Name: Herminiimonas fonticola S-94
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 11304

Type strain:

Species: Herminiimonas fonticola

Strain Designation: S-94

Culture col. no.: CCUG 52513, DSM 18555, CIP 108398, LMG 22527

Strain history: CIP <- 2004, M. Costa, Coimbra Univ., Coimbra, Portugal: strain S-94

NCBI tax ID(s): 303380 (species)

SI-ID 131987

LMG 22527, CIP 108398, CCUG 52513, DSM 18555

Section

Herminiimonas fonticola S-94 is an aerobe, mesophilic, motile bacterium that was isolated from bore hole of mineral water spring.

motile
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	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Oxalobacteraceae*
	Genus	*Herminiimonas*
	Species	**Herminiimonas fonticola**
	Full Scientific Name (LPSN)	Herminiimonas fonticola Fernandes et al. 2005

Information on morphological and physiological properties Morphology

[Ref.: #119418]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %100

[Ref.: #119418]	Cell shape	rod-shaped

[Ref.: #119418]	Motility	no
[Ref.: #69480]	Motility	yes Confidence in %96.94

[Ref.: #59574]

Incubation period

3 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7587]

Culture medium

HETEROTROPHIC MEDIUM H3P (DSMZ Medium 428)

[Ref.: #7587]

Culture medium growth

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Culture medium link

Medium recipe at MediaDive

[Ref.: #7587]

Culture medium composition

expand / minimize

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Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #7587]

Culture medium growth

[Ref.: #7587]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7587]

Culture medium composition

expand / minimize

[Ref.: #33957]

Culture medium

MEDIUM 584 - for Herminiimonas fonticola

[Ref.: #33957]

Culture medium growth

[Ref.: #33957]

Culture medium composition

expand / minimize

[Ref.: #119418]

Culture medium

CIP Medium 584

[Ref.: #119418]

Culture medium growth

[Ref.: #119418]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #7587]	growth	28 °C
[Ref.: #7587]	growth	30 °C
[Ref.: #33957]	growth	30 °C
[Ref.: #59574]	growth	30 °C

[Ref.: #7587]	Temperature range	mesophilic
[Ref.: #33957]	Temperature range	mesophilic
[Ref.: #59574]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #59574]	Oxygen tolerance	aerobe
[Ref.: #119418]	Oxygen tolerance	obligate aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %100

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #119418]		nitrate ChEBI	-	reduction
[Ref.: #119418]		nitrite ChEBI	-	reduction

	Metabolite production	Metabolite	Production
[Ref.: #119418]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[Ref.: #119418]	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.: #119418]	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.: #119418]	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.: #119418]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #119418]	oxidase	+
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #119418]	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.: #119418]	11149	-	-	+	-	-	+	-	-	-	-	-	+	-	-	-	-	-	-	-	-

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

[Ref.: #7587]	Sample type/isolated from	bore hole of mineral water spring
[Ref.: #7587]	Country	Portugal
[Ref.: #7587]	Country ISO 3 Code	PRT
[Ref.: #7587]	Continent	Europe

[Ref.: #59574]	Sample type/isolated from	Water,borehole mineral water
[Ref.: #59574]	Sampling date	1997
[Ref.: #59574]	Geographic location (country and/or sea, region)	Serra da Estrela
[Ref.: #59574]	Country	Portugal
[Ref.: #59574]	Country ISO 3 Code	PRT
[Ref.: #59574]	Continent	Europe

[Ref.: #119418]	Sample type/isolated from	Environment, Mineral water
[Ref.: #119418]	Geographic location (country and/or sea, region)	Serra da Esrela
[Ref.: #119418]	Country	Portugal
[Ref.: #119418]	Country ISO 3 Code	PRT
[Ref.: #119418]	Continent	Europe
[Ref.: #119418]	Isolation date	1997
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Spring

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB512142 (>99% sequence identity) for Herminiimonas fonticola from Microbeatlas

Aquatic Samples	3
Soil Samples
Animal Samples
Plant Samples	1
Total Samples	4

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

[Ref.: #7587]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #119418]	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.: #7587]	Herminiimonas fonticola 16S ribosomal RNA gene, partial sequence	AY676462	1426	ENA	303380 tax ID
[Ref.: #20218]	Herminiimonas fonticola gene for 16S rRNA, partial sequence, strain: da Costa S-94	AB512142	1485	ENA	303380 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Herminiimonas fonticola DSM 18555	GCA_004361795	contig	GenBank	303380 tax ID	*
[Ref.: #66792]	Herminiimonas fonticola S-94	GCA_003293745	contig	GenBank	303380 tax ID	*
[Ref.: #66792]	Herminiimonas fonticola strain DSM 18555	303380.4	wgs	PATRIC	303380 tax ID	*
[Ref.: #66792]	Herminiimonas fonticola DSM 18555	2802429731	draft	JGI IMG/M	303380 tax ID	*

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Herminiimonas fonticola strain DSM 18555 PATRIC: 303380.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Herminiimonas fonticola strain DSM 18555 PATRIC: 303380.4
[Ref.: #69480]	gram-positive	no	98.522	no
[Ref.: #69480]	anaerobic	no	98.725	yes
[Ref.: #69480]	halophile	no	93.88	no
[Ref.: #69480]	spore-forming	no	94.938	no
[Ref.: #69480]	glucose-util	no	76.836	no
[Ref.: #69480]	motile	yes	85.14	no
[Ref.: #69480]	flagellated	yes	66.749	no
[Ref.: #69480]	aerobic	yes	94.282	yes
[Ref.: #69480]	thermophile	no	98.739	yes
[Ref.: #69480]	glucose-ferment	no	92.391	no

Availability in culture collections External links

[Ref.: #7587]

Culture collection no.

CCUG 52513, DSM 18555, CIP 108398, LMG 22527

[Ref.: #80537]

SI-ID 131987

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Herminiimonas contaminans sp. nov., isolated as a contaminant of biopharmaceuticals.	Kampfer P, P Glaeser S, Lodders N, Busse HJ, Falsen E	Int J Syst Evol Microbiol	10.1099/ijs.0.039073-0	2012	*
Phylogeny	Herminiimonas saxobsidens sp. nov., isolated from a lichen-colonized rock.	Lang E, Swiderski J, Stackebrandt E, Schumann P, Sproer C, Sahin N	Int J Syst Evol Microbiol	10.1099/ijs.0.65163-0	2007	*
Phylogeny	Herminiimonas arsenicoxydans sp. nov., a metalloresistant bacterium.	Muller D, Simeonova DD, Riegel P, Mangenot S, Koechler S, Lievremont D, Bertin PN, Lett MC	Int J Syst Evol Microbiol	10.1099/ijs.0.64308-0	2006	*
Phylogeny	Herminiimonas fonticola gen. nov., sp. nov., a Betaproteobacterium isolated from a source of bottled mineral water.	Fernandes C, Rainey FA, Nobre MF, Pinhal I, Folhas F, da Costa MS	Syst Appl Microbiol	10.1016/j.syapm.2005.03.013	2005	*

References

#7587

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18555

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#33957 ; Curators of the CIP;
#59574 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 52513

#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) .

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#80537

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-ID131987.1 )

#119418 Collection of Institut Pasteur ; Curators of the CIP; CIP 108398
* These data were automatically processed and therefore are not curated

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Herminiimonas fonticola strain DSM 18555

Herminiimonas fonticola strain DSM 18555

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