Microbacterium profundi (DSM 22239, CGMCC 1.6777, CIP 109927)

Name: Microbacterium profundi (DSM 22239, CGMCC 1.6777, CIP 109927)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7444

Type strain

Strain Designation Shh49

Culture col. no. DSM 22239 CGMCC 1.6777 CIP 109927 JCM 14840 Shh49

NCBI tax ID(s) 450380

Special Collections DSMZ JCM CIP Literature strains

History <- JCM/RIKEN <- X.-W. Xu; Shh49 X.-W. Xu Shh49. CIP <- 2008, JCM <- 2007, X.W. Xu, Zhejiang Univ., Hangzhou, China: strain Shh49

Links

Microbacterium profundi Shh49 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from deep-sea sediment sample collected from a polymetallic nodule region.

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

Name and taxonomic classification

SI-ID 360277

CGMCC 1.6777,JCM 14840,CIP 109927,DSM 22239

@ref 20215

Last LPSN update 2026-02-09 11:19:28

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Microbacteriaceae

Genus Microbacterium

Species Microbacterium profundi

Full scientific name Microbacterium profundi Wu et al. 2008

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31189	positive	01-02 µm	0.4-0.6 µm	rod-shaped
121956	positive			rod-shaped
125438					91
125438	positive				91.529
125439	positive				94.8

Pigmentation

31189

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
16220	R2A MEDIUM (DSMZ Medium 830)	Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
16220	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)	Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
37695	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
121956	CIP Medium 13	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
16220	positive	growth	28
31189	positive	growth	04-35
31189	positive	optimum	28
37695	positive	growth	30
67770	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
31189	positive	optimum	07-08
31189	positive	growth	6-9.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31189	aerobe
121956	obligate aerobe
125439	obligate aerobe	98.6

Spore formation

31189

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31189	NaCl	positive	growth	0-7.5 %
31189	NaCl	positive	optimum	0-1 %

Observation

@ref	Observation
31189	aggregates in chains
67770	quinones: MK-12, MK-13

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31189	30089 ChEBI	acetate	+	carbon source
31189	22599 ChEBI	arabinose	+	carbon source
31189	29016 ChEBI	arginine	+	carbon source
31189	35391 ChEBI	aspartate	+	carbon source
31189	17057 ChEBI	cellobiose	+	carbon source
31189	4853 ChEBI	esculin	+	hydrolysis
31189	28757 ChEBI	fructose	+	carbon source
31189	28260 ChEBI	galactose	+	carbon source
31189	17234 ChEBI	glucose	+	carbon source
31189	17754 ChEBI	glycerol	+	carbon source
31189	24996 ChEBI	lactate	+	carbon source
31189	17716 ChEBI	lactose	+	carbon source
31189	25115 ChEBI	malate	+	carbon source
31189	17306 ChEBI	maltose	+	carbon source
31189	29864 ChEBI	mannitol	+	carbon source
31189	37684 ChEBI	mannose	+	carbon source
121956	17632 ChEBI	nitrate	-	reduction
121956	16301 ChEBI	nitrite	-	reduction
31189	17272 ChEBI	propionate	+	carbon source
31189	15361 ChEBI	pyruvate	+	carbon source
31189	16634 ChEBI	raffinose	+	carbon source
31189	26546 ChEBI	rhamnose	+	carbon source
31189	33942 ChEBI	ribose	+	carbon source
31189	17814 ChEBI	salicin	+	carbon source
31189	17822 ChEBI	serine	+	carbon source
31189	30031 ChEBI	succinate	+	carbon source
31189	17992 ChEBI	sucrose	+	carbon source
31189	27082 ChEBI	trehalose	+	carbon source
31189	18222 ChEBI	xylose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
121956	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
31189	catalase	+	1.11.1.6
121956	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	-		from API zym
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
121956	oxidase	-
68382	trypsin	-	3.4.21.4	from API zym
121956	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
121956	-	-	+	-	-	+	-	-	-	-	+	-	-	+	-	+	-	-	+	-

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Geographic location	Latitude	Longitude	Country
16220	deep-sea sediment sample collected from a polymetallic nodule region	East Pacific Ocean (station ES0301; 8° 22' 38'' N 145° 23' 56'' W) at a depth of 5280 m	8.3772	-145.399 8.3772/-145.399
67770	Deep-sea sediment from a polymetallic nodule region in the East Pacific Ocean
121956	Environment, Deep sea sediment, polymetallic nodule	East			Pacific Ocean

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16220	1	Risk group (German classification) According to TRBA 466
121956	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
67770	ASM76337v1 assembly for Microbacterium profundi Shh49	contig	GCA_000763375	450380.4	2617271234	450380	76.5

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16220	Microbacterium profundi strain Shh49 16S ribosomal RNA gene, partial sequence	EF623999	1488		450380

GC content

@ref	GC-content (mol%)	Method
16220	66.8	thermal denaturation, midpoint method (Tm)
31189	66.8

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Microbacterium profundi Shh49
NCBI: GCA_000763375

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	78.80	no
125439	motility	BacteriaNetⓘ	no	65.80	no
125439	gram_stain	BacteriaNetⓘ	positive	94.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Microbacterium profundi Shh49
PATRIC: 450380.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	91.53	yes
125438	anaerobic	anaerobicⓘ	no	98.13	yes
125438	spore-forming	spore-formingⓘ	no	76.99	no
125438	aerobic	aerobicⓘ	yes	88.69	yes
125438	thermophilic	thermophileⓘ	no	96.93	yes
125438	flagellated	motile2+ⓘ	no	91.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Draft Genome Sequence of Microbacterium profundi Shh49T, an Actinobacterium Isolated from Deep-Sea Sediment of a Polymetallic Nodule Environment.	Wu YH, Zhou P, Cheng H, Wang CS, Wu M, Xu XW	Genome Announc	10.1128/genomeA.00642-15	2015
Phylogeny	Microbacterium shaanxiense sp. nov., isolated from the nodule surface of soybean.	Peng S, Dongying L, Bingxin Y, Mingjun L, Gehong W	Int J Syst Evol Microbiol	10.1099/ijs.0.000116	2015
Phylogeny	Microbacterium murale sp. nov., isolated from an indoor wall.	Kampfer P, Schafer J, Lodders N, Martin K	Int J Syst Evol Microbiol	10.1099/ijs.0.037705-0	2011
Phylogeny	Microbacterium profundi sp. nov., isolated from deep-sea sediment of polymetallic nodule environments.	Wu YH, Wu M, Wang CS, Wang XG, Yang JY, Oren A, Xu XW	Int J Syst Evol Microbiol	10.1099/ijs.0.2008/000455-0	2008

References

#16220	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22239
#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 )
#27516	IJSEM 2930 2008 ( DOI 10.1099/ijs.0.2008/000455-0 , PubMed 19060085 )
#31189	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 #27516
#37695	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68382	Automatically annotated from API zym .
#121956	Collection of Institut Pasteur ; Curators of the CIP; CIP 109927
#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 profundi (DSM 22239, CGMCC 1.6777, CIP 109927)

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

Observation

Metabolite utilization

Metabolite production

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000763375

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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