Isoptericola hypogeus (DSM 16849, CIP 108902, HKI 0342)

Name: Isoptericola hypogeus (DSM 16849, CIP 108902, HKI 0342)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 12585

Type strain

Strain Designation CD12E2-119, CD12-119

Culture col. no. DSM 16849 CIP 108902 HKI 0342 NBRC 104396 NCIMB 14033 4 more

NCBI tax ID(s) 300179

Special Collections DSMZ JCM CIP Wink compendium Literature strains

Links

Isoptericola hypogeus CD12E2-119 is a microaerophile, mesophilic, Gram-positive prokaryote that was isolated from Tufa, catacomb Domitilla.

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

Name and taxonomic classification

SI-ID 237171

NBRC 104396,NCIMB 14033,DSM 16849,CIP 108902,JCM 14325,JCM 15589

@ref 20215

Last LPSN update 2025-12-16 09:49:53

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Promicromonosporaceae

Genus Isoptericola

Species Isoptericola hypogeus

Full scientific name Isoptericola hypogeus Groth et al. 2005

Morphology

Cell morphology

@ref	Gram stain	Cell width	Cell shape	Motility
31470	positive	0.9 µm	rod-shaped
120035	positive		rod-shaped

Colony morphology

@ref	Colony color	Incubation period	Medium used
18297	Colorless	10-14 days	ISP 2
18297	Light cadmium yellow	10-14 days	ISP 3
18297	Light cadmium yellow	10-14 days	ISP 4
18297	Light cadmium yellow	10-14 days	ISP 5
18297	Sulfur yellow (1016)	10-14 days	ISP 6
18297	Light cadmium yellow	10-14 days	ISP 7
120035

Multicellular morphology

@ref	Forms multicellular complex	Medium name
18297		ISP 2
18297		ISP 3
18297		ISP 4
18297		ISP 5
18297		ISP 6
18297		ISP 7

Pigmentation

31470

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6633	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
18297	ISP 2		Name: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
18297	ISP 3		Name: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
18297	ISP 4		Name: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
18297	ISP 5		Name: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
18297	ISP 7		Name: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
18297	ISP 6		Name: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
37329	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
6633	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
120035	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
6633	positive	growth	28	mesophilic
18297	positive	optimum	28	mesophilic
31470	positive	growth	10-40
31470	positive	optimum	28	mesophilic
37329	positive	growth	30	mesophilic
67770	positive	growth	28	mesophilic
120035	positive	growth	10-37
120035	negative	growth	41
120035	negative	growth	45

Culture pH

@ref	Ability	Type	PH	PH range
31470	positive	optimum	7.5
31470	positive	growth	06-09	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
31470	microaerophile
120035	obligate aerobe

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31470	NaCl	positive	growth	<10 %
31470	NaCl	positive	optimum	5 %
120035	NaCl	positive	growth	0-10 %

Murein

@ref	Murein short key	Type
6633	A11.33	A4alpha L-Lys-D-Glu

Observation

@ref	Observation
31470	aggregates in clumps
67770	quinones: MK-9(H₂), MK-9, MK-9(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31470	37054 ChEBI	3-hydroxybutyrate	+	carbon source
18297	22599 ChEBI	arabinose	-
18297	62968 ChEBI	cellulose	-
120035	16947 ChEBI	citrate	-	carbon source
68379	4853 ChEBI	esculin	+	hydrolysis	from API Coryne
120035	4853 ChEBI	esculin	+	hydrolysis
18297	28757 ChEBI	fructose	+
68379	5291 ChEBI	gelatin	+	hydrolysis	from API Coryne
18297	17234 ChEBI	glucose	-
120035	606565 ChEBI	hippurate	+	hydrolysis
31470	25115 ChEBI	malate	+	carbon source
18297	29864 ChEBI	mannitol	+
18297	17268 ChEBI	myo-inositol	+
120035	17632 ChEBI	nitrate	+	reduction
120035	17632 ChEBI	nitrate	-	respiration
120035	16301 ChEBI	nitrite	-	reduction
18297	16634 ChEBI	raffinose	-
18297	26546 ChEBI	rhamnose	+
18297	17992 ChEBI	sucrose	+
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
68379	16199 ChEBI	urea	+	hydrolysis	from API Coryne
18297	18222 ChEBI	xylose	-

Metabolite production

@ref	Chebi-ID	Metabolite	Production
120035	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
120035	15688 ChEBI	acetoin	-
120035	17234 ChEBI	glucose		+

