Name: Agromyces lapidis CD55
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 7274

Type strain:

Species: Agromyces lapidis

Strain Designation: CD55

Culture col. no.: DSM 16390, NCIMB 14013, HKI 0324, JCM 14321, IAM 15275, CIP 108739

Strain history: CIP <- 2005, V. Jurado, CSIC, Sevilla, Spain: strain CD55 <- I. Groth, Hans Knöll Inst., Jena, Germany: strain HKI 0324

NCBI tax ID(s): 279574 (species)

SI-ID 137994

DSM 16390, NCIMB 14013, JCM 14321, IAM 15275, CIP 108739

Section

Agromyces lapidis CD55 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from carved stone wall.

Gram-positive
rod-shaped
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 lapidis**
	Full Scientific Name (LPSN)	Agromyces lapidis Jurado et al. 2005

Information on morphological and physiological properties Morphology

[Ref.: #31369]	Gram stain	positive
[Ref.: #120559]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #31369]	Cell width	0.5 µm

[Ref.: #31369]	Cell shape	rod-shaped
[Ref.: #120559]	Cell shape	rod-shaped

[Ref.: #31369]	Motility	no
[Ref.: #120559]	Motility	no

[Ref.: #31369]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6423]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #6423]

Culture medium growth

[Ref.: #6423]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6423]

Culture medium composition

expand / minimize

[Ref.: #6423]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #6423]

Culture medium growth

[Ref.: #6423]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6423]

Culture medium composition

expand / minimize

[Ref.: #37633]

Culture medium

MEDIUM 56 - for Micromonospora purpurea

[Ref.: #37633]

Culture medium growth

[Ref.: #37633]

Culture medium composition

expand / minimize

[Ref.: #120559]

Culture medium

CIP Medium 56

[Ref.: #120559]

Culture medium growth

[Ref.: #120559]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #120559]

Culture medium

CIP Medium 72

[Ref.: #120559]

Culture medium growth

[Ref.: #120559]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #6423]	growth	28 °C
[Ref.: #31369]	growth	10-37 °C
[Ref.: #31369]	optimum	28 °C
[Ref.: #37633]	growth	30 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #6423]	Temperature range	mesophilic
[Ref.: #31369]	Temperature range	mesophilic
[Ref.: #37633]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31369]			optimum	7.25
[Ref.: #31369]			growth	5-9.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31369]	Oxygen tolerance	aerobe
[Ref.: #120559]	Oxygen tolerance	obligate aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.99

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31369]		NaCl		growth	<4	%
[Ref.: #31369]		NaCl		optimum	2	%

[Ref.: #6423]	Murein short key	B07
[Ref.: #6423]	Murein types	B2gamma {Gly} [L-Dab] D-Glu-D-Dab

[Ref.: #67770]

Observation

quinones: MK-12, MK-13

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31369]	arabinose ChEBI	+	carbon source
[Ref.: #31369]	cellobiose ChEBI	+	carbon source
[Ref.: #31369]	fucose ChEBI	+	carbon source
[Ref.: #31369]	galactose ChEBI	+	carbon source
[Ref.: #31369]	glucose ChEBI	+	carbon source
[Ref.: #31369]	glycerol ChEBI	+	carbon source
[Ref.: #31369]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #31369]	nitrate ChEBI	+	reduction
[Ref.: #120559]	nitrate ChEBI	+	reduction
[Ref.: #120559]	nitrate ChEBI	-	respiration
[Ref.: #120559]	nitrite ChEBI	-	reduction
[Ref.: #31369]	raffinose ChEBI	+	carbon source
[Ref.: #31369]	salicin ChEBI	+	carbon source
[Ref.: #31369]	sucrose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #120559]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	-	3.1.3.1	* from API zym
[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
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	+	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	+	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #31369]	catalase	+	1.11.1.6
[Ref.: #120559]	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.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #120559]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #120559]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #120559]	oxidase	+
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #120559]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

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.: #120559]	11425	-	-	+	+	-	+	+	+	-	-	+	+	+	+	-	+	+	-	-	-

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

[Ref.: #6423]	Sample type/isolated from	carved stone wall
[Ref.: #6423]	Geographic location (country and/or sea, region)	Rome, Domitilla catacombs
[Ref.: #6423]	Country	Italy
[Ref.: #6423]	Country ISO 3 Code	ITA
[Ref.: #6423]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Stone wall of a tomb
[Ref.: #67770]	Geographic location (country and/or sea, region)	Domitilla Catacombs, Rome
[Ref.: #67770]	Country	Italy
[Ref.: #67770]	Country ISO 3 Code	ITA
[Ref.: #67770]	Continent	Europe

[Ref.: #120559]	Sample type/isolated from	Carved stone wall
[Ref.: #120559]	Geographic location (country and/or sea, region)	Rome
[Ref.: #120559]	Country	Italy
[Ref.: #120559]	Country ISO 3 Code	ITA
[Ref.: #120559]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

What are isolation sources categories?

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

[Ref.: #6423]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #120559]	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.: #6423]	Agromyces lapidis 16S ribosomal RNA gene, partial sequence	AY618217	1470	ENA	279574 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Agromyces lapidis JCM 14321	GCA_009749405	contig	GenBank	279574 tax ID
[Ref.: #66792]	Agromyces lapidis strain JCM 14321	279574.3	wgs	PATRIC	279574 tax ID	*

[Ref.: #6423]	GC-content	70.4 mol%
[Ref.: #67770]	GC-content	70.4 mol%	thermal denaturation, midpoint method (Tm)

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 lapidis strain JCM 14321 PATRIC: 279574.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Agromyces lapidis strain JCM 14321 PATRIC: 279574.3
[Ref.: #69480]	motile	no	88.131	no
[Ref.: #69480]	gram-positive	yes	90.631	no
[Ref.: #69480]	anaerobic	no	99.688	yes
[Ref.: #69480]	halophile	no	91.238	no
[Ref.: #69480]	spore-forming	no	88.664	no
[Ref.: #69480]	glucose-util	yes	86.159	no
[Ref.: #69480]	flagellated	no	97.489	yes
[Ref.: #69480]	aerobic	yes	95.762	yes
[Ref.: #69480]	thermophile	no	99.413	no
[Ref.: #69480]	glucose-ferment	no	91.607	no

Availability in culture collections External links

[Ref.: #6423]

Culture collection no.

DSM 16390, NCIMB 14013, HKI 0324, JCM 14321, IAM 15275, CIP 108739

[Ref.: #76725]

SI-ID 137994

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Agromyces agglutinans sp. nov., isolated from saline lake sediment.	Yi BF, Xia TT, Niu MM, Zhao ZY, Su QY, Ming H, Nie GX	Int J Syst Evol Microbiol	10.1099/ijsem.0.005208	2022	*
Phylogeny	Agromyces italicus sp. nov., Agromyces humatus sp. nov. and Agromyces lapidis sp. nov., isolated from Roman catacombs.	Jurado V, Groth I, Gonzalez JM, Laiz L, Schuetze B, Saiz-Jimenez C	Int J Syst Evol Microbiol	10.1099/ijs.0.63414-0	2005	*

References

#6423

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16390

#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 )

#31369

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 #27682 (see below)

#37633 ; 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;

#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 )

#76725

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-ID137994.1 )

#120559 Collection of Institut Pasteur ; Curators of the CIP; CIP 108739

#27682

IJSEM 871 2005 ( DOI 10.1099/ijs.0.63414-0 , PubMed 15774677 )

* These data were automatically processed and therefore are not curated

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Agromyces lapidis strain JCM 14321

Agromyces lapidis strain JCM 14321

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