Name: Microbacterium sediminis YLB-01
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 7467

Type strain:

Species: Microbacterium sediminis

Strain Designation: YLB-01

Culture col. no.: DSM 23767, CCTCC AB 2010363, JCM 19554, MCCC 1A06153

Strain history: DSM 23767 <-- L. Yu YLB-01.

NCBI tax ID(s): 904291 (species)

SI-ID 398690

DSM 23767

Section

Microbacterium sediminis YLB-01 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from deep-sea sediment.

Gram-positive
motile
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	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micrococcales*
	Family	*Microbacteriaceae*
	Genus	*Microbacterium*
	Species	**Microbacterium sediminis**
	Full Scientific Name (LPSN)	Microbacterium sediminis Yu et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #30121]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #30121]	Cell length	5.5 µm

[Ref.: #30121]	Cell width	1.25 µm

[Ref.: #30121]	Cell shape	rod-shaped

[Ref.: #30121]	Motility	yes

[Ref.: #30121]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #17367]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #17367]

Culture medium growth

[Ref.: #17367]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17367]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #17367]	growth	28 °C
[Ref.: #30121]	growth	04-50 °C
[Ref.: #30121]	optimum	28 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #17367]	Temperature range	mesophilic
[Ref.: #30121]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30121]			optimum	7
[Ref.: #30121]			growth	5.0-10.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30121]

Oxygen tolerance

aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.979

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30121]		NaCl		growth	0-8	%

[Ref.: #67770]

Observation

quinones: MK-10, MK-11, MK-8, MK-9

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30121]	alanine ChEBI	+	carbon source
[Ref.: #30121]	esculin ChEBI	+	hydrolysis
[Ref.: #30121]	fructose ChEBI	+	carbon source
[Ref.: #30121]	galactonate ChEBI	+	carbon source
[Ref.: #30121]	galactose ChEBI	+	carbon source
[Ref.: #30121]	gluconate ChEBI	+	carbon source
[Ref.: #30121]	glucose ChEBI	+	carbon source
[Ref.: #30121]	glycine ChEBI	+	carbon source
[Ref.: #30121]	L-alaninamide ChEBI	+	carbon source
[Ref.: #30121]	leucine ChEBI	+	carbon source
[Ref.: #30121]	mannitol ChEBI	+	carbon source
[Ref.: #30121]	mannose ChEBI	+	carbon source
[Ref.: #30121]	sodium citrate ChEBI	+	carbon source
[Ref.: #30121]	sorbitol ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #30121]	acid phosphatase	+	3.1.3.2
[Ref.: #30121]	alkaline phosphatase	+	3.1.3.1
[Ref.: #30121]	catalase	+	1.11.1.6
[Ref.: #30121]	cytochrome oxidase	+	1.9.3.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	pentose phosphate pathway	100	11 of 11
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	glutamate and glutamine metabolism	85.71	24 of 28
[Ref.: #66794]	purine metabolism	80.85	76 of 94
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	4-hydroxymandelate degradation	77.78	7 of 9
[Ref.: #66794]	allantoin degradation	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	pyrimidine metabolism	75.56	34 of 45
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	peptidoglycan biosynthesis	73.33	11 of 15
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	isoprenoid biosynthesis	69.23	18 of 26
[Ref.: #66794]	degradation of sugar alcohols	68.75	11 of 16
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	NAD metabolism	66.67	12 of 18
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	alanine metabolism	65.52	19 of 29
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	tryptophan metabolism	63.16	24 of 38
[Ref.: #66794]	C4 and CAM-carbon fixation	62.5	5 of 8
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	oxidative phosphorylation	60.44	55 of 91
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	3-chlorocatechol degradation	60	3 of 5
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	metabolism of disaccharids	54.55	6 of 11
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	lysine metabolism	50	21 of 42
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	methionine metabolism	50	13 of 26
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	lipid metabolism	48.39	15 of 31
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	d-xylose degradation	45.45	5 of 11
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	degradation of pentoses	42.86	12 of 28
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	phenol degradation	40	8 of 20
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	vitamin B1 metabolism	38.46	5 of 13
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	3-phenylpropionate degradation	33.33	5 of 15
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	degradation of sugar acids	28	7 of 25
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
[Ref.: #66794]	ascorbate metabolism	22.73	5 of 22
[Ref.: #66794]	carotenoid biosynthesis	22.73	5 of 22
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #17367]	Sample type/isolated from	deep-sea sediment
[Ref.: #17367]	Geographic location (country and/or sea, region)	Indian Ocean (49.8405° E 37.8111° S) at 2327 m water depth
[Ref.: #17367]	Country	China
[Ref.: #17367]	Country ISO 3 Code	CHN
[Ref.: #17367]	Continent	Asia
[Ref.: #17367]	Geographic location	-37.8111°/49.8405°

[Ref.: #67770]	Sample type/isolated from	Sediment of the Indian Ocean
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence HQ219727 (>99% sequence identity) for Microbacterium sediminis from Microbeatlas

Aquatic Samples	14
Soil Samples	8
Animal Samples	20
Plant Samples	3
Total Samples	45

