Name: Agromyces humatus CD 5
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 7275

Type strain:

Species: Agromyces humatus

Strain Designation: CD 5, CD5

Culture col. no.: DSM 16389, NBRC 109085, NCIMB 14012, HKI 0327, JCM 14319, CIP 108741, IAM 15274

Strain history: CIP <- 2005, V. Jurado, CSIC, Sevilla, Spain: strain CD5 <- I. Groth: strain HKI 0327

NCBI tax ID(s): 279573 (species)

SI-ID 137992

DSM 16389, NCIMB 14012, JCM 14319, CIP 108741, IAM 15274

Section

Agromyces humatus CD 5 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 humatus**
	Full Scientific Name (LPSN)	Agromyces humatus Jurado et al. 2005

Information on morphological and physiological properties Morphology

[Ref.: #31369]	Gram stain	positive
[Ref.: #119981]	Gram stain	positive

[Ref.: #31369]	Cell width	0.4 µm

[Ref.: #31369]	Cell shape	rod-shaped
[Ref.: #119981]	Cell shape	rod-shaped

[Ref.: #31369]	Motility	no
[Ref.: #119981]	Motility	no

[Ref.: #31369]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6422]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #6422]

Culture medium growth

[Ref.: #6422]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6422]

Culture medium composition

expand / minimize

[Ref.: #6422]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #6422]

Culture medium growth

[Ref.: #6422]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6422]

Culture medium composition

expand / minimize

[Ref.: #37635]

Culture medium

MEDIUM 56 - for Micromonospora purpurea

[Ref.: #37635]

Culture medium growth

[Ref.: #37635]

Culture medium composition

expand / minimize

[Ref.: #119981]

Culture medium

CIP Medium 72

[Ref.: #119981]

Culture medium growth

[Ref.: #119981]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #119981]

Culture medium

CIP Medium 56

[Ref.: #119981]

Culture medium growth

[Ref.: #119981]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #6422]	growth	28 °C
[Ref.: #31369]	growth	15-37 °C
[Ref.: #31369]	optimum	28 °C
[Ref.: #37635]	growth	30 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #6422]	Temperature range	mesophilic
[Ref.: #31369]	Temperature range	mesophilic
[Ref.: #37635]	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.: #119981]	Oxygen tolerance	obligate aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31369]		NaCl		growth	<2	%
[Ref.: #31369]		NaCl		optimum	1	%

[Ref.: #6422]	Murein short key	B07
[Ref.: #6422]	Murein types	B2gamma {Gly} [L-Dab] D-Glu-D-Dab

[Ref.: #67770]

Observation

quinones: MK-13, MK-12

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31369]	arabinose 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]	malate ChEBI	+	carbon source
[Ref.: #31369]	mannitol ChEBI	+	carbon source
[Ref.: #31369]	nitrate ChEBI	+	reduction
[Ref.: #119981]	nitrate ChEBI	+	reduction
[Ref.: #119981]	nitrite ChEBI	-	reduction
[Ref.: #31369]	raffinose ChEBI	+	carbon source
[Ref.: #31369]	rhamnose ChEBI	+	carbon source
[Ref.: #31369]	succinate 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.: #119981]	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.: #119981]	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.: #119981]	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.: #119981]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #119981]	oxidase	-
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #119981]	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.: #119981]	11427	-	+	+	+	-	+	+	-	+	-	+	+	+	+	+	+	+	-	+	-

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

[Ref.: #6422]	Sample type/isolated from	wall of a tomb
[Ref.: #6422]	Geographic location (country and/or sea, region)	Rome, Domitilla Catacombs, Little Apostle cubicle
[Ref.: #6422]	Country	Italy
[Ref.: #6422]	Country ISO 3 Code	ITA
[Ref.: #6422]	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.: #119981]	Sample type/isolated from	Wall of a tomb
[Ref.: #119981]	Geographic location (country and/or sea, region)	Rome
[Ref.: #119981]	Country	Italy
[Ref.: #119981]	Country ISO 3 Code	ITA
[Ref.: #119981]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered

#Built environment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AY618216 (>99% sequence identity) for Agromyces from Microbeatlas

Aquatic Samples	192
Soil Samples	3011
Animal Samples	261
Plant Samples	900
Total Samples	4364

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

[Ref.: #6422]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #119981]	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.: #6422]	Agromyces humatus 16S ribosomal RNA gene, partial sequence	AY618216	1388	ENA	279573 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Agromyces humatus JCM 14319	GCA_021228295	contig	GenBank	279573 tax ID	*

[Ref.: #6422]	GC-content	70.6 mol%
[Ref.: #67770]	GC-content	70.6 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 Diaspora project based on: Agromyces humatus JCM 14319 NCBI: GCA_021228295.1
[Ref.: #69480]	flagellated	no	97.897	yes
[Ref.: #69480]	gram-positive	yes	93.941	no
[Ref.: #69480]	anaerobic	no	99.625	yes
[Ref.: #69480]	aerobic	yes	94.121	yes
[Ref.: #69480]	halophile	no	89.379	yes
[Ref.: #69480]	spore-forming	no	91.985	no
[Ref.: #69480]	motile	no	90.594	yes
[Ref.: #69480]	thermophile	no	98.479	yes
[Ref.: #69480]	glucose-util	yes	86.848	no
[Ref.: #69480]	glucose-ferment	no	87.94	no

Availability in culture collections External links

[Ref.: #6422]

Culture collection no.

DSM 16389, NBRC 109085, NCIMB 14012, HKI 0327, JCM 14319, CIP 108741, IAM 15274

[Ref.: #76726]

SI-ID 137992

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Agromyces insulae sp. nov., an actinobacterium isolated from a soil sample.	Huang JR, Ming H, Li S, Meng XL, Zhang JX, Khieu TN, Tang Z, Li WJ, Nie GX	Int J Syst Evol Microbiol	10.1099/ijsem.0.000978	2016	*
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	*
Phylogeny	Agromyces cavernae sp. nov., a novel member of the genus Agromyces isolated from a karstic cave in Shaoguan.	Fang BZ, Gao L, Jiao JY, Zhang ZT, Li MM, Mohamad OAA, Ahmed I, Li L, Liu YH, Li WJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.005503	2022	*

References

#6422

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16389

#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)

#37635 ; 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) .

#76726

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-ID137992.1 )

#119981 Collection of Institut Pasteur ; Curators of the CIP; CIP 108741

#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 humatus JCM 14319

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