Calidifontibacter indicus (DSM 22967, JCM 16038, MTCC 8338)

Name: Calidifontibacter indicus (DSM 22967, JCM 16038, MTCC 8338)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 3934

Type strain

Strain Designation PC IW-02, PC IW02

Culture col. no. DSM 22967 JCM 16038 MTCC 8338 NBRC 109629 PC IW-02 1 more

NCBI tax ID(s) 419650

Special Collections DSMZ JCM Wink compendium

Links

Calidifontibacter indicus PC IW-02 is a mesophilic prokaryote that has a Sand yellow pigmentation and was isolated from warm spring water.

pigmented mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 288188

MTCC 8338,JCM 16038

@ref 20215

Last LPSN update 2025-12-16 09:47:41

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Dermacoccaceae

Genus Calidifontibacter

Species Calidifontibacter indicus

Full scientific name Calidifontibacter indicus Ruckmani et al. 2011

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	positive	99.3
125438		93
125438	positive	93.344

Colony morphology

@ref	Colony color	Medium used
69216	Ivory (1014)	ISP 4
69216	Ivory (1014)	ISP 5
69216	Ivory (1014)	suter without tyrosine
69216	Ivory (1014), sand yellow (1002)	ISP 2
69216	Light ivory (1015), sand yellow (1002)	ISP 7
69216	Sand yellow (1002)	ISP 3
69216	Sand yellow (1002)	ISP 6
69216	Sand yellow (1002)	suter with tyrosine

Multicellular morphology

@ref	Complex name	Medium name
69216	Aerial mycelium	suter without tyrosine
69216	Aerial mycelium	suter with tyrosine
69216	Aerial mycelium	ISP 4
69216	Aerial mycelium	ISP 3
69216	Aerial mycelium	ISP 2
69216	Aerial mycelium	ISP 7
69216	Aerial mycelium	ISP 6
69216	Aerial mycelium	ISP 5

Pigmentation

@ref	Production	Color	Name
69216		Sand yellow (1002)	soluble pigment

Multimedia

@ref:	69216
multimedia content:	DSM_22967_image5.jpeg
multimedia.multimedia content:	DSM_22967_image5.jpeg
caption:	(ISP6, SSM+T, SSM-T)
intellectual property rights:	Helmholtz-Zentrum für Infektionsforschung GmbH
manual_annotation:	1

@ref:	69216
multimedia content:	DSM_22967_image6.jpeg
multimedia.multimedia content:	DSM_22967_image6.jpeg
caption:	(ISP6, SSM+T, SSM-T)
intellectual property rights:	Helmholtz-Zentrum für Infektionsforschung GmbH
manual_annotation:	1

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
67770	positive	growth	28	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.5

Halophily

@ref	Salt	Growth	Tested relation	Concentration
69216	NaCl	positive	growth	0-7.5 %

Observation

67770

Observationquinones: MK-8(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
69216	22599 ChEBI	arabinose	-	growth
69216	62968 ChEBI	cellulose	-	growth
68379	17634 ChEBI	D-glucose	-	fermentation	from API Coryne
68379	16899 ChEBI	D-mannitol	-	fermentation	from API Coryne
68379	16988 ChEBI	D-ribose	-	fermentation	from API Coryne
68379	65327 ChEBI	D-xylose	-	fermentation	from API Coryne
68379	4853 ChEBI	esculin	-	hydrolysis	from API Coryne
69216	28757 ChEBI	fructose	+	growth
68379	5291 ChEBI	gelatin	-	hydrolysis	from API Coryne
69216	17234 ChEBI	glucose	+	growth
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
69216	17268 ChEBI	inositol	+/-	growth
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
69216	37684 ChEBI	mannose	-	growth
68379	17632 ChEBI	nitrate	-	reduction	from API Coryne
69216	16634 ChEBI	raffinose	-	growth
69216	26546 ChEBI	rhamnose	-	growth
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
69216	17992 ChEBI	sucrose	+	growth
68379	16199 ChEBI	urea	+	hydrolysis	from API Coryne
69216	18222 ChEBI	xylose	-	growth

