Name: Micromonospora avicenniae 268506
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 23119

Type strain:

Species: Micromonospora avicenniae

Strain Designation: 268506

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

Strain history: DSM 45758 <-- L. Li; Wuhan Univ., China; 268506.

NCBI tax ID(s): 1198245 (species)

SI-ID 397886

DSM 45758

Section

Micromonospora avicenniae 268506 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from root of the mangrove Avicennia marina.

Gram-positive
spore-forming
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micromonosporales*
	Family	*Micromonosporaceae*
	Genus	*Micromonospora*
	Species	**Micromonospora avicenniae**
	Full Scientific Name (LPSN)	Micromonospora avicenniae Li et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	positive Confidence in %100

Information on culture and growth conditions Culture and growth conditions

[Ref.: #19357]

Culture medium

GPHF-MEDIUM (DSMZ Medium 553)

[Ref.: #19357]

Culture medium growth

[Ref.: #19357]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #19357]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #19357]

Culture medium growth

[Ref.: #19357]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #19357]

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

[Ref.: #19357]

Culture medium growth

[Ref.: #19357]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #19357]

Culture medium

N-Z-AMINE-MEDIUM (DSMZ Medium 554)

[Ref.: #19357]

Culture medium growth

[Ref.: #19357]

Culture medium link

Medium recipe at MediaDive

[Ref.: #19357]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #19357]			growth	28 °C
[Ref.: #67770]			growth	28 °C

[Ref.: #19357]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	yes Confidence in %100

[Ref.: #67770]

Observation

quinones: MK-9(H₈), MK-9(H₆)

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	4-hydroxymandelate degradation	100	9 of 9
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	glycolate and glyoxylate degradation	100	6 of 6
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	pentose phosphate pathway	100	11 of 11
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	aerobactin biosynthesis	100	1 of 1
[Ref.: #66794]	resorcinol degradation	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	ketogluconate metabolism	87.5	7 of 8
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	flavin biosynthesis	86.67	13 of 15
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	phenol degradation	85	17 of 20
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	urea cycle	84.62	11 of 13
[Ref.: #66794]	tryptophan metabolism	84.21	32 of 38
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	selenocysteine biosynthesis	83.33	5 of 6
[Ref.: #66794]	glycolysis	82.35	14 of 17
[Ref.: #66794]	pyrimidine metabolism	82.22	37 of 45
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	purine metabolism	80.85	76 of 94
[Ref.: #66794]	3-chlorocatechol degradation	80	4 of 5
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	tyrosine metabolism	78.57	11 of 14
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	methionine metabolism	76.92	20 of 26
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	degradation of sugar acids	76	19 of 25
[Ref.: #66794]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	degradation of pentoses	75	21 of 28
[Ref.: #66794]	vitamin B12 metabolism	73.53	25 of 34
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	non-pathway related	71.05	27 of 38
[Ref.: #66794]	lipid metabolism	70.97	22 of 31
[Ref.: #66794]	oxidative phosphorylation	70.33	64 of 91
[Ref.: #66794]	myo-inositol biosynthesis	70	7 of 10
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	degradation of sugar alcohols	68.75	11 of 16
[Ref.: #66794]	carotenoid biosynthesis	68.18	15 of 22
[Ref.: #66794]	glutamate and glutamine metabolism	67.86	19 of 28
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	degradation of hexoses	66.67	12 of 18
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	arginine metabolism	66.67	16 of 24
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	61.54	8 of 13
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	vitamin K metabolism	60	3 of 5
[Ref.: #66794]	lysine metabolism	57.14	24 of 42
[Ref.: #66794]	androgen and estrogen metabolism	56.25	9 of 16
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	cholesterol biosynthesis	54.55	6 of 11
[Ref.: #66794]	3-phenylpropionate degradation	53.33	8 of 15
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	47.06	8 of 17
[Ref.: #66794]	phenylpropanoid biosynthesis	46.15	6 of 13
[Ref.: #66794]	ascorbate metabolism	45.45	10 of 22
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	chlorophyll metabolism	38.89	7 of 18
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	polyamine pathway	26.09	6 of 23
[Ref.: #66794]	biotin biosynthesis	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	allantoin degradation	22.22	2 of 9
[Ref.: #66794]	daunorubicin biosynthesis	22.22	2 of 9
		Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #19357]	Sample type/isolated from	root of the mangrove Avicennia marina
[Ref.: #19357]	Host species	Avicennia marina
[Ref.: #19357]	Geographic location (country and/or sea, region)	Hainan Province, Wenchang, mangrove forest
[Ref.: #19357]	Country	China
[Ref.: #19357]	Country ISO 3 Code	CHN
[Ref.: #19357]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Root of Avicennia marina from mangrove forest
[Ref.: #67770]	Host species	Avicennia marina
[Ref.: #67770]	Geographic location (country and/or sea, region)	Wengchang, Hainan Province
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #19357]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #19357]	Micromonospora avicenniae strain 2685R06 16S ribosomal RNA gene, partial sequence	JQ867183	1477	ENA	1198245 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Micromonospora avicenniae DSM 45758	GCA_900156065	contig	GenBank	1198245 tax ID
[Ref.: #66792]	Micromonospora avicenniae strain DSM 45758	1198245.3	wgs	PATRIC	1198245 tax ID	*
[Ref.: #66792]	Micromonospora avicenniae DSM 45758	2681813563	draft	JGI IMG/M	1198245 tax ID	*

[Ref.: #67770]	GC-content	71.5 mol%	genome sequence analysis
[Ref.: #67770]	GC-content	70.3 mol%	high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Micromonospora avicenniae strain DSM 45758 PATRIC: 1198245.3
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Micromonospora avicenniae strain DSM 45758 PATRIC: 1198245.3
[Ref.: #69480]	motile	no	93.053	no
[Ref.: #69480]	gram-positive	yes	90.523	no
[Ref.: #69480]	anaerobic	no	98.936	no
[Ref.: #69480]	aerobic	yes	93.921	no
[Ref.: #69480]	halophile	no	92.905	no
[Ref.: #69480]	spore-forming	yes	93.222	no
[Ref.: #69480]	glucose-util	yes	88.201	no
[Ref.: #69480]	flagellated	no	97.943	no
[Ref.: #69480]	thermophile	no	98.746	yes
[Ref.: #69480]	glucose-ferment	no	92.236	no

Availability in culture collections External links

[Ref.: #19357]

Culture collection no.

DSM 45758, CCTCC AA 2012010, JCM 31034, NBRC 110452

[Ref.: #87355]

SI-ID 397886

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 )

#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;

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#87355

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID397886.1 )

* These data were automatically processed and therefore are not curated

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Micromonospora avicenniae strain DSM 45758

Micromonospora avicenniae strain DSM 45758

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