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

[Ref.: #17367]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #17367]	Microbacterium sediminis strain YLB-01 16S ribosomal RNA gene, partial sequence	HQ219727	1487	ENA	904291 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Microbacterium sediminis YLB-01	GCA_002741995	scaffold	GenBank	904291 tax ID
[Ref.: #67770]	Microbacterium sediminis YLB-01	GCA_001689915	scaffold	GenBank	904291 tax ID
[Ref.: #66792]	Microbacterium sediminis YLB-01	GCA_004564075	complete	GenBank	904291 tax ID	*
[Ref.: #66792]	Microbacterium sediminis strain YLB-01	904291.4	wgs	PATRIC	904291 tax ID	*
[Ref.: #66792]	Microbacterium sediminis ylb-01	2877021139	draft	JGI IMG/M	904291 tax ID	*
[Ref.: #66792]	Microbacterium sediminis ylb-01	2847293147	complete	JGI IMG/M	904291 tax ID	*

[Ref.: #17367]	GC-content	71 mol%
[Ref.: #67770]	GC-content	71 mol%	high performance liquid chromatography (HPLC)

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: Microbacterium sediminis YLB-01 NCBI: GCA_004564075.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Microbacterium sediminis YLB-01 NCBI: GCA_004564075.1
[Ref.: #69480]	motile	yes	57.238	yes
[Ref.: #69480]	flagellated	no	90.627	no
[Ref.: #69480]	gram-positive	yes	92.192	yes
[Ref.: #69480]	anaerobic	no	99.357	yes
[Ref.: #69480]	aerobic	yes	93.802	yes
[Ref.: #69480]	halophile	no	84.112	no
[Ref.: #69480]	spore-forming	no	94.366	no
[Ref.: #69480]	glucose-util	yes	85.247	yes
[Ref.: #69480]	thermophile	no	98.138	yes
[Ref.: #69480]	glucose-ferment	no	89.383	no

Availability in culture collections External links

[Ref.: #17367]

Culture collection no.

DSM 23767, CCTCC AB 2010363, JCM 19554, MCCC 1A06153

[Ref.: #76912]

SI-ID 398690

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Transcriptome	Transcriptomic Analysis Reveals that Changes in Gene Expression Contribute to Microbacterium sediminis YLB-01 Adaptation at Low Temperature Under High Hydrostatic Pressure.	Qiu X, Cao X, Jian H, Wu H, Xu G, Tang X	Curr Microbiol	10.1007/s00284-022-02786-9	2022	*
Genetics	Genomic analysis of Microbacterium sediminis YLB-01(T) reveals backgrounds related to its deep-sea environment adaptation.	Yi Z, Cao X, Li H, Jian H, Xu X, Yu L, Tang X	Mar Genomics	10.1016/j.margen.2020.100818	2020	*
Enzymology	Characterization of cold-tolerant trehalose-6-phosphate synthase from the deep-sea bacterium Microbacterium sediminis YLB-01.	Tang X, Yi Z, Xu X, Xu R, Huang P, Yu L	Biosci Biotechnol Biochem	10.1080/09168451.2020.1713044	2020	*
Metabolism	Metabolic profiling of cold adaptation of a deep-sea psychrotolerant Microbacterium sediminis to prolonged low temperature under high hydrostatic pressure.	Xia JM, Hu XM, Huang CH, Yu LB, Xu RF, Tang XX, Lin DH	Appl Microbiol Biotechnol	10.1007/s00253-019-10134-4	2019	*
Phylogeny	Microbacterium gilvum sp. nov., isolated from civet faeces.	Chen X, Li QY, Li GD, Xu FJ, Jiang Y, Han L, Jiang CL, Huang XS	Antonie Van Leeuwenhoek	10.1007/s10482-016-0718-1	2016	*
Phylogeny	Microbacterins A and B, new peptaibols from the deep sea actinomycete Microbacterium sediminis sp. nov. YLB-01(T).	Liu D, Lin H, Proksch P, Tang X, Shao Z, Lin W	Org Lett	10.1021/acs.orglett.5b00172	2015	*
Phylogeny	Microbacterium petrolearium sp. nov., isolated from an oil-contaminated water sample.	Wang H, Xiang T, Wang Y, Song J, Zhai Y, Chen X, Li Y, Zhao B, Zhao B, Ruan Z	Int J Syst Evol Microbiol	10.1099/ijs.0.061119-0	2014	*
Phylogeny	Microbacterium sediminis sp. nov., a psychrotolerant, thermotolerant, halotolerant and alkalitolerant actinomycete isolated from deep-sea sediment.	Yu L, Lai Q, Yi Z, Zhang L, Huang Y, Gu L, Tang X	Int J Syst Evol Microbiol	10.1099/ijs.0.029652-0	2012	*

References

#17367

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23767

#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 )

#30121

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 #26475 (see below)

#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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

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

#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 .

#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 )

#76912

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-ID398690.1 )

#26475

IJSEM 25 2013 ( DOI 10.1099/ijs.0.029652-0 , PubMed 22328608 )

* These data were automatically processed and therefore are not curated

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