Micromonospora krabiensis (DSM 45344, JCM 12869, TISTR 1565)

Name: Micromonospora krabiensis (DSM 45344, JCM 12869, TISTR 1565)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 8014

Type strain

Strain Designation MA-2

Culture col. no. DSM 45344 JCM 12869 TISTR 1565 PCU 268 MA-2 2 more

NCBI tax ID(s) 307121

Special Collections DSMZ JCM

History DSMZ <- JCM/RIKEN <- S. Tanasupawat; MA-2 JCM <-- S. Tanasupawat; Chulalongkorn Univ., Thailand; MA-2.

Links

Micromonospora krabiensis MA-2 is a bacterium that was isolated from marine soil.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 403991

JCM 12869,DSM 45344

@ref 20215

Last LPSN update 2026-05-29 08:26:46

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micromonosporales

Family Micromonosporaceae

Genus Micromonospora

Species Micromonospora krabiensis

Full scientific name Micromonospora krabiensis Jongrungruangchok et al. 2008

BacDive ID	Other strains from **Micromonospora krabiensis** (1)	Type strain
161274	M. krabiensis JCM 12868

Morphology

Cell morphology

@ref	Confidence	Gram stain
125439	91.875
125439	99.576	positive
125438	92.279	positive

Multimedia

@ref:	16337
multimedia content:	DSM_45344.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_45344.jpg
caption:	Medium 554 28°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
16337	N-Z-AMINE-MEDIUM (DSMZ Medium 554)	Medium recipe at MediaDive	Name: N-Z-AMINE-MEDIUM (DSMZ Medium 554) Composition: Starch 20.0 g/l Agar 20.0 g/l Glucose 10.0 g/l N-Z amine 5.0 g/l Yeast extract 5.0 g/l CaCO3 1.0 g/l Distilled water
16337	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
16337	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
16337	YEAST-STARCH-AGAR(B) (DSMZ Medium 656)	Medium recipe at MediaDive	Name: YEAST-STARCH-AGAR(B) (DSMZ Medium 656) Composition: Starch 15.0 g/l Agar 15.0 g/l Yeast extract 4.0 g/l MgSO4 x 7 H2O 0.5 g/l K2HPO4 0.5 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
16337	positive	growth	28
67770	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.502

Spore formation

@ref	Spore formation	Confidence
125438		93.033

Observation

67770

Observationquinones: MK-10(H₄), MK-10(H₆), MK-9(H₄)

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	palmitate biosynthesis	100	22 of 22
66794	ribulose monophosphate pathway	100	2 of 2
66794	biotin biosynthesis	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	ethanol fermentation	100	2 of 2
66794	glycolate and glyoxylate degradation	100	6 of 6
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	pentose phosphate pathway	100	11 of 11
66794	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
66794	methylglyoxal degradation	100	5 of 5
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	cardiolipin biosynthesis	100	7 of 7
66794	ppGpp biosynthesis	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	threonine metabolism	100	10 of 10
66794	acetate fermentation	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	kanosamine biosynthesis II	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	aerobactin biosynthesis	100	1 of 1
66794	cellulose degradation	100	5 of 5
66794	ceramide biosynthesis	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	sulfopterin metabolism	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	starch degradation	100	10 of 10
66794	NAD metabolism	94.44	17 of 18
66794	flavin biosynthesis	93.33	14 of 15
66794	phenylalanine metabolism	92.31	12 of 13
66794	propionate fermentation	90	9 of 10
66794	Entner Doudoroff pathway	90	9 of 10
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	gluconeogenesis	87.5	7 of 8
66794	dTDPLrhamnose biosynthesis	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	isoleucine metabolism	87.5	7 of 8
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	heme metabolism	85.71	12 of 14
66794	photosynthesis	85.71	12 of 14
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	leucine metabolism	84.62	11 of 13
66794	urea cycle	84.62	11 of 13
66794	tryptophan metabolism	84.21	32 of 38
66794	selenocysteine biosynthesis	83.33	5 of 6
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	phenol degradation	80	16 of 20
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	factor 420 biosynthesis	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	purine metabolism	78.72	74 of 94
66794	glutathione metabolism	78.57	11 of 14
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	tyrosine metabolism	78.57	11 of 14
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	methionine metabolism	76.92	20 of 26
66794	glycolysis	76.47	13 of 17
66794	degradation of sugar acids	76	19 of 25
66794	glycogen biosynthesis	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	proline metabolism	72.73	8 of 11
66794	metabolism of disaccharids	72.73	8 of 11
66794	alanine metabolism	72.41	21 of 29
66794	degradation of pentoses	71.43	20 of 28
66794	citric acid cycle	71.43	10 of 14
66794	pyrimidine metabolism	71.11	32 of 45
66794	non-pathway related	71.05	27 of 38
66794	lipid metabolism	70.97	22 of 31
66794	arginine metabolism	70.83	17 of 24
66794	oxidative phosphorylation	70.33	64 of 91
66794	myo-inositol biosynthesis	70	7 of 10
66794	vitamin B1 metabolism	69.23	9 of 13
66794	degradation of sugar alcohols	68.75	11 of 16
66794	carotenoid biosynthesis	68.18	15 of 22
66794	lysine metabolism	66.67	28 of 42
66794	octane oxidation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	3-phenylpropionate degradation	66.67	10 of 15
66794	histidine metabolism	65.52	19 of 29
66794	d-xylose degradation	63.64	7 of 11
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	ketogluconate metabolism	62.5	5 of 8
66794	phosphatidylethanolamine bioynthesis	61.54	8 of 13
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	cysteine metabolism	61.11	11 of 18
66794	vitamin K metabolism	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	D-cycloserine biosynthesis	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	glycine metabolism	60	6 of 10
66794	gallate degradation	60	3 of 5
66794	polyamine pathway	56.52	13 of 23
66794	nitrate assimilation	55.56	5 of 9
66794	toluene degradation	50	2 of 4
66794	coenzyme M biosynthesis	50	5 of 10
66794	pantothenate biosynthesis	50	3 of 6
66794	lactate fermentation	50	2 of 4
66794	cyclohexanol degradation	50	2 of 4
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	androgen and estrogen metabolism	50	8 of 16
66794	phenylmercury acetate degradation	50	1 of 2
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	quinate degradation	50	1 of 2
66794	degradation of hexoses	50	9 of 18
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	sulfate reduction	46.15	6 of 13
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	vitamin B6 metabolism	45.45	5 of 11
66794	chlorophyll metabolism	44.44	8 of 18
66794	4-hydroxymandelate degradation	44.44	4 of 9
66794	lipid A biosynthesis	44.44	4 of 9
66794	propanol degradation	42.86	3 of 7
66794	vitamin B12 metabolism	41.18	14 of 34
66794	arachidonate biosynthesis	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	carnitine metabolism	37.5	3 of 8
66794	ascorbate metabolism	36.36	8 of 22
66794	cholesterol biosynthesis	36.36	4 of 11
66794	sphingosine metabolism	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	arachidonic acid metabolism	33.33	6 of 18
66794	IAA biosynthesis	33.33	1 of 3
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	catecholamine biosynthesis	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	allantoin degradation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
16337	marine soil	Krabi Province	Thailand	THA	Asia
67770	Marine soil	Krabi Province	Thailand	THA	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16337	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	IMG-taxon 2617270872 annotated assembly for Micromonospora krabiensis DSM 45344	chromosome	GCA_900091425	307121.4	2617270872	307121	86.36
124043	ASM4264782v1 assembly for Micromonospora krabiensis PCU 268	contig	GCA_042647825			307121	67.65