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
120035	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68379	alkaline phosphatase	+	3.1.3.1	from API Coryne
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	+	3.2.1.24	from API zym
120035	amylase	+
68382	beta-galactosidase	+	3.2.1.23	from API zym
120035	beta-galactosidase	+	3.2.1.23
68379	beta-galactosidase	+	3.2.1.23	from API Coryne
68382	beta-glucosidase	+	3.2.1.21	from API zym
68379	beta-glucosidase	+	3.2.1.21	from API Coryne
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
120035	caseinase	+	3.4.21.50
120035	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
120035	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
120035	gamma-glutamyltransferase	+	2.3.2.2
120035	gelatinase	+/-
68379	gelatinase	+		from API Coryne
120035	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
120035	lipase	-
68382	lipase (C 14)	-		from API zym
120035	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
120035	ornithine decarboxylase	-	4.1.1.17
120035	oxidase	-
120035	phenylalanine ammonia-lyase	-	4.3.1.24
120035	protease	+
68379	pyrazinamidase	-	3.5.1.B15	from API Coryne
68379	pyrrolidonyl arylamidase	-	3.4.19.3	from API Coryne
68382	trypsin	-	3.4.21.4	from API zym
120035	tryptophan deaminase	-
120035	tween esterase	-
120035	urease	-	3.5.1.5
68379	urease	+	3.5.1.5	from API Coryne

API coryne

@ref	Reduction of nitrateNIT	PYZ	PYRA	PAL	beta GUR	beta GAL	alpha GLU	beta NAG	ESC	URE	GEL	Control fermentationControl	GLU	RIB	XYL	MAN	MAL	LAC	SAC	GLYG	CAT
18297	not determinedn.d.	-	-	+	-	+	+/-	+/-	+	+	+	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	-	not determinedn.d.	not determinedn.d.

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
18297	not determinedn.d.	+	+	+	-	+	+	-	-	+	-	+	+	+	-	+	+	+	+	-
120035	-	+	+	+	-	+	-	-	-	-	-	+	-	+	-	+	+	+	+	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Built environment	-
#Environmental	#Terrestrial	#Geologic

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
6633	Tufa, catacomb Domitilla	Rom	Italy	ITA	Europe
67770	Tufa from a burial chamber in the catacomb of Domitilla	Rome	Italy	ITA	Europe
120035	Tufa, Roman catacomb	Domitilla, Rome	Italy	ITA	Europe

Taxonmaps

69479

Global distribution of 16S sequence AJ854061 (>99% sequence identity) for Isoptericola from Microbeatlas

Aquatic Samples	100
Soil Samples	472
Animal Samples	365
Plant Samples	124
Total Samples	1061

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
18297	1	Risk group (German classification) According to TRBA 466
6633	1	Risk group (German classification) According to TRBA 466
120035	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	NCBI tax ID	Score
124043	ASM3953114v1 assembly for Isoptericola hypogeus JCM 15589	scaffold	GCA_039531145	300179	13.97

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6633	Isoptericola hypogeus 16S rRNA gene, type strain HKI 0342T	AJ854061	1426		300179
124043	Isoptericola hypogeus gene for 16S rRNA, partial sequence, strain: NBRC 104396.	AB489223	1476		300179

GC content

@ref	GC-content (mol%)	Method
6633	73.8
67770	73.8	high performance liquid chromatography (HPLC)

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Succession of lignocellulolytic bacterial consortia bred anaerobically from lake sediment.	Korenblum E, Jimenez DJ, van Elsas JD.	Microb Biotechnol	10.1111/1751-7915.12338	2016
Genetics	(Meta)genomic insights into the pathogenome of Cellulosimicrobium cellulans.	Sharma A, Gilbert JA, Lal R.	Sci Rep	10.1038/srep25527	2016
Phylogeny	Isoptericola luteus sp. nov., a novel yellow bacterium isolated from soil.	Bing H, Ling L, Gu J, Cai Y, Zhang Y, Cui L, Li A, Kong X, Luo Y, Xiang W, Zhao J.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006324	2024
Phylogeny	Isoptericola hypogeus sp. nov., isolated from the Roman catacomb of Domitilla.	Groth I, Schumann P, Schutze B, Gonzalez JM, Laiz L, Saiz-Jimenez C, Stackebrandt E	Int J Syst Evol Microbiol	10.1099/ijs.0.63632-0	2005

References

#6633	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16849
#18297	Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .
#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 )
#27770	IJSEM 1715 2005 ( DOI 10.1099/ijs.0.63632-0 , PubMed 16014507 )
#31470	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 #27770
#37329	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68379	Automatically annotated from API Coryne .
#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 .
#120035	Collection of Institut Pasteur ; Curators of the CIP; CIP 108902
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Isoptericola hypogeus (DSM 16849, CIP 108902, HKI 0342)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Halophily

Murein

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API coryne

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_039531145

16S sequences

GC content

Genome-based predictions

Literature

Literature

References

BacDive

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