Name: Agromyces subbeticus Z33
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 7277

Type strain:

Species: Agromyces subbeticus

Strain Designation: Z33

Culture col. no.: DSM 16689, NCIMB 14025, HKI 0340, JCM 14324, IAM 15298, CIP 108957

Strain history: CIP <- 2005, NCIMB

NCBI tax ID(s): 1120960 (strain), 293890 (species)

SI-ID 237163

NCIMB 14025, DSM 16689, JCM 14324, IAM 15298, CIP 108957

Section

Agromyces subbeticus Z33 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from cyanobacterial biofilm, cave of bats.

coccus-shaped
Gram-positive
aerobe
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	*Micrococcales*
	Family	*Microbacteriaceae*
	Genus	*Agromyces*
	Species	**Agromyces subbeticus**
	Full Scientific Name (LPSN)	Agromyces subbeticus Jurado et al. 2005

Information on morphological and physiological properties Morphology

[Ref.: #31475]	Gram stain	positive
[Ref.: #123342]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #31475]	Cell length	2.5-4 µm

[Ref.: #31475]	Cell width	0.3-0.5 µm

[Ref.: #31475]	Cell shape	coccus-shaped
[Ref.: #123342]	Cell shape	rod-shaped

[Ref.: #123342]	Motility	no

[Ref.: #19742]	Colony color	Zinc yellow (1018)
[Ref.: #19742]	Incubation period	10-14 days
[Ref.: #19742]	Cultivation medium used	ISP 2

[Ref.: #19742]	Colony color	Zinc yellow (1018)
[Ref.: #19742]	Incubation period	10-14 days
[Ref.: #19742]	Cultivation medium used	ISP 3

[Ref.: #19742]	Colony color	Zinc yellow (1018)
[Ref.: #19742]	Incubation period	10-14 days
[Ref.: #19742]	Cultivation medium used	ISP 4

[Ref.: #19742]	Colony color	Zinc yellow (1018)
[Ref.: #19742]	Incubation period	10-14 days
[Ref.: #19742]	Cultivation medium used	ISP 6

[Ref.: #19742]	Incubation period	10-14 days
[Ref.: #19742]	Cultivation medium used	ISP 5

[Ref.: #19742]	Incubation period	10-14 days
[Ref.: #19742]	Cultivation medium used	ISP 7

[Ref.: #31475]

Pigment production

yes

[Ref.: #19742]	Multicellular complex forming ability	no
[Ref.: #19742]	Medium Name (multicellularity)	ISP 2

[Ref.: #19742]	Multicellular complex forming ability	no
[Ref.: #19742]	Medium Name (multicellularity)	ISP 3

[Ref.: #19742]	Multicellular complex forming ability	no
[Ref.: #19742]	Medium Name (multicellularity)	ISP 4

[Ref.: #19742]	Multicellular complex forming ability	no
[Ref.: #19742]	Medium Name (multicellularity)	ISP 5

[Ref.: #19742]	Multicellular complex forming ability	no
[Ref.: #19742]	Medium Name (multicellularity)	ISP 6

[Ref.: #19742]	Multicellular complex forming ability	no
[Ref.: #19742]	Medium Name (multicellularity)	ISP 7

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6568]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #6568]

Culture medium growth

[Ref.: #6568]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6568]

Culture medium composition

expand / minimize

[Ref.: #19742]

Culture medium

ISP 2

[Ref.: #19742]

Culture medium growth

[Ref.: #19742]

Culture medium composition

expand / minimize

[Ref.: #19742]

Culture medium

ISP 3

[Ref.: #19742]

Culture medium growth

[Ref.: #19742]

Culture medium composition

expand / minimize

[Ref.: #19742]

Culture medium

ISP 4

[Ref.: #19742]

Culture medium growth

[Ref.: #19742]

Culture medium composition

expand / minimize

[Ref.: #19742]

Culture medium

ISP 5

[Ref.: #19742]

Culture medium growth

[Ref.: #19742]

Culture medium composition

expand / minimize

[Ref.: #19742]

Culture medium

ISP 6

[Ref.: #19742]

Culture medium growth

[Ref.: #19742]

Culture medium composition

expand / minimize

[Ref.: #19742]

Culture medium

ISP 7

[Ref.: #19742]

Culture medium growth

[Ref.: #19742]

Culture medium composition

expand / minimize

[Ref.: #33272]

Culture medium

MEDIUM 11 - for Agromyces

[Ref.: #33272]

Culture medium growth

[Ref.: #33272]

