

[Ref.: #32148]	Cell shape	rod-shaped
[Ref.: #122534]	Cell shape	rod-shaped

[Ref.: #122534]	Motility	no

[Ref.: #18414]	Incubation period	10-14 days
[Ref.: #18414]	Cultivation medium used	ISP 2

[Ref.: #18414]	Incubation period	10-14 days
[Ref.: #18414]	Cultivation medium used	ISP 3

[Ref.: #18414]	Incubation period	10-14 days
[Ref.: #18414]	Cultivation medium used	ISP 4

[Ref.: #18414]	Incubation period	10-14 days
[Ref.: #18414]	Cultivation medium used	ISP 5

[Ref.: #18414]	Incubation period	10-14 days
[Ref.: #18414]	Cultivation medium used	ISP 6

[Ref.: #18414]	Incubation period	10-14 days
[Ref.: #18414]	Cultivation medium used	ISP 7

[Ref.: #32148]

Pigment production

yes

[Ref.: #18414]	Multicellular complex forming ability	no
[Ref.: #18414]	Medium Name (multicellularity)	ISP 2

[Ref.: #18414]	Multicellular complex forming ability	no
[Ref.: #18414]	Medium Name (multicellularity)	ISP 3

[Ref.: #18414]	Multicellular complex forming ability	no
[Ref.: #18414]	Medium Name (multicellularity)	ISP 4

[Ref.: #18414]	Multicellular complex forming ability	no
[Ref.: #18414]	Medium Name (multicellularity)	ISP 5

[Ref.: #18414]	Multicellular complex forming ability	no
[Ref.: #18414]	Medium Name (multicellularity)	ISP 6

[Ref.: #18414]	Multicellular complex forming ability	no
[Ref.: #18414]	Medium Name (multicellularity)	ISP 7

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7614]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #7614]

Culture medium growth

[Ref.: #7614]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7614]

Culture medium composition

expand / minimize

[Ref.: #18414]

Culture medium

ISP 2

[Ref.: #18414]

Culture medium growth

[Ref.: #18414]

Culture medium composition

expand / minimize

[Ref.: #18414]

Culture medium

ISP 3

[Ref.: #18414]

Culture medium growth

[Ref.: #18414]

Culture medium composition

expand / minimize

[Ref.: #18414]

Culture medium

ISP 5

[Ref.: #18414]

Culture medium growth

[Ref.: #18414]

Culture medium composition

expand / minimize

[Ref.: #18414]

Culture medium

ISP 4

[Ref.: #18414]

Culture medium growth

[Ref.: #18414]

Culture medium composition

expand / minimize

[Ref.: #18414]

Culture medium

ISP 6

[Ref.: #18414]

Culture medium growth

[Ref.: #18414]

Culture medium composition

expand / minimize

[Ref.: #18414]

Culture medium

ISP 7

[Ref.: #18414]

Culture medium growth

[Ref.: #18414]

Culture medium composition

expand / minimize

[Ref.: #37848]

Culture medium

MEDIUM 338 - for Sanguibacter keddieii

[Ref.: #37848]

Culture medium growth

[Ref.: #37848]

Culture medium composition

expand / minimize

[Ref.: #122534]

Culture medium

CIP Medium 338

[Ref.: #122534]

Culture medium growth

[Ref.: #122534]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #7614]	growth	28 °C
[Ref.: #32148]	growth	19-38 °C
[Ref.: #32148]	optimum	28.5 °C
[Ref.: #37848]	growth	30 °C
[Ref.: #67770]	growth	28 °C

	pH	Kind of pH		pH
[Ref.: #32148]			optimum	9
[Ref.: #32148]			growth	06-11

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32148]	Oxygen tolerance	aerobe
[Ref.: #122534]	Oxygen tolerance	obligate aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32148]		NaCl		growth	<7	%
[Ref.: #32148]		NaCl		optimum	3.5	%

[Ref.: #67770]

Observation

quinones: MK-10, MK-11

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68371]	amygdalin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32148]	arabinose ChEBI	+	carbon source
[Ref.: #68371]	arbutin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	cellobiose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fructose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-galactose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-glucose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-lyxose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannitol ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-ribose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-sorbitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-tagatose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	erythritol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	esculin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32148]	galactose ChEBI	+	carbon source
[Ref.: #68371]	gentiobiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	gluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32148]	glucose ChEBI	+	carbon source
[Ref.: #68371]	glycerol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycogen ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	inulin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabinose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-rhamnose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-sorbose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	lactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32148]	maltose ChEBI	+	carbon source
[Ref.: #68371]	maltose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32148]	mannitol ChEBI	+	carbon source
[Ref.: #32148]	mannose ChEBI	+	carbon source
[Ref.: #68371]	melezitose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	melibiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-mannoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	myo-inositol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32148]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #68371]	N-acetylglucosamine ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #122534]	nitrate ChEBI	-	reduction
[Ref.: #122534]	nitrite ChEBI	-	reduction
[Ref.: #32148]	ornithine ChEBI	+	carbon source
[Ref.: #68371]	Potassium 2-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	Potassium 5-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	raffinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32148]	rhamnose ChEBI	+	carbon source
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	salicin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	starch ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	sucrose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32148]	trehalose ChEBI	+	carbon source
[Ref.: #68371]	trehalose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	turanose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32148]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #122534]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[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.: #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.: #32148]	catalase	+	1.11.1.6
[Ref.: #122534]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API zym
[Ref.: #122534]	oxidase	+
[Ref.: #122534]	urease	-	3.5.1.5
	Only first 10 entries are displayed. Click here to see all.

