Micromonospora avicenniae (DSM 45758, CCTCC AA 2012010, JCM 31034)

Name: Micromonospora avicenniae (DSM 45758, CCTCC AA 2012010, JCM 31034)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 23119

Type strain

Strain Designation 268506

Culture col. no. DSM 45758 CCTCC AA 2012010 JCM 31034 NBRC 110452 268506

NCBI tax ID(s) 1198245

Special Collections DSMZ JCM

Links

Micromonospora avicenniae 268506 is a mesophilic prokaryote that was isolated from root of the mangrove Avicennia marina.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 397886

NBRC 110452,JCM 31034,DSM 45758

@ref 20215

Last LPSN update 2025-12-16 09:52:35

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Micromonosporales

Family Micromonosporaceae

Genus Micromonospora

Species Micromonospora avicenniae

Full scientific name Micromonospora avicenniae Li et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	positive	99

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
19357	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
19357	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
19357	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)	Medium recipe at MediaDive	Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 20.0 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
19357	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

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
19357	positive	growth	28	mesophilic
67770	positive	growth	28	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125438	aerobe	90.074
125439	obligate aerobe	99.6

Spore formation

@ref	Spore formation	Confidence
125438		91.172

Observation

67770

Observationquinones: MK-9(H₈), MK-9(H₆)

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cellulose degradation	100	5 of 5
66794	starch degradation	100	10 of 10
66794	coenzyme A metabolism	100	4 of 4
66794	4-hydroxymandelate degradation	100	9 of 9
66794	ethanol fermentation	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	ribulose monophosphate pathway	100	2 of 2
66794	cardiolipin biosynthesis	100	7 of 7
66794	glycolate and glyoxylate degradation	100	6 of 6
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	threonine metabolism	100	10 of 10
66794	pentose phosphate pathway	100	11 of 11
66794	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
66794	adipate degradation	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	acetate fermentation	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	butanoate fermentation	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	aerobactin biosynthesis	100	1 of 1
66794	resorcinol degradation	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	phenylalanine metabolism	92.31	12 of 13
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	C4 and CAM-carbon fixation	87.5	7 of 8
66794	gluconeogenesis	87.5	7 of 8
66794	ketogluconate metabolism	87.5	7 of 8
66794	isoleucine metabolism	87.5	7 of 8
66794	flavin biosynthesis	86.67	13 of 15
66794	propanol degradation	85.71	6 of 7
66794	photosynthesis	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	heme metabolism	85.71	12 of 14
66794	phenol degradation	85	17 of 20
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	NAD metabolism	83.33	15 of 18
66794	selenocysteine biosynthesis	83.33	5 of 6
66794	glycolysis	82.35	14 of 17
66794	pyrimidine metabolism	82.22	37 of 45
66794	proline metabolism	81.82	9 of 11
66794	purine metabolism	80.85	76 of 94
66794	3-chlorocatechol degradation	80	4 of 5
66794	gallate degradation	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	factor 420 biosynthesis	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	tetrahydrofolate metabolism	78.57	11 of 14
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	vitamin B1 metabolism	76.92	10 of 13
66794	degradation of sugar acids	76	19 of 25
66794	alanine metabolism	75.86	22 of 29
66794	CMP-KDO biosynthesis	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	degradation of pentoses	75	21 of 28
66794	vitamin B12 metabolism	73.53	25 of 34
66794	histidine metabolism	72.41	21 of 29
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	glutathione metabolism	71.43	10 of 14
66794	citric acid cycle	71.43	10 of 14
66794	non-pathway related	71.05	27 of 38
66794	lipid metabolism	70.97	22 of 31
66794	oxidative phosphorylation	70.33	64 of 91
66794	myo-inositol biosynthesis	70	7 of 10
66794	propionate fermentation	70	7 of 10
66794	degradation of sugar alcohols	68.75	11 of 16
66794	carotenoid biosynthesis	68.18	15 of 22
66794	glutamate and glutamine metabolism	67.86	19 of 28
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	degradation of hexoses	66.67	12 of 18
66794	cyanate degradation	66.67	2 of 3
66794	arginine metabolism	66.67	16 of 24
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	d-xylose degradation	63.64	7 of 11
66794	metabolism of disaccharids	63.64	7 of 11
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	phosphatidylethanolamine bioynthesis	61.54	8 of 13
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	vitamin K metabolism	60	3 of 5
66794	lysine metabolism	57.14	24 of 42
66794	androgen and estrogen metabolism	56.25	9 of 16
66794	cysteine metabolism	55.56	10 of 18
66794	cholesterol biosynthesis	54.55	6 of 11
66794	3-phenylpropionate degradation	53.33	8 of 15
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	coenzyme M biosynthesis	50	5 of 10
66794	phenylmercury acetate degradation	50	1 of 2
66794	toluene degradation	50	2 of 4
66794	quinate degradation	50	1 of 2
66794	lactate fermentation	50	2 of 4
66794	kanosamine biosynthesis II	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	cyclohexanol degradation	50	2 of 4
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	ascorbate metabolism	45.45	10 of 22
66794	vitamin B6 metabolism	45.45	5 of 11
66794	lipid A biosynthesis	44.44	4 of 9
66794	nitrate assimilation	44.44	4 of 9
66794	lipoate biosynthesis	40	2 of 5
66794	D-cycloserine biosynthesis	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	glycine betaine biosynthesis	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	chlorophyll metabolism	38.89	7 of 18
66794	sulfate reduction	38.46	5 of 13
66794	carnitine metabolism	37.5	3 of 8
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	mevalonate metabolism	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	polyamine pathway	26.09	6 of 23
66794	biotin biosynthesis	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	methanogenesis from CO2	25	3 of 12
66794	catecholamine biosynthesis	25	1 of 4
66794	allantoin degradation	22.22	2 of 9
66794	daunorubicin biosynthesis	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Mangrove
#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Root (Rhizome)