Culture medium composition

expand / minimize

[Ref.: #123342]

Culture medium

CIP Medium 11

[Ref.: #123342]

Culture medium growth

[Ref.: #123342]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #123342]

Culture medium

CIP Medium 72

[Ref.: #123342]

Culture medium growth

[Ref.: #123342]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #6568]	growth	28 °C
[Ref.: #19742]	optimum	28 °C
[Ref.: #31475]	growth	06-37 °C
[Ref.: #31475]	optimum	21.5 °C
[Ref.: #33272]	growth	30 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #6568]	Temperature range	mesophilic
[Ref.: #19742]	Temperature range	mesophilic
[Ref.: #31475]	Temperature range	psychrophilic
[Ref.: #33272]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31475]			optimum	7.25
[Ref.: #31475]			growth	5-9.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31475]	Oxygen tolerance	aerobe
[Ref.: #123342]	Oxygen tolerance	obligate aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %97
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.95

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31475]		NaCl		growth	0-4	%
[Ref.: #31475]		NaCl		optimum	2	%

[Ref.: #6568]	Murein short key	B07
[Ref.: #6568]	Murein types	B2gamma {Gly} [L-Dab] D-Glu-D-Dab

[Ref.: #31475]	Observation	aggregates in chains
[Ref.: #67770]	Observation	quinones: MK-12, MK-13

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31475]	acetate ChEBI	+	carbon source
[Ref.: #31475]	alanine ChEBI	+	carbon source
[Ref.: #19742]	arabinose ChEBI	+
[Ref.: #19742]	cellulose ChEBI	+
[Ref.: #31475]	esculin ChEBI	+	hydrolysis
[Ref.: #68379]	esculin ChEBI	+	hydrolysis	* from API Coryne
[Ref.: #19742]	fructose ChEBI	+
[Ref.: #31475]	fructose ChEBI	+	carbon source
[Ref.: #68379]	gelatin ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #19742]	glucose ChEBI	+
[Ref.: #31475]	glycine ChEBI	+	carbon source
[Ref.: #31475]	glycogen ChEBI	+	carbon source
[Ref.: #31475]	leucine ChEBI	+	carbon source
[Ref.: #19742]	mannitol ChEBI	+
[Ref.: #19742]	myo-inositol ChEBI	+
[Ref.: #123342]	nitrate ChEBI	-	reduction
[Ref.: #123342]	nitrite ChEBI	-	reduction
[Ref.: #19742]	raffinose ChEBI	-
[Ref.: #19742]	rhamnose ChEBI	-
[Ref.: #31475]	rhamnose ChEBI	+	carbon source
[Ref.: #19742]	sucrose ChEBI	+
[Ref.: #68379]	sucrose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	urea ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #19742]	xylose ChEBI	-
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #31475]		hydrogen sulfide ChEBI	yes
[Ref.: #123342]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #31475]	acid phosphatase	+	3.1.3.2
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #123342]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #31475]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68379]	alkaline phosphatase	-	3.1.3.1	* from API Coryne
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym, API Coryne
[Ref.: #68382]	beta-galactosidase	+	3.2.1.23	* from API zym, API Coryne
[Ref.: #68382]	beta-glucosidase	+	3.2.1.21	* from API zym, API Coryne
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym, API Coryne
[Ref.: #123342]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68379]	gelatinase	-		* from API Coryne
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #123342]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API zym, API Coryne
[Ref.: #123342]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #123342]	oxidase	-
[Ref.: #68379]	pyrazinamidase	+	3.5.1.B15	* from API Coryne
[Ref.: #68379]	pyrrolidonyl arylamidase	-	3.4.19.3	* from API Coryne
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #123342]	urease	-	3.5.1.5
[Ref.: #68379]	urease	-	3.5.1.5	* from API Coryne
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® Coryne:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitrateNIT	PyrazinamidasePYZ	Pyrrolidonyl arylamidasePYRA	Alkaline phosphatasePAL	beta-Glucuronidasebeta GUR	beta-Galactosidasebeta GAL	alpha-Glucosidasealpha GLU	N-Acetyl-beta-Glucosidasebeta NAG	Esculin hydrolysis/beta-GlucosidaseESC	Urease/urea hydrolysisURE	Gelatinase/gelatin hydrolysisGEL	Control fermentationControl	Fermentation of D-glucoseGLU	Fermentation of D-riboseRIB	Fermentation of D-xyloseXYL	Fermentation of D-mannitolMAN	Fermentation of maltoseMAL	Fermentation of lactoseLAC	Fermentation of sucroseSAC	Fermentation of glycogenGLYG	CatalaseCAT
[Ref.: #19742]	284	not determinedn.d.	+	-	-	-	+	+	+	+	-	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	-	not determinedn.d.	not determinedn.d.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #19742]	566	not determinedn.d.	+	+	+	-	+	+	-	-	-	+	-	-	+	-	+	+	+	+	-
[Ref.: #123342]	11574	-	+	+	+	-	+	+	-	-	-	+	+	-	+	-	+	+	+	-	-

