Name: Actinocorallia herbida DSM 44254
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 16911

Type strain:

Species: Actinocorallia herbida

Culture col. no.: DSM 44254, ATCC 51528, IFO 15485, JCM 9647, NBRC 15485, NCIMB 13337, VKM Ac-1994, IMSNU 21271

Strain history: IFO 15485 <-- Takeda Chem. Ind., Ltd.; AL-50780.

NCBI tax ID(s): 58109 (species)

SI-ID 93001

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

Special Collections

DSMZ
JCM

Other strains from Actinocorallia herbida

Section

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

spore-forming
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	*Streptosporangiales*
	Family	*Thermomonosporaceae*
	Genus	*Actinocorallia*
	Species	**Actinocorallia herbida**
	Full Scientific Name (LPSN)	Actinocorallia herbida Iinuma et al. 1994

Information on culture and growth conditions Culture and growth conditions

[Ref.: #11626]

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

[Ref.: #11626]

Culture medium growth

[Ref.: #11626]

Culture medium link

Medium recipe at MediaDive

[Ref.: #11626]

Culture medium composition

expand / minimize

[Ref.: #11626]

Culture medium

CORYNEBACTERIUM AGAR (DSMZ Medium 53)

[Ref.: #11626]

Culture medium growth

[Ref.: #11626]

Culture medium link

Medium recipe at MediaDive

[Ref.: #11626]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #11626]			growth	28 °C
[Ref.: #67770]			growth	28 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]

Ability of spore formation

yes Confidence in %100

[Ref.: #11626]

Name of produced compound

azaserine-like antibiotic

[Ref.: #67770]	Observation	Production of Azaserine-like antibiotic
[Ref.: #67770]	Observation	quinones: MK-9(H₄), MK-9(H₆)

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	hydrogen production	100	5 of 5
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	resorcinol degradation	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	ethylmalonyl-CoA pathway	100	5 of 5
[Ref.: #66794]	pentose phosphate pathway	100	11 of 11
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	glycine betaine biosynthesis	100	5 of 5
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	propanol degradation	100	7 of 7
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	CO2 fixation in Crenarchaeota	100	9 of 9
[Ref.: #66794]	cyanate degradation	100	3 of 3
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	photosynthesis	100	14 of 14
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	NAD metabolism	94.44	17 of 18
[Ref.: #66794]	flavin biosynthesis	93.33	14 of 15
[Ref.: #66794]	citric acid cycle	92.86	13 of 14
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	urea cycle	92.31	12 of 13
[Ref.: #66794]	leucine metabolism	92.31	12 of 13
[Ref.: #66794]	propionate fermentation	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	88.89	8 of 9
[Ref.: #66794]	allantoin degradation	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	methionine metabolism	88.46	23 of 26
[Ref.: #66794]	dTDPLrhamnose biosynthesis	87.5	7 of 8
[Ref.: #66794]	ketogluconate metabolism	87.5	7 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	3-phenylpropionate degradation	86.67	13 of 15
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	phenol degradation	85	17 of 20
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	tryptophan metabolism	84.21	32 of 38
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	purine metabolism	82.98	78 of 94
[Ref.: #66794]	vitamin B12 metabolism	82.35	28 of 34
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	3-chlorocatechol degradation	80	4 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	80	8 of 10
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	glutathione metabolism	78.57	11 of 14
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	sulfate reduction	76.92	10 of 13
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	75	9 of 12
[Ref.: #66794]	toluene degradation	75	3 of 4
[Ref.: #66794]	degradation of sugar alcohols	75	12 of 16
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	catecholamine biosynthesis	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	lipid metabolism	74.19	23 of 31
[Ref.: #66794]	non-pathway related	73.68	28 of 38
[Ref.: #66794]	pyrimidine metabolism	73.33	33 of 45
[Ref.: #66794]	cysteine metabolism	72.22	13 of 18
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	tyrosine metabolism	71.43	10 of 14
[Ref.: #66794]	arginine metabolism	70.83	17 of 24
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	myo-inositol biosynthesis	70	7 of 10
[Ref.: #66794]	oxidative phosphorylation	69.23	63 of 91
[Ref.: #66794]	histidine metabolism	68.97	20 of 29
[Ref.: #66794]	androgen and estrogen metabolism	68.75	11 of 16
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	daunorubicin biosynthesis	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]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	carnitine metabolism	62.5	5 of 8
[Ref.: #66794]	degradation of pentoses	60.71	17 of 28
[Ref.: #66794]	arachidonate biosynthesis	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	creatinine degradation	60	3 of 5
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	starch degradation	60	6 of 10
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	58.82	10 of 17
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	degradation of hexoses	55.56	10 of 18
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	lysine metabolism	54.76	23 of 42
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	arachidonic acid metabolism	50	9 of 18
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	alginate biosynthesis	50	2 of 4
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	46.15	6 of 13
[Ref.: #66794]	ascorbate metabolism	45.45	10 of 22
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	aclacinomycin biosynthesis	42.86	3 of 7
[Ref.: #66794]	carotenoid biosynthesis	40.91	9 of 22
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	chlorophyll metabolism	38.89	7 of 18
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	cholesterol biosynthesis	36.36	4 of 11
[Ref.: #66794]	degradation of sugar acids	36	9 of 25
[Ref.: #66794]	methane metabolism	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate 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]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	polyamine pathway	30.43	7 of 23
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	diterpene phytoalexins precursors biosynthesis	25	4 of 16
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	lactate fermentation	25	1 of 4
		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.: #11626]	Sample type/isolated from	soil
[Ref.: #11626]	Geographic location (country and/or sea, region)	Bangkok
[Ref.: #11626]	Country	Thailand
[Ref.: #11626]	Country ISO 3 Code	THA
[Ref.: #11626]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Soil
[Ref.: #67770]	Geographic location (country and/or sea, region)	Bangkok
[Ref.: #67770]	Country	Thailand
[Ref.: #67770]	Country ISO 3 Code	THA
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #11626]