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
19357	root of the mangrove Avicennia marina	Avicennia marina	Hainan Province, Wenchang, mangrove forest	China	CHN	Asia
67770	Root of Avicennia marina from mangrove forest	Avicennia marina	Wengchang, Hainan Province	China	CHN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
19357	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
67770	IMG-taxon 2681813563 annotated assembly for Micromonospora avicenniae DSM 45758	contig	GCA_900156065	1198245.3	2681813563	1198245	62.81

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
19357	Micromonospora avicenniae strain 2685R06 16S ribosomal RNA gene, partial sequence	JQ867183	1477		1198245

GC content

@ref	GC-content (mol%)	Method
67770	71.5	genome sequence analysis
67770	70.3	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: Micromonospora avicenniae DSM 45758
NCBI: GCA_900156065

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	75.70	no
125439	motility	BacteriaNetⓘ	no	82.90	no
125439	gram_stain	BacteriaNetⓘ	positive	99.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Micromonospora avicenniae strain DSM 45758
PATRIC: 1198245.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	87.93	no
125438	anaerobic	anaerobicⓘ	no	94.82	no
125438	spore-forming	spore-formingⓘ	yes	91.17	no
125438	aerobic	aerobicⓘ	yes	90.07	no
125438	thermophilic	thermophileⓘ	no	95.00	yes
125438	flagellated	motile2+ⓘ	no	88.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Micromonospora azadirachtae sp. nov., isolated from roots of Azadirachta indica A. Juss. var. siamensis Valeton.	Kuncharoen N, Kudo T, Ohkuma M, Tanasupawat S	Antonie Van Leeuwenhoek	10.1007/s10482-018-1152-3	2018
Phylogeny	Micromonospora avicenniae sp. nov., isolated from a root of Avicennia marina.	Li L, Mao YJ, Xie QY, Deng Z, Hong K	Antonie Van Leeuwenhoek	10.1007/s10482-013-9888-2	2013

References

#19357	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45758
#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 )
#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;
#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 avicenniae (DSM 45758, CCTCC AA 2012010, JCM 31034)

Name and taxonomic classification

Morphology

Cell morphology

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_900156065

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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