Microbacterium sediminis (DSM 23767, CCTCC AB 2010363, JCM 19554)

Name: Microbacterium sediminis (DSM 23767, CCTCC AB 2010363, JCM 19554)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7467

Type strain

Strain Designation YLB-01

Culture col. no. DSM 23767 CCTCC AB 2010363 JCM 19554 MCCC 1A06153 YLB-01

NCBI tax ID(s) 904291

Special Collections DSMZ JCM Literature strains

Links

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

Gram-positive motile rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 398690

JCM 19554,DSM 23767

@ref 20215

Last LPSN update 2025-12-16 09:48:35

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Microbacteriaceae

Genus Microbacterium

Species Microbacterium sediminis

Full scientific name Microbacterium sediminis Yu et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
30121	positive	5.5 µm	1.25 µm	rod-shaped
125439	positive					93.4

Pigmentation

30121

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
17367	TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)		Medium recipe at MediaDive	Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
17367	positive	growth	28	mesophilic
30121	positive	growth	04-50
30121	positive	optimum	28	mesophilic
67770	positive	growth	28	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
30121	positive	optimum	7
30121	positive	growth	5.0-10.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30121	aerobe
125439	obligate aerobe	99.8

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30121	NaCl	positive	growth	0-8 %

Observation

67770

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

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30121	16449 ChEBI	alanine	+	carbon source
30121	4853 ChEBI	esculin	+	hydrolysis
30121	28757 ChEBI	fructose	+	carbon source
30121	24148 ChEBI	galactonate	+	carbon source
30121	28260 ChEBI	galactose	+	carbon source
30121	24265 ChEBI	gluconate	+	carbon source
30121	17234 ChEBI	glucose	+	carbon source
30121	15428 ChEBI	glycine	+	carbon source
30121	21217 ChEBI	L-alaninamide	+	carbon source
30121	25017 ChEBI	leucine	+	carbon source
30121	29864 ChEBI	mannitol	+	carbon source
30121	37684 ChEBI	mannose	+	carbon source
30121	53258 ChEBI	sodium citrate	+	carbon source
30121	30911 ChEBI	sorbitol	+	carbon source

Enzymes

@ref	Value	Activity	Ec
30121	acid phosphatase	+	3.1.3.2
30121	alkaline phosphatase	+	3.1.3.1
30121	catalase	+	1.11.1.6
30121	cytochrome oxidase	+	1.9.3.1

Pathway annotation

Computationally determined by

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

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
17367	deep-sea sediment	Indian Ocean (49.8405° E 37.8111° S) at 2327 m water depth	China	CHN	Asia	-37.8111	49.8405 -37.8111/49.8405
67770	Sediment of the Indian Ocean

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17367	1	Risk group (German 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	ASM456407v1 assembly for Microbacterium sediminis YLB-01	complete	GCA_004564075	904291.8	2847293147	904291	98.16
67770	ASM274199v1 assembly for Microbacterium sediminis YLB-01	scaffold	GCA_002741995	904291.5	2765235862	904291	73.12
67770	ASM168991v1 assembly for Microbacterium sediminis YLB-01	scaffold	GCA_001689915	904291.4	2877021139	904291	73.1

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17367	Microbacterium sediminis strain YLB-01 16S ribosomal RNA gene, partial sequence	HQ219727	1487		904291

GC content

@ref	GC-content (mol%)	Method
17367	71
67770	71	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Microbacterium sediminis ylb-01
IMG: 2847293147

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	85.50	no
125439	motility	BacteriaNetⓘ	yes	55.70	no
125439	gram_stain	BacteriaNetⓘ	positive	93.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Microbacterium sediminis YLB-01
NCBI: GCA_004564075.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	86.67	yes
125438	anaerobic	anaerobicⓘ	no	96.40	yes
125438	aerobic	aerobicⓘ	yes	86.64	no
125438	spore-forming	spore-formingⓘ	no	75.52	no
125438	thermophilic	thermophileⓘ	no	95.13	yes
125438	flagellated	motile2+ⓘ	no	77.50	no

Literature

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 .
#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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Microbacterium sediminis (DSM 23767, CCTCC AB 2010363, JCM 19554)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Halophily

Observation

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_004564075

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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