Microbacterium azadirachtae (DSM 23848, JCM 15681, KCTC 19668)

Name: Microbacterium azadirachtae (DSM 23848, JCM 15681, KCTC 19668)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7452

Type strain

Strain Designation AI-S262

Culture col. no. DSM 23848 JCM 15681 KCTC 19668 LMG 24772 AI-S262

NCBI tax ID(s) 582680

Special Collections DSMZ JCM KCTC Literature strains

History DSMZ <- JCM <- M. Madhaiyan, Tamil Nadu Agric. Univ., Coimbatore, India JCM <-- M. Madhaiyan AI-S262. KCTC <- M Madhaiyan, Tamilnadu Agri. Univ., India

Links

Microbacterium azadirachtae AI-S262 is an aerobe, Gram-positive, motile bacterium that was isolated from rhizoplane of neem Azadirachta indica seedlings.

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

Name and taxonomic classification

SI-ID 27524

KCTC 19668,JCM 15681

@ref 20215

Last LPSN update 2026-05-29 08:26:39

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Microbacteriaceae

Genus Microbacterium

Species Microbacterium azadirachtae

Full scientific name Microbacterium azadirachtae Madhaiyan et al. 2010

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29556	positive	0.6-0.7 µm	0.3-0.4 µm	rod-shaped
67771	positive
125439	positive				90.972
125438	positive				90.211

Pigmentation

29556

Productionyes

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
29556	positive	growth	10-37
29556	positive	optimum	28
67770	positive	growth	28
67771	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
29556	positive	optimum	07-08
29556	positive	growth	05-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29556	aerobe
67771	aerobe
125439	obligate aerobe	95.472

Spore formation

@ref	Spore formation	Confidence
29556
125439		93.928

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29556	NaCl	positive	growth	0-5.5 %
29556	NaCl	positive	optimum	0-1 %

Observation

67770

Observationquinones: MK-12, MK-13

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29556	16449 ChEBI	alanine	+	carbon source
29556	22599 ChEBI	arabinose	+	carbon source
29556	16947 ChEBI	citrate	+	carbon source
29556	4853 ChEBI	esculin	+	hydrolysis
29556	25115 ChEBI	malate	+	carbon source

Enzymes

@ref	Value	Activity	Ec
29556	catalase	+	1.11.1.6

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cellulose degradation	100	5 of 5
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	gallate degradation	100	5 of 5
66794	threonine metabolism	100	10 of 10
66794	lipoate biosynthesis	100	5 of 5
66794	acetate fermentation	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	valine metabolism	100	9 of 9
66794	glycogen metabolism	100	5 of 5
66794	pentose phosphate pathway	100	11 of 11
66794	adipate degradation	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	teichoic acid biosynthesis	100	1 of 1
66794	coenzyme A metabolism	100	4 of 4
66794	vitamin K metabolism	100	5 of 5
66794	ribulose monophosphate pathway	100	2 of 2
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	butanoate fermentation	100	4 of 4
66794	glutamate and glutamine metabolism	89.29	25 of 28
66794	serine metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	dTDPLrhamnose biosynthesis	87.5	7 of 8
66794	gluconeogenesis	87.5	7 of 8
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	photosynthesis	85.71	12 of 14
66794	propanol degradation	85.71	6 of 7
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	phenylalanine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	starch degradation	80	8 of 10
66794	citric acid cycle	78.57	11 of 14
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	heme metabolism	78.57	11 of 14
66794	d-mannose degradation	77.78	7 of 9
66794	purine metabolism	77.66	73 of 94
66794	leucine metabolism	76.92	10 of 13
66794	glycolysis	76.47	13 of 17
66794	tryptophan metabolism	76.32	29 of 38
66794	glycogen biosynthesis	75	3 of 4
66794	phenol degradation	75	15 of 20
66794	isoleucine metabolism	75	6 of 8
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	3-phenylpropionate degradation	73.33	11 of 15
66794	flavin biosynthesis	73.33	11 of 15
66794	pyrimidine metabolism	73.33	33 of 45
66794	histidine metabolism	72.41	21 of 29
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	myo-inositol biosynthesis	70	7 of 10
66794	propionate fermentation	70	7 of 10
66794	vitamin B1 metabolism	69.23	9 of 13
66794	alanine metabolism	68.97	20 of 29
66794	degradation of sugar alcohols	68.75	11 of 16
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	enterobactin biosynthesis	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	allantoin degradation	66.67	6 of 9
66794	degradation of hexoses	66.67	12 of 18
66794	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
66794	acetoin degradation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	formaldehyde oxidation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	lipid A biosynthesis	66.67	6 of 9
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	d-xylose degradation	63.64	7 of 11
66794	proline metabolism	63.64	7 of 11
66794	non-pathway related	63.16	24 of 38
66794	ketogluconate metabolism	62.5	5 of 8
66794	arginine metabolism	62.5	15 of 24
66794	oxidative phosphorylation	61.54	56 of 91
66794	methionine metabolism	61.54	16 of 26
66794	cysteine metabolism	61.11	11 of 18
66794	degradation of pentoses	60.71	17 of 28
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	4-hydroxyphenylacetate degradation	60	6 of 10
66794	Entner Doudoroff pathway	60	6 of 10
66794	3-chlorocatechol degradation	60	3 of 5
66794	lipid metabolism	58.06	18 of 31
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	vitamin B6 metabolism	54.55	6 of 11
66794	metabolism of disaccharids	54.55	6 of 11
66794	carotenoid biosynthesis	50	11 of 22
66794	pantothenate biosynthesis	50	3 of 6
66794	quinate degradation	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	tyrosine metabolism	50	7 of 14
66794	androgen and estrogen metabolism	50	8 of 16
66794	toluene degradation	50	2 of 4
66794	kanosamine biosynthesis II	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	lysine metabolism	50	21 of 42
66794	ethanol fermentation	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	urea cycle	46.15	6 of 13
66794	polyamine pathway	43.48	10 of 23
66794	glutathione metabolism	42.86	6 of 14
66794	arachidonate biosynthesis	40	2 of 5
66794	degradation of sugar acids	40	10 of 25
66794	factor 420 biosynthesis	40	2 of 5
66794	sulfate reduction	38.46	5 of 13
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	arachidonic acid metabolism	33.33	6 of 18
66794	nitrate assimilation	33.33	3 of 9
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	IAA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	ascorbate metabolism	31.82	7 of 22
66794	coenzyme M biosynthesis	30	3 of 10
66794	mevalonate metabolism	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	lactate fermentation	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	CMP-KDO biosynthesis	25	1 of 4
66794	biotin biosynthesis	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	daunorubicin biosynthesis	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Rhizoplane