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

[Ref.: #6568]	Sample type/isolated from	cyanobacterial biofilm, cave of bats
[Ref.: #6568]	Geographic location (country and/or sea, region)	Zuheros, Cordoba
[Ref.: #6568]	Country	Spain
[Ref.: #6568]	Country ISO 3 Code	ESP
[Ref.: #6568]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Blue-gray cyanobacterial biofilm covering the walls of the Cave of Bats
[Ref.: #67770]	Geographic location (country and/or sea, region)	Zuheros, Cordoba
[Ref.: #67770]	Country	Spain
[Ref.: #67770]	Country ISO 3 Code	ESP
[Ref.: #67770]	Continent	Europe

[Ref.: #123342]	Sample type/isolated from	Cyanobacterial film
[Ref.: #123342]	Geographic location (country and/or sea, region)	Cordoba
[Ref.: #123342]	Country	Spain
[Ref.: #123342]	Country ISO 3 Code	ESP
[Ref.: #123342]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental	#Biofilm	-
#Host	#Microbial	#Bacteria

What are isolation sources categories?

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

[Ref.: #6568]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #19742]	Biosafety level	1	Risk group (German classification)
[Ref.: #123342]	Biosafety level	1	Risk group (French classification)

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.: #6568]	Agromyces subbeticus strain Z33 16S ribosomal RNA gene, partial sequence	AY737778	1468	ENA	293890 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Agromyces subbeticus DSM 16689	GCA_000421565	contig	GenBank	1120960 tax ID
[Ref.: #66792]	Agromyces subbeticus DSM 16689	1120960.3	wgs	PATRIC	1120960 tax ID	*
[Ref.: #66792]	Agromyces subbeticus DSM 16689	2524023187	draft	JGI IMG/M	1120960 tax ID	*

[Ref.: #6568]	GC-content	71.2 mol%
[Ref.: #67770]	GC-content	71.2 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #67770]	GC-content	69.1 mol%	genome sequence analysis

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: Agromyces subbeticus DSM 16689 PATRIC: 1120960.3
[Ref.: #69481]	spore-forming	no	97	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Agromyces subbeticus DSM 16689 PATRIC: 1120960.3
[Ref.: #69480]	motile	no	88.761	no
[Ref.: #69480]	flagellated	no	98.266	no
[Ref.: #69480]	gram-positive	yes	93.452	yes
[Ref.: #69480]	anaerobic	no	99.69	yes
[Ref.: #69480]	aerobic	yes	95.793	yes
[Ref.: #69480]	halophile	no	91.696	no
[Ref.: #69480]	spore-forming	no	87.895	no
[Ref.: #69480]	thermophile	no	99.427	yes
[Ref.: #69480]	glucose-util	yes	88.673	yes
[Ref.: #69480]	glucose-ferment	no	90.414	no

Availability in culture collections External links

[Ref.: #6568]

Culture collection no.

DSM 16689, NCIMB 14025, HKI 0340, JCM 14324, IAM 15298, CIP 108957

[Ref.: #76728]

SI-ID 237163

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Agromyces subbeticus sp. nov., isolated from a cave in southern Spain.	Jurado V, Groth I, Gonzalez JM, Laiz L, Saiz-Jimenez C	Int J Syst Evol Microbiol	10.1099/ijs.0.63637-0	2005	*

References

#6568

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16689

#19742

Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .

#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 )

#31475

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 #27775 (see below)

#33272 ; Curators of the CIP;

#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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68379

Automatically annotated from API Coryne .

#68382

Automatically annotated from API zym .

#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 )

#76728

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-ID237163.1 )

#123342 Collection of Institut Pasteur ; Curators of the CIP; CIP 108957

#27775

IJSEM 1897 2005 ( DOI 10.1099/ijs.0.63637-0 , PubMed 16166685 )

* These data were automatically processed and therefore are not curated

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Agromyces subbeticus DSM 16689

Agromyces subbeticus DSM 16689

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