Agromyces italicus (DSM 16388, NCIMB 14011, HKI 0325)

Name: Agromyces italicus (DSM 16388, NCIMB 14011, HKI 0325)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7276

Type strain

Strain Designation CD1

Culture col. no. DSM 16388 NCIMB 14011 HKI 0325 CD1 IAM 15273 2 more

NCBI tax ID(s) 1120959 279572

Special Collections DSMZ JCM Literature strains CIP

History <- I. Groth; HKI 0325 <- Ch. Weigel; CD1 I. Groth CD1 (=HKI 0325) <-- Ch. Weigel. CIP <- 2005, V. Jurado, CSIC, Sevilla, Spain: stain CD1 <- I. Groth, Hans Knöll Inst., Jena, Germany: strain HKI 0325

Links

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

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

Name and taxonomic classification

SI-ID 362278

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

@ref 20215

Last LPSN update 2026-02-09 11:19:26

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Microbacteriaceae

Genus Agromyces

Species Agromyces italicus

Full scientific name Agromyces italicus Jurado et al. 2005

Morphology

Cell morphology

@ref	Gram stain	Cell width	Cell shape	Confidence
31369	positive	0.5 µm	rod-shaped
120290	positive		rod-shaped
125438				94.5
125439	positive			99.2

Colony morphology

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6421	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
6421	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
37634	MEDIUM 56 - for Micromonospora purpurea		Distilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (10.000g);Yeast extract (5.000 g);Starch maize (20.000 g);Calcium carbonate (1.000 g);Casamino acids (5.000 g)
120290	CIP Medium 56	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
6421	positive	growth	28	mesophilic
31369	positive	growth	10-37
31369	positive	optimum	28	mesophilic
37634	positive	growth	30	mesophilic
67770	positive	growth	28	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
31369	positive	optimum	7.25
31369	positive	growth	5-9.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31369	aerobe
120290	obligate aerobe
125439	obligate aerobe	99.1

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31369	NaCl	positive	growth	<4 %
31369	NaCl	positive	optimum	2 %

Murein

@ref	Murein short key	Type
6421	B07	B2gamma {Gly} [L-Dab] D-Glu-D-Dab

Observation

67770

Observationquinones: MK-12, MK-13

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31369	22599 ChEBI	arabinose	+	carbon source
31369	17057 ChEBI	cellobiose	+	carbon source
31369	33984 ChEBI	fucose	+	carbon source
31369	28260 ChEBI	galactose	+	carbon source
31369	5291 ChEBI	gelatin	+	carbon source
31369	17234 ChEBI	glucose	+	carbon source
31369	17754 ChEBI	glycerol	+	carbon source
31369	17716 ChEBI	lactose	+	carbon source
31369	17632 ChEBI	nitrate	+	reduction
120290	17632 ChEBI	nitrate	+	reduction
120290	17632 ChEBI	nitrate	-	respiration
120290	16301 ChEBI	nitrite	-	reduction
31369	17814 ChEBI	salicin	+	carbon source
31369	18222 ChEBI	xylose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
120290	alcohol dehydrogenase	-	1.1.1.1
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
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	+	3.2.1.23	from API zym
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
31369	catalase	+	1.11.1.6
120290	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
31369	cytochrome oxidase	+	1.9.3.1
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
120290	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
120290	ornithine decarboxylase	-	4.1.1.17
120290	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
120290	urease	-	3.5.1.5
68382	valine arylamidase	+		from API zym

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
120290	-	-	+	+	-	+	+	+	-	-	+	+	-	+	-	+	+	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Engineered	#Built environment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
6421	wall of a tomb	Rome, Domitilla Catacombs, Little Apostle cubicle	Italy	ITA	Europe
67770	Wall of a tomb located in the Little Apostle cubicle	Domitilla Catacombs, Rome	Italy	ITA	Europe
120290	Wall of a tomb	Rome	Italy	ITA	Europe

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6421	1	Risk group (German classification) According to TRBA 466
120290	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM42154v1 assembly for Agromyces italicus DSM 16388	contig	GCA_000421545	1120959.3	2524023150	1120959	76.75
67770	ASM974937v1 assembly for Agromyces italicus JCM 14320	contig	GCA_009749375	279572.3	2895207311	279572	73.45

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6421	Agromyces italicus 16S ribosomal RNA gene, partial sequence	AY618215	1429		279572

GC content

@ref	GC-content (mol%)	Method
6421	70.8
67770	70.8	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: Agromyces italicus DSM 16388
NCBI: GCA_000421545

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	70.80	no
125439	motility	BacteriaNetⓘ	no	72.40	no
125439	gram_stain	BacteriaNetⓘ	positive	99.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Agromyces italicus DSM 16388
PATRIC: 1120959.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	89.12	yes
125438	anaerobic	anaerobicⓘ	no	97.45	yes
125438	spore-forming	spore-formingⓘ	no	70.75	no
125438	aerobic	aerobicⓘ	yes	88.75	yes
125438	thermophilic	thermophileⓘ	no	96.38	no
125438	flagellated	motile2+ⓘ	no	94.50	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	Genomic Insights of Cryobacterium Isolated From Ice Core Reveal Genome Dynamics for Adaptation in Glacier.	Liu Y, Shen L, Zeng Y, Xing T, Xu B, Wang N.	Front Microbiol	10.3389/fmicb.2020.01530	2020
	Evaluation of the anti-infective potential of the seed endophytic fungi of Corchorus olitorius through metabolomics and molecular docking approach.	Ahmed AM, Ibrahim AM, Yahia R, Shady NH, Mahmoud BK, Abdelmohsen UR, Fouad MA.	BMC Microbiol	10.1186/s12866-023-03092-5	2023
	Lactonase-mediated inhibition of quorum sensing largely alters phenotypes, proteome, and antimicrobial activities in Burkholderia thailandensis E264.	Gonzales M, Plener L, Armengaud J, Armstrong N, Chabriere E, Daude D.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1190859	2023
Enzymology	Rare bacterium of new genus isolated with prolonged enrichment culture.	Hashizume A, Fudou R, Jojima Y, Nakai R, Hiraishi A, Tabuchi A, Sen K, Shibai H.	Biosci Biotechnol Biochem	10.1271/bbb.68.28	2004
	Antibacterial, antifungal and antioxidant activities of the ethanol extract of the stem bark of Clausena heptaphylla.	Fakruddin M, Mannan KS, Mazumdar RM, Afroz H.	BMC Complement Altern Med	10.1186/1472-6882-12-232	2012
Phylogeny	Agromyces seonyuensis sp. nov., isolated from island soil.	Kim YS, Kim SB.	Int J Syst Evol Microbiol	10.1099/ijsem.0.005689	2023
	Agromyces chromiiresistens sp. nov., Novosphingobium album sp. nov., Sphingobium arseniciresistens sp. nov., Sphingomonas pollutisoli sp. nov., and Salinibacterium metalliresistens sp. nov.: five new members of Microbacteriaceae and Sphingomonadaceae from polluted soil.	Liu ZS, Wang KH, Cai M, Yang ML, Wang XK, Ma HL, Yuan YH, Wu LH, Li DF, Liu SJ.	Front Microbiol	10.3389/fmicb.2023.1289110	2023
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 )
#27682	IJSEM 871 2005 ( DOI 10.1099/ijs.0.63414-0 , PubMed 15774677 )
#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
#37634	; Curators of the CIP;
#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 .
#120290	Collection of Institut Pasteur ; Curators of the CIP; CIP 108740
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#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 italicus (DSM 16388, NCIMB 14011, HKI 0325)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Halophily

Murein

Observation

Metabolite utilization

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000421545

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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