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.: #67770]	Actinocorallia herbida gene for 16S ribosomal RNA, partial sequence, strain: JCM 9647	LC066303	1452	GenBank ENA	58109 tax ID
[Ref.: #20218]	Actinocorallia herbida 16S-23S ribosomal RNA intergenic spacer region, partial sequence	AF134109	403	GenBank ENA	58109 tax ID	*
[Ref.: #20218]	Actinocorallia herbida gene for 16S ribosomal RNA, partial sequence	D85473	1465	GenBank ENA	58109 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Actinocorallia herbida DSM 44254	GCA_003751225	contig	GenBank ENA	58109 tax ID
[Ref.: #66792]	Actinocorallia herbida strain DSM 44254	58109.3	wgs	PATRIC	58109 tax ID	*
[Ref.: #66792]	Actinocorallia herbida DSM 44254	2784132147	draft	JGI IMG/M	58109 tax ID	*

[Ref.: #11626]

GC-content

73 mol%

high performance liquid chromatography (HPLC)

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Actinocorallia herbida strain DSM 44254 PATRIC: 58109.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	yes	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Actinocorallia herbida strain DSM 44254 PATRIC: 58109.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	87.155	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	95.902	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	yes	82.968	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	88.803	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	95.1	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	86	no

Availability in culture collections External links

[Ref.: #11626]

Culture collection no.

DSM 44254, ATCC 51528, IFO 15485, JCM 9647, NBRC 15485, NCIMB 13337, VKM Ac-1994, IMSNU 21271

[Ref.: #85916]

SI-ID 93001

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 )

#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 )

#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;

#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 .

#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 )

#85916

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-ID93001.1 )

* These data were automatically processed and therefore are not curated

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Actinocorallia herbida strain DSM 44254

Actinocorallia herbida strain DSM 44254

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