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
17402	rhizoplane of neem Azadirachta indica seedlings	Azadirachta indica	Coimbatore, Tamilnadu, Botanical Garden	India	IND	Asia
67770	Rhizoplane of neem (Azadirachta indica) seedlings at Tamilnadu Agric. Univ.	Azadirachta indica	Coimbatore, Tamilnadu	India	IND	Asia
67771	From Neem (`Azadirachta indica` A. Juss), rhizoplane	Azadirachta indica	Tamilnadu Agricultural University, Coimbatore, Taminadu	India	IND	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17402	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	ASM95654v1 assembly for Microbacterium azadirachtae DSM 23848	contig	GCA_000956545	582680.7	2773857981	582680	61.56

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17402	Microbacterium azadirachtae strain AI-S262 16S ribosomal RNA gene, partial sequence	EU912487	1373		582680

GC content

@ref	GC-content (mol%)	Method
17402	69.5	high performance liquid chromatography (HPLC)
29556	69.5

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM95654v1 assembly for Microbacterium azadirachtae DSM 23848
NCBI: GCA_000956545

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	95.47	no
125439	gram_stain	BacteriaNetⓘ	positive	90.97	no
125439	motility	BacteriaNetⓘ	no	71.34	no
125439	spore_formation	BacteriaNetⓘ	no	93.93	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Microbacterium azadirachtae strain DSM 23848
PATRIC: 582680.7

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.21	yes
125438	anaerobic	anaerobicⓘ	no	97.67	yes
125438	spore-forming	spore-formingⓘ	no	79.07	yes
125438	aerobic	aerobicⓘ	yes	87.25	yes
125438	thermophilic	thermophileⓘ	no	98.47	yes
125438	flagellated	motile2+ⓘ	no	89.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Comparative Genomics of Microbacterium Species to Reveal Diversity, Potential for Secondary Metabolites and Heavy Metal Resistance.	Corretto E, Antonielli L, Sessitsch A, Hofer C, Puschenreiter M, Widhalm S, Swarnalakshmi K, Brader G.	Front Microbiol	10.3389/fmicb.2020.01869	2020
Genetics	Genome Sequences of 72 Bacterial Strains Isolated from Ectocarpus subulatus: A Resource for Algal Microbiology.	Karimi E, Geslain E, KleinJan H, Tanguy G, Legeay E, Corre E, Dittami SM.	Genome Biol Evol	10.1093/gbe/evz278	2020
Phylogeny	Microbacterium panaciterrae sp. nov., isolated from the rhizosphere of ginseng.	Nguyen NL, Kim YJ, Hoang VA, Min JW, Hwang KH, Yang DC	Int J Syst Evol Microbiol	10.1099/ijs.0.000041	2015
Phylogeny	Microbacterium azadirachtae sp. nov., a plant-growth-promoting actinobacterium isolated from the rhizoplane of neem seedlings.	Madhaiyan M, Poonguzhali S, Lee JS, Lee KC, Saravanan VS, Santhanakrishnan P	Int J Syst Evol Microbiol	10.1099/ijs.0.015800-0	2009

References

#17402	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23848
#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 )
#25951	IJSEM 1687 2010 ( DOI 10.1099/ijs.0.015800-0 , PubMed 19734284 )
#29556	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 #25951
#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;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 azadirachtae (DSM 23848, JCM 15681, KCTC 19668)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000956545

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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