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68379	alkaline phosphatase	+	3.1.3.1	from API Coryne
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
68379	alpha-glucosidase	-	3.2.1.20	from API Coryne
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
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
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68379	gelatinase	-		from API Coryne
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68379	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API Coryne
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
68379	urease	+	3.5.1.5	from API Coryne

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	palmitate biosynthesis	100	22 of 22
66794	methylglyoxal degradation	100	5 of 5
66794	ppGpp biosynthesis	100	4 of 4
66794	lipoate biosynthesis	100	5 of 5
66794	phenylmercury acetate degradation	100	2 of 2
66794	acetate fermentation	100	4 of 4
66794	starch degradation	100	10 of 10
66794	glycogen metabolism	100	5 of 5
66794	biotin biosynthesis	100	4 of 4
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	adipate degradation	100	2 of 2
66794	threonine metabolism	100	10 of 10
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	suberin monomers biosynthesis	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	phenylalanine metabolism	92.31	12 of 13
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	allantoin degradation	88.89	8 of 9
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	heme metabolism	85.71	12 of 14
66794	photosynthesis	85.71	12 of 14
66794	vitamin B12 metabolism	85.29	29 of 34
66794	vitamin B1 metabolism	84.62	11 of 13
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	pentose phosphate pathway	81.82	9 of 11
66794	factor 420 biosynthesis	80	4 of 5
66794	vitamin K metabolism	80	4 of 5
66794	flavin biosynthesis	80	12 of 15
66794	peptidoglycan biosynthesis	80	12 of 15
66794	myo-inositol biosynthesis	80	8 of 10
66794	serine metabolism	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	purine metabolism	77.66	73 of 94
66794	leucine metabolism	76.92	10 of 13
66794	glycolysis	76.47	13 of 17
66794	histidine metabolism	75.86	22 of 29
66794	alanine metabolism	75.86	22 of 29
66794	glycogen biosynthesis	75	3 of 4
66794	gluconeogenesis	75	6 of 8
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	butanoate fermentation	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	pyrimidine metabolism	73.33	33 of 45
66794	proline metabolism	72.73	8 of 11
66794	citric acid cycle	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	propionate fermentation	70	7 of 10
66794	cysteine metabolism	66.67	12 of 18
66794	d-mannose degradation	66.67	6 of 9
66794	enterobactin biosynthesis	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	octane oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	lipid metabolism	64.52	20 of 31
66794	tyrosine metabolism	64.29	9 of 14
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	glutathione metabolism	64.29	9 of 14
66794	tryptophan metabolism	63.16	24 of 38
66794	non-pathway related	63.16	24 of 38
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	ketogluconate metabolism	62.5	5 of 8
66794	methionine metabolism	61.54	16 of 26
66794	urea cycle	61.54	8 of 13
66794	cellulose degradation	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	lysine metabolism	57.14	24 of 42
66794	propanol degradation	57.14	4 of 7
66794	oxidative phosphorylation	57.14	52 of 91
66794	metabolism of disaccharids	54.55	6 of 11
66794	carotenoid biosynthesis	54.55	12 of 22
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	Entner Doudoroff pathway	50	5 of 10
66794	kanosamine biosynthesis II	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	coenzyme M biosynthesis	50	5 of 10
66794	pantothenate biosynthesis	50	3 of 6
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	androgen and estrogen metabolism	50	8 of 16
66794	CMP-KDO biosynthesis	50	2 of 4
66794	arginine metabolism	50	12 of 24
66794	toluene degradation	50	2 of 4
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	ethanol fermentation	50	1 of 2
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	sulfate reduction	46.15	6 of 13
66794	vitamin B6 metabolism	45.45	5 of 11
66794	d-xylose degradation	45.45	5 of 11
66794	lipid A biosynthesis	44.44	4 of 9
66794	nitrate assimilation	44.44	4 of 9
66794	polyamine pathway	43.48	10 of 23
66794	bacilysin biosynthesis	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	chlorophyll metabolism	38.89	7 of 18
66794	degradation of sugar alcohols	37.5	6 of 16
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	methane metabolism	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	ascorbate metabolism	31.82	7 of 22
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	degradation of pentoses	28.57	8 of 28
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	degradation of hexoses	27.78	5 of 18
66794	arachidonic acid metabolism	27.78	5 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	cholesterol biosynthesis	27.27	3 of 11
66794	lactate fermentation	25	1 of 4
66794	phenol degradation	25	5 of 20
66794	catecholamine biosynthesis	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	4-hydroxymandelate degradation	22.22	2 of 9

