Name: Agromyces italicus CD1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 7276

Type strain:

Species: Agromyces italicus

Strain Designation: CD1

Culture col. no.: DSM 16388, NCIMB 14011, HKI 0325, JCM 14320, IAM 15273, CIP 108740

Strain history: CIP <- 2005, V. Jurado, CSIC, Sevilla, Spain: stain CD1 <- I. Groth, Hans Knöll Inst., Jena, Germany: strain HKI 0325

NCBI tax ID(s): 1120959 (strain), 279572 (species)

SI-ID 362278

DSM 16388, NCIMB 14011, CIP 108740, JCM 14320, IAM 15273

Section

Agromyces italicus CD1 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from wall of a tomb.

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 italicus**
	Full Scientific Name (LPSN)	Agromyces italicus Jurado et al. 2005

Information on morphological and physiological properties Morphology

[Ref.: #31369]	Gram stain	positive
[Ref.: #120290]	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.: #120290]	Cell shape	rod-shaped

[Ref.: #31369]	Motility	no
[Ref.: #120290]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6421]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #6421]

Culture medium growth

[Ref.: #6421]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6421]

Culture medium composition

expand / minimize

[Ref.: #6421]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #6421]

Culture medium growth

[Ref.: #6421]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6421]

Culture medium composition

expand / minimize

[Ref.: #37634]

Culture medium

MEDIUM 56 - for Micromonospora purpurea

[Ref.: #37634]

Culture medium growth

[Ref.: #37634]

Culture medium composition

expand / minimize

[Ref.: #120290]

Culture medium

CIP Medium 56

[Ref.: #120290]

Culture medium growth

[Ref.: #120290]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #6421]	growth	28 °C
[Ref.: #31369]	growth	10-37 °C
[Ref.: #31369]	optimum	28 °C
[Ref.: #37634]	growth	30 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #6421]	Temperature range	mesophilic
[Ref.: #31369]	Temperature range	mesophilic
[Ref.: #37634]	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.: #120290]	Oxygen tolerance	obligate aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.969

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

[Ref.: #6421]	Murein short key	B07
[Ref.: #6421]	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]	gelatin ChEBI	+	carbon source
[Ref.: #31369]	glucose ChEBI	+	carbon source
[Ref.: #31369]	glycerol ChEBI	+	carbon source
[Ref.: #31369]	lactose ChEBI	+	carbon source
[Ref.: #31369]	nitrate ChEBI	+	reduction
[Ref.: #120290]	nitrate ChEBI	+	reduction
[Ref.: #120290]	nitrate ChEBI	-	respiration
[Ref.: #120290]	nitrite ChEBI	-	reduction
[Ref.: #31369]	salicin ChEBI	+	carbon source
[Ref.: #31369]	xylose 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.: #120290]	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.: #120290]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	+	3.4.11.3	* from API zym
[Ref.: #31369]	cytochrome oxidase	+	1.9.3.1
[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.: #120290]	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.: #120290]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #120290]	oxidase	+
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #120290]	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.: #120290]	11426	-	-	+	+	-	+	+	+	-	-	+	+	-	+	-	+	+	-	-	-

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

[Ref.: #6421]	Sample type/isolated from	wall of a tomb
[Ref.: #6421]	Geographic location (country and/or sea, region)	Rome, Domitilla Catacombs, Little Apostle cubicle
[Ref.: #6421]	Country	Italy
[Ref.: #6421]	Country ISO 3 Code	ITA
[Ref.: #6421]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Wall of a tomb located in the Little Apostle cubicle
[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.: #120290]	Sample type/isolated from	Wall of a tomb
[Ref.: #120290]	Geographic location (country and/or sea, region)	Rome
[Ref.: #120290]	Country	Italy
[Ref.: #120290]	Country ISO 3 Code	ITA
[Ref.: #120290]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered

#Built environment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AY618215 (>99% sequence identity) for Agromyces from Microbeatlas

Aquatic Samples	150
Soil Samples	603
Animal Samples	312
Plant Samples	24
Total Samples	1089

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

[Ref.: #6421]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #120290]	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.: #6421]	Agromyces italicus 16S ribosomal RNA gene, partial sequence	AY618215	1429	ENA	279572 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Agromyces italicus DSM 16388	GCA_000421545	contig	GenBank	1120959 tax ID
[Ref.: #67770]	Agromyces italicus JCM 14320	GCA_009749375	contig	GenBank	279572 tax ID
[Ref.: #66792]	Agromyces italicus DSM 16388	1120959.3	wgs	PATRIC	1120959 tax ID	*
[Ref.: #66792]	Agromyces italicus strain JCM 14320	279572.3	wgs	PATRIC	279572 tax ID	*
[Ref.: #66792]	Agromyces italicus JCM 14320	2895207311	draft	JGI IMG/M	279572 tax ID	*
[Ref.: #66792]	Agromyces italicus DSM 16388	2524023150	draft	JGI IMG/M	1120959 tax ID	*

[Ref.: #6421]	GC-content	70.8 mol%
[Ref.: #67770]	GC-content	70.8 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 italicus DSM 16388 PATRIC: 1120959.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Agromyces italicus DSM 16388 PATRIC: 1120959.3
[Ref.: #69480]	motile	no	90.957	yes
[Ref.: #69480]	flagellated	no	97.674	yes
[Ref.: #69480]	gram-positive	yes	93.043	no
[Ref.: #69480]	anaerobic	no	99.693	yes
[Ref.: #69480]	aerobic	yes	95.234	no
[Ref.: #69480]	halophile	no	87.965	no
[Ref.: #69480]	spore-forming	no	90.77	no
[Ref.: #69480]	glucose-util	yes	83.46	yes
[Ref.: #69480]	thermophile	no	98.706	yes
[Ref.: #69480]	glucose-ferment	no	90.039	no

Availability in culture collections External links

[Ref.: #6421]

Culture collection no.

DSM 16388, NCIMB 14011, HKI 0325, JCM 14320, IAM 15273, CIP 108740

[Ref.: #76727]

SI-ID 362278

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

#6421

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16388

#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)

#37634 ; 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 .

#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 )

#76727

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-ID362278.1 )

#120290 Collection of Institut Pasteur ; Curators of the CIP; CIP 108740

#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 italicus DSM 16388

Agromyces italicus DSM 16388

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