Agromyces humatus (DSM 16389, NBRC 109085, NCIMB 14012)

Name: Agromyces humatus (DSM 16389, NBRC 109085, NCIMB 14012)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7275

Type strain

Strain Designation CD 5, CD5

Culture col. no. DSM 16389 NBRC 109085 NCIMB 14012 HKI 0327 CD 5 4 more

NCBI tax ID(s) 279573

Special Collections DSMZ JCM CIP Literature strains

History <- I. Groth; HKI 0327 <- Ch. Weigel; CD 5 I. Groth CD5 (=HKI 0327) <-- Ch. Weigel. CIP <- 2005, V. Jurado, CSIC, Sevilla, Spain: strain CD5 <- I. Groth: strain HKI 0327

Links

Agromyces humatus CD 5 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from wall of a tomb.

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

Name and taxonomic classification

SI-ID 137992

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

@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 humatus

Full scientific name Agromyces humatus Jurado et al. 2005

Morphology

Cell morphology

@ref	Gram stain	Cell width	Cell shape	Confidence
31369	positive	0.4 µm	rod-shaped
119981	positive		rod-shaped
125439	positive			99.3
125438				92.5
125438	positive			92.216

Colony morphology

Pigmentation

31369

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6422	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
6422	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
37635	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)
119981	CIP Medium 72	Medium recipe at CIP
119981	CIP Medium 56	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
6422	positive	growth	28
31369	positive	growth	15-37
31369	positive	optimum	28
37635	positive	growth	30
67770	positive	growth	28

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
119981	obligate aerobe
125439	obligate aerobe	99.7

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31369	NaCl	positive	growth	<2 %
31369	NaCl	positive	optimum	1 %

Murein

@ref	Murein short key	Type
6422	B07	B2gamma {Gly} [L-Dab] D-Glu-D-Dab

Observation

67770

Observationquinones: MK-13, MK-12

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31369	22599 ChEBI	arabinose	+	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	25115 ChEBI	malate	+	carbon source
31369	29864 ChEBI	mannitol	+	carbon source
31369	17632 ChEBI	nitrate	+	reduction
119981	17632 ChEBI	nitrate	+	reduction
119981	16301 ChEBI	nitrite	-	reduction
31369	16634 ChEBI	raffinose	+	carbon source
31369	26546 ChEBI	rhamnose	+	carbon source
31369	30031 ChEBI	succinate	+	carbon source
31369	17992 ChEBI	sucrose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
119981	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
119981	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
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
119981	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
119981	ornithine decarboxylase	-	4.1.1.17
119981	oxidase	-
68382	trypsin	+	3.4.21.4	from API zym
119981	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
119981	-	+	+	+	-	+	+	-	+	-	+	+	+	+	+	+	+	-	+	-

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
6422	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
119981	Wall of a tomb	Rome	Italy	ITA	Europe

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6422	1	Risk group (German classification) According to TRBA 466
119981	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
66792	ASM2122829v1 assembly for Agromyces humatus JCM 14319	contig	GCA_021228295	279573.3	8067983834	279573	68.1
124043	ASM3952969v1 assembly for Agromyces humatus JCM 14319	scaffold	GCA_039529695			279573	52.99

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6422	Agromyces humatus 16S ribosomal RNA gene, partial sequence	AY618216	1388		279573

GC content

@ref	GC-content (mol%)	Method
6422	70.6
67770	70.6	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 humatus JCM 14319
NCBI: GCA_021228295

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	72.20	no
125439	motility	BacteriaNetⓘ	no	66.40	no
125439	gram_stain	BacteriaNetⓘ	positive	99.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Agromyces humatus JCM 14319
NCBI: GCA_021228295.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	92.22	yes
125438	anaerobic	anaerobicⓘ	no	97.56	yes
125438	aerobic	aerobicⓘ	yes	89.21	yes
125438	spore-forming	spore-formingⓘ	no	71.91	no
125438	thermophilic	thermophileⓘ	no	98.00	no
125438	flagellated	motile2+ⓘ	no	92.50	yes

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 )
#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
#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 .
#119981	Collection of Institut Pasteur ; Curators of the CIP; CIP 108741
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 humatus (DSM 16389, NBRC 109085, NCIMB 14012)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

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_021228295

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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