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
69216	-	-	-	+	-	-	-	-	-	+	-	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
69216	not determinedn.d.	+	+	+/-	-	+	+/-	-	-	-	+	+/-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Thermal spring

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
16563	warm spring water	Western Ghats (N 12.77° E 75.22°)	India	IND	Asia	12.77	75.22 12.77/75.22
67770	Warm spring of Western Ghats		India	IND	Asia

Taxonmaps

69479

Global distribution of 16S sequence EF187228 (>99% sequence identity) for Calidifontibacter indicus subclade from Microbeatlas

Aquatic Samples	118
Soil Samples	138
Animal Samples	797
Plant Samples	36
Total Samples	1089

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16563	1	Risk group (German 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	ASM338686v1 assembly for Calidifontibacter indicus DSM 22967	contig	GCA_003386865	419650.3	2778260926	419650	75.02

Genome browser: GCA_003386865

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16563	Calidifontibacter indicus strain PC IW02 16S ribosomal RNA gene, partial sequence	EF187228	1400		419650

GC content

16563

GC-content (mol%)77

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Calidifontibacter indicus DSM 22967
NCBI: GCA_003386865

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	50.00	no
125439	motility	BacteriaNetⓘ	no	79.80	no
125439	gram_stain	BacteriaNetⓘ	positive	99.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Calidifontibacter indicus strain DSM 22967
PATRIC: 419650.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	93.34	no
125438	anaerobic	anaerobicⓘ	no	97.38	no
125438	spore-forming	spore-formingⓘ	no	72.94	no
125438	aerobic	aerobicⓘ	yes	87.98	no
125438	thermophilic	thermophileⓘ	no	96.00	yes
125438	flagellated	motile2+ⓘ	no	93.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Allobranchiibius huperziae gen. nov., sp. nov., a member of Dermacoccaceae isolated from the root of a medicinal plant Huperzia serrata (Thunb.).	Ai MJ, Sun Y, Sun HM, Liu HY, Yu LY, Zhang YQ	Int J Syst Evol Microbiol	10.1099/ijsem.0.002284	2017
Phylogeny	Calidifontibacter terrae sp. nov., an actinomycete isolated from soil, with potential applications in cosmetics.	Dahal RH, Shim DS, Kim JY, Kim J	Int J Syst Evol Microbiol	10.1099/ijsem.0.001893	2017
Phylogeny	Calidifontibacter indicus gen. nov., sp. nov., a member of the family Dermacoccaceae isolated from a hot spring, and emended description of the family Dermacoccaceae.	Ruckmani A, Kaur I, Schumann P, Klenk HP, Mayilraj S	Int J Syst Evol Microbiol	10.1099/ijs.0.025593-0	2010

References

#16563	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22967
#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 )
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68379	Automatically annotated from API Coryne .
#68382	Automatically annotated from API zym .
#69216	Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .
#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 .
#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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Calidifontibacter indicus (DSM 22967, JCM 16038, MTCC 8338)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture temp

Physiology and metabolism

Oxygen tolerance

Halophily

Observation

Metabolite utilization

Enzymes

Pathway annotation

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_003386865

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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