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
16337	Micromonospora krabiensis gene for 16S rRNA, partial sequence, strain: MA-2	AB196716	1437	307121
124043	Micromonospora krabiensis strain PCU 268 16S ribosomal RNA gene, partial sequence.	MT758140	1334	307121
124043	Micromonospora krabiensis strain PCU 268 16S ribosomal RNA gene, partial sequence.	MT760024	1334	307121

GC content

@ref	GC-content (mol%)	Method
16337	72.1
67770	72.1	high performance liquid chromatography (HPLC)
67770	72.81	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: IMG-taxon 2617270872 annotated assembly for Micromonospora krabiensis DSM 45344
BV-BRC: 307121.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.50	no
125439	gram_stain	BacteriaNetⓘ	positive	99.58	no
125439	motility	BacteriaNetⓘ	no	91.88	no
125439	spore_formation	BacteriaNetⓘ	yes	82.96	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Micromonospora krabiensis strain DSM 45344
PATRIC: 307121.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	92.28	no
125438	anaerobic	anaerobicⓘ	no	95.89	no
125438	spore-forming	spore-formingⓘ	yes	93.03	no
125438	aerobic	aerobicⓘ	yes	89.09	no
125438	thermophilic	thermophileⓘ	no	95.50	no
125438	flagellated	motile2+ⓘ	no	87.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Marine Actinobacteria from the Gulf of California: diversity, abundance and secondary metabolite biosynthetic potential.	Becerril-Espinosa A, Freel KC, Jensen PR, Soria-Mercado IE.	Antonie Van Leeuwenhoek	10.1007/s10482-012-9863-3	2013
Phylogeny	Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential.	Carro L, Nouioui I, Sangal V, Meier-Kolthoff JP, Trujillo ME, Montero-Calasanz MDC, Sahin N, Smith DL, Kim KE, Peluso P, Deshpande S, Woyke T, Shapiro N, Kyrpides NC, Klenk HP, Goker M, Goodfellow M.	Sci Rep	10.1038/s41598-017-17392-0	2018
Phylogeny	Micromonospora oryzae sp. nov., isolated from roots of upland rice.	Kittiwongwattana C, Thanaboripat D, Laosinwattana C, Koohakan P, Parinthawong N, Thawai C	Int J Syst Evol Microbiol	10.1099/ijsem.0.000500	2015
Phylogeny	Two new species of the genus Micromonospora: Micromonospora palomenae sp. nov. and Micromonospora harpali sp. nov. isolated from the insects.	Fang B, Liu C, Guan X, Song J, Zhao J, Liu H, Li C, Ning W, Wang X, Xiang W	Antonie Van Leeuwenhoek	10.1007/s10482-015-0472-9	2015

References

#16337	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45344
#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 )
#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;
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 krabiensis (DSM 45344, JCM 12869, TISTR 1565)

Name and taxonomic classification

Morphology

Cell morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900091425

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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