Agromyces neolithicus (DSM 16197, CIP 108987, NBRC 109084)

Name: Agromyces neolithicus (DSM 16197, CIP 108987, NBRC 109084)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7272

Type strain

Strain Designation 23-23

Culture col. no. DSM 16197 CIP 108987 NBRC 109084 HKI 0321 23-23 6 more

NCBI tax ID(s) 269420

Special Collections DSMZ JCM CIP Wink compendium Literature strains JMRC

History DSMZ <- I. Groth; HKI 0321 <- Ch. Weigel; 23-23 JCM <-- I. Groth 23-23 (=HKI 0321) <-- Ch. Weigel. CIP <- 2005, DSMZ <- I. Groth, Hans Knöll Inst., Jena, Germany <- C. Weigel: strain 23-23

Links

Agromyces neolithicus 23-23 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from soil sample.

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

Name and taxonomic classification

SI-ID 135102

NBRC 109084,DSM 16197,NCIMB 13990,CIP 108987,JCM 14322,IAM 15296

@ref 20215

Last LPSN update 2026-05-29 08:26:36

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Microbacteriaceae

Genus Agromyces

Species Agromyces neolithicus

Full scientific name Agromyces neolithicus Jurado et al. 2005

Morphology

Cell morphology

@ref	Gram stain	Cell width	Cell shape	Confidence
31281	positive	0.4 µm	rod-shaped
121268	positive		rod-shaped
125439	positive			95.318

Colony morphology

@ref	Colony color	Incubation period	Medium used	Hemolysis ability
18399	Beige (1001)	10-14 days	ISP 2
18399	Beige (1001)	10-14 days	ISP 3
18399	Beige (1001)	10-14 days	ISP 4
18399	Beige (1001)	10-14 days	ISP 5
18399	Beige (1001)	10-14 days	ISP 6
18399	Beige (1001)	10-14 days	ISP 7
121268				0

Multicellular morphology

@ref	Forms multicellular complex	Medium name
18399		ISP 2
18399		ISP 3
18399		ISP 4
18399		ISP 5
18399		ISP 6
18399		ISP 7

Pigmentation

31281

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6319	R2A MEDIUM (DSMZ Medium 830)	Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
6319	TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)	Medium recipe at MediaDive	Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
18399	ISP 2		Name: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
18399	ISP 3		Name: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
18399	ISP 4		Name: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
18399	ISP 5		Name: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
18399	ISP 6		Name: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
18399	ISP 7		Name: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
121268	CIP Medium 338	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
6319	positive	growth	28
18399	positive	optimum	28
31281	positive	growth	15-37
31281	positive	optimum	28
67770	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31281	aerobe
121268	obligate aerobe
125439	obligate aerobe	99.691

Observation

@ref	Observation
31281	aggregates in clumps
67770	quinones: MK-13, MK-12

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31281	22599 ChEBI	arabinose	+	carbon source
31281	17057 ChEBI	cellobiose	+	carbon source
31281	4853 ChEBI	esculin	+	hydrolysis
68379	4853 ChEBI	esculin	+	hydrolysis	from API Coryne
31281	28757 ChEBI	fructose	+	carbon source
31281	33984 ChEBI	fucose	+	carbon source
31281	28260 ChEBI	galactose	+	carbon source
68379	5291 ChEBI	gelatin	-	hydrolysis	from API Coryne
31281	17234 ChEBI	glucose	+	carbon source
31281	17754 ChEBI	glycerol	+	carbon source
31281	28087 ChEBI	glycogen	+	carbon source
31281	17306 ChEBI	maltose	+	carbon source
31281	29864 ChEBI	mannitol	+	carbon source
31281	37684 ChEBI	mannose	+	carbon source
31281	28053 ChEBI	melibiose	+	carbon source
31281	506227 ChEBI	N-acetylglucosamine	+	carbon source
31281	17632 ChEBI	nitrate	+	reduction
121268	17632 ChEBI	nitrate	+	reduction
121268	16301 ChEBI	nitrite	-	reduction
31281	16634 ChEBI	raffinose	+	carbon source
31281	17992 ChEBI	sucrose	+	carbon source
68379	17992 ChEBI	sucrose	+	fermentation	from API Coryne
68379	16199 ChEBI	urea	+	hydrolysis	from API Coryne

