Actinocorallia herbida (DSM 44254, ATCC 51528, IFO 15485)

Name: Actinocorallia herbida (DSM 44254, ATCC 51528, IFO 15485)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 16911

Type strain

Culture col. no. DSM 44254 ATCC 51528 IFO 15485 JCM 9647 NBRC 15485 6 more

NCBI tax ID(s) 58109

Special Collections DSMZ JCM JMRC

History DSMZ <- IFO <- S. Iinuma, Takeda Chem. Ind., AL-50780 JCM <-- IFO 15485 <-- Takeda Chem. Ind., Ltd.; AL-50780.

Links

Actinocorallia herbida DSM 44254 is a bacterium that was isolated from soil.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 93001

ATCC 51528,IFO 15485,DSM 44254,JCM 9647,NCIMB 13337,VKM Ac-1994,NBRC 15485

@ref 20215

Last LPSN update 2026-05-29 08:28:53

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Streptosporangiales

Family Thermomonosporaceae

Genus Actinocorallia

Species Actinocorallia herbida

Full scientific name Actinocorallia herbida Iinuma et al. 1994

Morphology

Cell morphology

@ref	Motility	Confidence	Gram stain
125439		95.396
125439		99.766	positive

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
11626	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
11626	CORYNEBACTERIUM AGAR (DSMZ Medium 53)		Medium recipe at MediaDive	Name: CORYNEBACTERIUM AGAR (DSMZ Medium 53) Composition: Agar 15.0 g/l Casein peptone 10.0 g/l NaCl 5.0 g/l Glucose 5.0 g/l Yeast extract 5.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
11626	positive	growth	28
67770	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	facultative anaerobe	98.511

Spore formation

@ref	Spore formation	Confidence
125439		97.9

Compound production

11626

Compoundazaserine-like antibiotic

Observation

@ref	Observation
67770	Production of Azaserine-like antibiotic
67770	quinones: MK-9(H₄), MK-9(H₆)

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	hydrogen production	100	5 of 5
66794	ceramide biosynthesis	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	resorcinol degradation	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	cardiolipin biosynthesis	100	7 of 7
66794	Entner Doudoroff pathway	100	10 of 10
66794	coenzyme A metabolism	100	4 of 4
66794	ethylmalonyl-CoA pathway	100	5 of 5
66794	pentose phosphate pathway	100	11 of 11
66794	formaldehyde oxidation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	glycine betaine biosynthesis	100	5 of 5
66794	biotin biosynthesis	100	4 of 4
66794	propanol degradation	100	7 of 7
66794	vitamin K metabolism	100	5 of 5
66794	ribulose monophosphate pathway	100	2 of 2
66794	CO2 fixation in Crenarchaeota	100	9 of 9
66794	cyanate degradation	100	3 of 3
66794	acetate fermentation	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	photosynthesis	100	14 of 14
66794	palmitate biosynthesis	100	22 of 22
66794	folate polyglutamylation	100	1 of 1
66794	aspartate and asparagine metabolism	100	9 of 9
66794	octane oxidation	100	3 of 3
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	taurine degradation	100	1 of 1
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	valine metabolism	100	9 of 9
66794	cellulose degradation	100	5 of 5
66794	ethanol fermentation	100	2 of 2
66794	NAD metabolism	94.44	17 of 18
66794	flavin biosynthesis	93.33	14 of 15
66794	citric acid cycle	92.86	13 of 14
66794	phenylalanine metabolism	92.31	12 of 13
66794	urea cycle	92.31	12 of 13
66794	leucine metabolism	92.31	12 of 13
66794	propionate fermentation	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	4-hydroxymandelate degradation	88.89	8 of 9
66794	allantoin degradation	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	methionine metabolism	88.46	23 of 26
66794	dTDPLrhamnose biosynthesis	87.5	7 of 8
66794	ketogluconate metabolism	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	gluconeogenesis	87.5	7 of 8
66794	3-phenylpropionate degradation	86.67	13 of 15
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	heme metabolism	85.71	12 of 14
66794	phenol degradation	85	17 of 20
66794	vitamin B1 metabolism	84.62	11 of 13
66794	tryptophan metabolism	84.21	32 of 38
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	purine metabolism	82.98	78 of 94
66794	vitamin B12 metabolism	82.35	28 of 34
66794	proline metabolism	81.82	9 of 11
66794	threonine metabolism	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	3-chlorocatechol degradation	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	4-hydroxyphenylacetate degradation	80	8 of 10
66794	gallate degradation	80	4 of 5
66794	factor 420 biosynthesis	80	4 of 5
66794	alanine metabolism	79.31	23 of 29
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	glutathione metabolism	78.57	11 of 14
66794	d-mannose degradation	77.78	7 of 9
66794	sulfate reduction	76.92	10 of 13
66794	glycogen biosynthesis	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	degradation of aromatic, nitrogen containing compounds	75	9 of 12
66794	toluene degradation	75	3 of 4
66794	degradation of sugar alcohols	75	12 of 16
66794	sulfopterin metabolism	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	catecholamine biosynthesis	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	lipid metabolism	74.19	23 of 31
66794	non-pathway related	73.68	28 of 38
66794	pyrimidine metabolism	73.33	33 of 45
66794	cysteine metabolism	72.22	13 of 18
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	tyrosine metabolism	71.43	10 of 14
66794	arginine metabolism	70.83	17 of 24
66794	glycolysis	70.59	12 of 17
66794	myo-inositol biosynthesis	70	7 of 10
66794	oxidative phosphorylation	69.23	63 of 91
66794	histidine metabolism	68.97	20 of 29
66794	androgen and estrogen metabolism	68.75	11 of 16
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	daunorubicin biosynthesis	66.67	6 of 9
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	IAA biosynthesis	66.67	2 of 3
66794	d-xylose degradation	63.64	7 of 11
66794	metabolism of disaccharids	63.64	7 of 11
66794	carnitine metabolism	62.5	5 of 8
66794	degradation of pentoses	60.71	17 of 28
66794	arachidonate biosynthesis	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	creatinine degradation	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	starch degradation	60	6 of 10
66794	bile acid biosynthesis, neutral pathway	58.82	10 of 17
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	degradation of hexoses	55.56	10 of 18
66794	nitrate assimilation	55.56	5 of 9
66794	lysine metabolism	54.76	23 of 42
66794	glycine metabolism	50	5 of 10
66794	cyclohexanol degradation	50	2 of 4
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	arachidonic acid metabolism	50	9 of 18
66794	selenocysteine biosynthesis	50	3 of 6
66794	vitamin E metabolism	50	2 of 4
66794	alginate biosynthesis	50	2 of 4
66794	kanosamine biosynthesis II	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	ascorbate metabolism	45.45	10 of 22
66794	lipid A biosynthesis	44.44	4 of 9
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	aclacinomycin biosynthesis	42.86	3 of 7
66794	carotenoid biosynthesis	40.91	9 of 22
66794	coenzyme M biosynthesis	40	4 of 10
66794	D-cycloserine biosynthesis	40	2 of 5
66794	chlorophyll metabolism	38.89	7 of 18
66794	vitamin B6 metabolism	36.36	4 of 11
66794	cholesterol biosynthesis	36.36	4 of 11
66794	degradation of sugar acids	36	9 of 25
66794	methane metabolism	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	pantothenate biosynthesis	33.33	2 of 6
66794	polyamine pathway	30.43	7 of 23
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	diterpene phytoalexins precursors biosynthesis	25	4 of 16
66794	methanogenesis from CO2	25	3 of 12
66794	lactate fermentation	25	1 of 4