API® 50CH acid:

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

	API ID	ControlQ	Acid from glycerolGLY	Acid from erythritolERY	Acid from D-arabinoseDARA	Acid from L-arabinoseLARA	Acid from D-riboseRIB	Acid from D-xyloseDXYL	Acid from L-xyloseLXYL	Acid from D-adonitolADO	Acid from methyl beta-D-xylopyranosideMDX	Acid from D-galactoseGAL	Acid from D-glucoseGLU	Acid from D-fructoseFRU	Acid from D-mannoseMNE	Acid from L-sorboseSBE	Acid from L-rhamnoseRHA	Acid from dulcitolDUL	Acid from inositolINO	Acid from D-mannitolMAN	Acid from D-sorbitolSOR	Acid from methyl alpha-D-mannopyranosideMDM	Acid from methyl alpha-D-glucopyranosideMDG	Acid from N-acetyl-glucosamineNAG	Acid from amygdalinAMY	Acid from arbutinARB	Acid from esculinESC	Acid from salicinSAL	Acid from cellobioseCEL	Acid from maltoseMAL	Acid from lactoseLAC	Acid from melibioseMEL	Acid from sucroseSAC	Acid from trehaloseTRE	Acid from inulinINU	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from starchAMD	Acid from glycogenGLYG	Acid from xylitolXLT	Acid from gentiobioseGEN	Acid from turanoseTUR	Acid from D-lyxoseLYX	Acid from D-tagatoseTAG	Acid from D-fucoseDFUC	Acid from L-fucoseLFUC	Acid from D-arabitolDARL	Acid from L-arabitolLARL	Acid from gluconateGNT	Acid from 2-Ketogluconate2KG	Acid from 5-Ketogluconate5KG
[Ref.: #7614]	14384	-	-	-	-	+	-	-	-	-	-	+	+	-	-	-	-	-	-	+	-	-	-	-	-	+	+	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

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.: #18414]	124	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	+	+	-	+	+	+	-	-
[Ref.: #122534]	12124	-	-	+	+	-	+	+	-	+	-	+	+	+	+	-	+	+	+	-	-

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

[Ref.: #7614]	Sample type/isolated from	sediment
[Ref.: #7614]	Geographic location (country and/or sea, region)	Samambula River, Fiji
[Ref.: #7614]	Country	Fiji
[Ref.: #7614]	Country ISO 3 Code	FJI
[Ref.: #7614]	Continent	Australia and Oceania

[Ref.: #67770]	Sample type/isolated from	Sediment from the mouth of the Samambula River
[Ref.: #67770]	Country	Fiji
[Ref.: #67770]	Country ISO 3 Code	FJI
[Ref.: #67770]	Continent	Australia and Oceania

[Ref.: #122534]	Sample type/isolated from	Environment, River sediment, marine lake
[Ref.: #122534]	Geographic location (country and/or sea, region)	Samambula river
[Ref.: #122534]	Country	Fiji
[Ref.: #122534]	Country ISO 3 Code	FJI
[Ref.: #122534]	Continent	Australia and Oceania
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Sediment
#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.: #18414]	Biosafety level	1	German classification
[Ref.: #7614]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #122534]	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.: #7614]	Microbacterium sediminicola gene for 16S rRNA, partial sequence	AB286021	1472	GenBank ENA	415210 tax ID

[Ref.: #7614]	GC-content	67.8 mol%
[Ref.: #67770]	GC-content	67.8 mol%	high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #7614]

Culture collection no.

DSM 18905, CIP 109809, JCM 15577, MBIC 08264, MBIC 07778, DSM 18904

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Microbacterium sediminicola sp. nov. and Microbacterium marinilacus sp. nov., isolated from marine environments.	Kageyama A, Takahashi Y, Matsuo Y, Kasai H, Shizuri Y, Omura S	Int J Syst Evol Microbiol	10.1099/ijs.0.65038-0	2007	*

References

#7614

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18905

#18414

Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .

#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 )

#32148

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 #28391 (see below)

#37848 ; Curators of the CIP;
#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68371

Automatically annotated from API 50CH acid .

#68382

Automatically annotated from API zym .

#122534 Collection of Institut Pasteur ; Curators of the CIP; CIP 109809

#28391

IJSEM 2355 2007 ( DOI 10.1099/ijs.0.65038-0 , PubMed 17911310 )

* These data were automatically processed and therefore are not curated

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