Metabolite production

@ref	Chebi-ID	Metabolite	Production
31281	16136 ChEBI	hydrogen sulfide
121268	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
121268	alcohol dehydrogenase	-	1.1.1.1
31281	alkaline phosphatase	+	3.1.3.1
68379	alkaline phosphatase	-	3.1.3.1	from API Coryne
68382	alkaline phosphatase	-	3.1.3.1	from API zym
68382	alpha-chymotrypsin	+	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	+	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68379	alpha-glucosidase	+	3.2.1.20	from API Coryne
68382	alpha-mannosidase	+	3.2.1.24	from API zym
68379	beta-galactosidase	+	3.2.1.23	from API Coryne
68379	beta-glucosidase	+	3.2.1.21	from API Coryne
68382	beta-glucuronidase	+	3.2.1.31	from API zym
68379	beta-glucuronidase	+	3.2.1.31	from API Coryne
31281	catalase	+	1.11.1.6
121268	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
31281	cytochrome oxidase	+	1.9.3.1
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68379	gelatinase	-		from API Coryne
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
121268	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68379	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API Coryne
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
121268	ornithine decarboxylase	-	4.1.1.17
121268	oxidase	-
68379	pyrazinamidase	+	3.5.1.B15	from API Coryne
68379	pyrrolidonyl arylamidase	+	3.4.19.3	from API Coryne
121268	urease	-	3.5.1.5
68379	urease	+	3.5.1.5	from API Coryne
68382	valine arylamidase	+		from API zym

API coryne

@ref	Reduction of nitrateNIT	PYZ	PYRA	PAL	beta GUR	beta GAL	alpha GLU	beta NAG	ESC	URE	GEL	Control fermentationControl	GLU	RIB	XYL	MAN	MAL	LAC	SAC	GLYG	CAT
18399	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

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
18399	not determinedn.d.	-	+	+	-	+	+	+	+	+	+	+	+	+	+	+	+	+	+	-
121268	-	-	+	+	-	+	+	+	-	+	+	+	+	-	+	+	-	+	+	-

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
6319	soil sample	Porto Badisco	Italy	ITA	Europe
67770	Soil sample inside the cave	Grotta dei Cervi, Porto Badisco	Italy	ITA	Europe
121268	Environment, Soil sample	Grotta dei Cervi	Italy	ITA	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6319	1	Risk group (German classification) According to TRBA 466
121268	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	NCBI tax ID	Score
124043	ASM3952973v1 assembly for Agromyces neolithicus JCM 14322	scaffold	GCA_039529735	269420	53.02

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6319	Agromyces neolithicus strain 23-23 16S ribosomal RNA gene, partial sequence	AY507128	1479		269420

GC content

@ref	GC-content (mol%)	Method
6319	65.3
67770	65.3	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM3952973v1 assembly for Agromyces neolithicus JCM 14322
NCBI: GCA_039529735

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.69	no
125439	gram_stain	BacteriaNetⓘ	positive	95.32	no
125439	motility	BacteriaNetⓘ	no	69.45	no
125439	spore_formation	BacteriaNetⓘ	no	88.44	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Agromyces salentinus sp. nov. and Agromyces neolithicus sp. nov.	Jurado V, Groth I, Gonzalez JM, Laiz L, Saiz-Jimenez C	Int J Syst Evol Microbiol	10.1099/ijs.0.63199-0	2005

References

#6319	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16197
#18399	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 )
#20216	Curators of the JMRC: Jena Microbial Resource Collection (JMRC):
#27601	IJSEM 153 2005 ( DOI 10.1099/ijs.0.63199-0 , PubMed 15653869 )
#31281	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 #27601
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68379	Automatically annotated from API Coryne .
#68382	Automatically annotated from API zym .
#121268	Collection of Institut Pasteur ; Curators of the CIP; CIP 108987
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Agromyces neolithicus (DSM 16197, CIP 108987, NBRC 109084)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Observation

Metabolite utilization

Metabolite production

Enzymes

API coryne

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_039529735

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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