Micromonospora sediminimaris (DSM 45558, CGMCC 4.3550, JCM 15670)

Name: Micromonospora sediminimaris (DSM 45558, CGMCC 4.3550, JCM 15670)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 8031

Type strain

Strain Designation MS 426

Culture col. no. DSM 45558 CGMCC 4.3550 JCM 15670 MS 426 NBRC 107745

NCBI tax ID(s) 547162

Special Collections DSMZ JCM Wink compendium Literature strains

History <- JCM <- J. Wang; MS 426 J. Wang MS426.

Links

Micromonospora sediminimaris MS 426 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from deep marine sediment.

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

Name and taxonomic classification

SI-ID 400987

JCM 15670,NBRC 107745,DSM 45558

@ref 20215

Last LPSN update 2026-02-09 11:19:37

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micromonosporales

Family Micromonosporaceae

Genus Micromonospora

Species Micromonospora sediminimaris

Full scientific name Micromonospora sediminimaris Nouioui et al. 2018

Synonyms (1)

Verrucosispora sediminis

Morphology

Cell morphology

@ref	Gram stain	Cell width	Cell shape	Confidence
29617	positive	0.2 µm	rod-shaped
125438				91
125438	positive			93.425
125439	positive			99.8
125439				93.5

Colony morphology

@ref	Colony color	Incubation period	Medium used
21434	Deep orange (2011)	10-14 days	ISP 2
21434	Deep orange (2011)	10-14 days	ISP 3
21434	Melon yellow (1028)	10-14 days	ISP 4
21434	Deep orange (2011)	10-14 days	ISP 5
21434	Deep orange (2011)	10-14 days	ISP 7
21434	Deep orange (2011)	10-14 days	Suter with tyrosine
21434	Deep orange (2011)	10-14 days	Suter without tyrosine

Pigmentation

29617

Productionno

Multimedia

@ref:	17644
multimedia content:	DSM_45558.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_45558.jpg
caption:	Medium 535 28°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
17644	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)	Medium recipe at MediaDive	Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
17644	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
17644	GPHF-MEDIUM (DSMZ Medium 553)	Medium recipe at MediaDive	Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water
21434	ISP 2		Name: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
21434	ISP 3		Name: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
21434	ISP 4		Name: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
21434	ISP 5		Name: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
21434	ISP 7		Name: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
21434	Suter with tyrosine		Name: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes
21434	Suter without tyrosine		Name: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes

Culture temp

@ref	Growth	Type	Temperature (°C)
17644	positive	growth	28
29617	positive	growth	20-45
29617	positive	optimum	28-37
67770	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
29617	positive	optimum	5-7.5
29617	positive	growth	3.5-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29617	aerobe
125439	aerobe	99.4

Spore formation

@ref	Spore formation	Confidence
29617
125438		91.048
125439		97.3

Halophily

@ref	Salt	Growth	Tested relation	Concentration
21434	NaCl	positive	maximum	5 %
29617	NaCl	positive	growth	0-6 %
29617	NaCl	positive	optimum	3.5 %

Observation

@ref	Observation
29617	aggregates in chains
67770	quinones: MK-9(H₄), MK-9(H₂)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
21434	22599 ChEBI	arabinose	+
29617	22599 ChEBI	arabinose	+	carbon source
21434	62968 ChEBI	cellulose	-
68379	17634 ChEBI	D-glucose	-	fermentation	from API Coryne
68379	16899 ChEBI	D-mannitol	-	fermentation	from API Coryne
68379	16988 ChEBI	D-ribose	-	fermentation	from API Coryne
68379	65327 ChEBI	D-xylose	-	fermentation	from API Coryne
68379	4853 ChEBI	esculin	+	hydrolysis	from API Coryne
21434	28757 ChEBI	fructose	+
68379	5291 ChEBI	gelatin	+	hydrolysis	from API Coryne
21434	17234 ChEBI	glucose	+
29617	17234 ChEBI	glucose	+	carbon source
29617	17754 ChEBI	glycerol	+	carbon source
68379	28087 ChEBI	glycogen	+	fermentation	from API Coryne
29617	18403 ChEBI	L-arabitol	+	carbon source
29617	17716 ChEBI	lactose	+	carbon source
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
21434	37684 ChEBI	mannose	-
29617	28053 ChEBI	melibiose	+	carbon source
21434	17268 ChEBI	myo-inositol	-
29617	17632 ChEBI	nitrate	+	reduction
68379	17632 ChEBI	nitrate	-	reduction	from API Coryne
21434	16634 ChEBI	raffinose	-
21434	26546 ChEBI	rhamnose	-
29617	33942 ChEBI	ribose	+	carbon source
29617	17814 ChEBI	salicin	+	carbon source
21434	17992 ChEBI	sucrose	+
68379	17992 ChEBI	sucrose	+	fermentation	from API Coryne
29617	27082 ChEBI	trehalose	+	carbon source
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne
21434	18222 ChEBI	xylose	+