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
11626	soil	Bangkok	Thailand	THA	Asia
67770	Soil	Bangkok	Thailand	THA	Asia

Taxonmaps

69479

Global distribution of 16S sequence LC066303 (>99% sequence identity) for Actinocorallia herbida from Microbeatlas

Aquatic Samples	1
Soil Samples	21
Animal Samples	3
Plant Samples	216
Total Samples	241

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
11626	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	ASM375122v1 assembly for Actinocorallia herbida DSM 44254	contig	GCA_003751225	58109.3	2784132147	58109	70.06

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Actinocorallia herbida 16S-23S ribosomal RNA intergenic spacer region, partial sequence	AF134109	403	58109
20218	Actinocorallia herbida gene for 16S ribosomal RNA, partial sequence	D85473	1465	58109
67770	Actinocorallia herbida gene for 16S ribosomal RNA, partial sequence, strain: JCM 9647	LC066303	1452	58109

GC content

@ref	GC-content (mol%)	Method
11626	73	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: ASM375122v1 assembly for Actinocorallia herbida DSM 44254
NCBI: GCA_003751225

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	positive	99.77	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	98.51	no
125439	motility	BacteriaNetⓘ	no	95.40	no
125439	spore_formation	BacteriaNetⓘ	yes	97.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Actinocorallia herbida strain DSM 44254
PATRIC: 58109.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	87.16	no
125438	anaerobic	anaerobicⓘ	no	95.90	no
125438	spore-forming	spore-formingⓘ	yes	82.97	no
125438	aerobic	aerobicⓘ	yes	88.80	no
125438	thermophilic	thermophileⓘ	no	95.10	yes
125438	flagellated	motile2+ⓘ	no	86.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Distribution and phylogenetic analysis of family 19 chitinases in Actinobacteria.	Kawase T, Saito A, Sato T, Kanai R, Fujii T, Nikaidou N, Miyashita K, Watanabe T.	Appl Environ Microbiol	10.1128/aem.70.2.1135-1144.2004	2004
	Improving the C_beta Stereoselectivity of l-Threonine Aldolase for the Synthesis of l-threo-4-Methylsulfonylphenylserine by Modulating the Substrate-Binding Pocket To Control the Orientation of the Substrate Entrance.	Wang L, Xu L, Su B, Lin W, Xu X, Lin J.	Chemistry	10.1002/chem.202100752	2021
Phylogeny	Cell wall teichoic acids of actinomycetes of three genera of the order actinomycetales.	Streshinskaya GM, Shashkov AS, Usov AI, Evtushenko LI, Naumova IB	Biochemistry (Mosc)	10.1023/a:1016348724308	2002

References

#11626	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44254
#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 )
#20216	Curators of the JMRC: Jena Microbial Resource Collection (JMRC):
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#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;
#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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Actinocorallia herbida (DSM 44254, ATCC 51528, IFO 15485)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Compound production

Observation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003751225

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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