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
68379	alkaline phosphatase	+	3.1.3.1	from API Coryne
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
68379	alpha-glucosidase	+	3.2.1.20	from API Coryne
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
68379	beta-galactosidase	-	3.2.1.23	from API Coryne
68382	beta-glucosidase	+	3.2.1.21	from API zym
68379	beta-glucosidase	+	3.2.1.21	from API Coryne
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68379	gelatinase	+		from API Coryne
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
68379	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API Coryne
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
68379	pyrazinamidase	-	3.5.1.B15	from API Coryne
68379	pyrrolidonyl arylamidase	-	3.4.19.3	from API Coryne
68382	trypsin	+	3.4.21.4	from API zym
68379	urease	-	3.5.1.5	from API Coryne
68382	valine arylamidase	+		from API zym

API coryne

@ref	Reduction of nitrateNIT	PYZ	PYRA	PAL	beta GUR	beta GAL	alpha GLU	beta NAG	ESC	URE	GEL	Control fermentationControl	GLU	RIB	XYL	MAN	MAL	LAC	SAC	GLYG	CAT
21434	-	-	-	+	-	-	+	+	+	-	+	not determinedn.d.	-	-	-	-	-	-	+	+	not determinedn.d.

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
21434	not determinedn.d.	+	+	+	-	+	+	+/-	+	+/-	+	+	-	-	-	+	+	+	-	-

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Geographic location	Continent
17644	deep marine sediment	South China Sea	Asia
67770	Deep marine sediment	South China Sea

Taxonmaps

69479

Global distribution of 16S sequence EU870859 (>99% sequence identity) for Micromonospora from Microbeatlas

Aquatic Samples	47
Soil Samples	308
Animal Samples	71
Plant Samples	23
Total Samples	449

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17644	1	Risk group (German classification) According to TRBA 466
21434	L1	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	ASM1686357v1 assembly for Micromonospora sediminimaris NBRC 107745	contig	GCA_016863575	547162.4	8048308550	547162	59.68
67770	IMG-taxon 2663762750 annotated assembly for Micromonospora sediminimaris CGMCC 4.3550	scaffold	GCA_900112325	547162.3	2663762750	547162	47.59

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17644	Verrucosispora sediminis strain MS426 16S ribosomal RNA gene, partial sequence	EU870859	1458		547162

GC content

@ref	GC-content (mol%)	Method
17644	66.8	thermal denaturation, midpoint method (Tm)
29617	66.8
67770	71	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Micromonospora sediminimaris CGMCC 4.3550
NCBI: GCA_900112325

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	97.30	no
125439	motility	BacteriaNetⓘ	no	93.50	no
125439	gram_stain	BacteriaNetⓘ	positive	99.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	99.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Micromonospora sediminimaris strain NBRC 107745
PATRIC: 547162.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	93.43	no
125438	anaerobic	anaerobicⓘ	no	95.77	yes
125438	spore-forming	spore-formingⓘ	yes	91.05	yes
125438	aerobic	aerobicⓘ	yes	86.89	yes
125438	thermophilic	thermophileⓘ	no	92.41	yes
125438	flagellated	motile2+ⓘ	no	91.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genome-Based Taxonomic Classification of the Phylum Actinobacteria.	Nouioui I, Carro L, Garcia-Lopez M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Goker M.	Front Microbiol	10.3389/fmicb.2018.02007	2018
Genetics	Genome analysis of cellulose and hemicellulose degrading Micromonospora sp. CP22.	Chen SJ, Lam MQ, Thevarajoo S, Abd Manan F, Yahya A, Chong CS.	3 Biotech	10.1007/s13205-020-2148-z	2020
Metabolism	Actinoplanes deserti sp. nov., isolated from a desert soil sample.	Habib N, Khan IU, Chu X, Xiao M, Li S, Fang BZ, Zhi XY, Li WJ	Antonie Van Leeuwenhoek	10.1007/s10482-018-1121-x	2018
Phylogeny	Verrucosispora maris sp. nov., a novel deep-sea actinomycete isolated from a marine sediment which produces abyssomicins.	Goodfellow M, Stach JE, Brown R, Bonda AN, Jones AL, Mexson J, Fiedler HP, Zucchi TD, Bull AT	Antonie Van Leeuwenhoek	10.1007/s10482-011-9651-5	2011
Phylogeny	Description of Verrucosispora qiuiae sp. nov., isolated from mangrove swamp sediment, and emended description of the genus Verrucosispora.	Xi L, Zhang L, Ruan J, Huang Y	Int J Syst Evol Microbiol	10.1099/ijs.0.033787-0	2011
Phylogeny	Verrucosispora sediminis sp. nov., a cyclodipeptide-producing actinomycete from deep-sea sediment.	Dai HQ, Wang J, Xin YH, Pei G, Tang SK, Ren B, Ward A, Ruan JS, Li WJ, Zhang LX	Int J Syst Evol Microbiol	10.1099/ijs.0.017053-0	2009

References

#17644	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45558
#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 )
#21434	Wink, J.: Compendium of Actinobacteria . HZI-Helmholtz-Centre for Infection Research, Braunschweig .
#26007	IJSEM 1807 2010 ( DOI 10.1099/ijs.0.017053-0 , PubMed 19767367 )
#29617	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 #26007
#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) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68379	Automatically annotated from API Coryne .
#68382	Automatically annotated from API zym .
#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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Micromonospora sediminimaris (DSM 45558, CGMCC 4.3550, JCM 15670)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

API coryne

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_016863575

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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