Name: Hymenobacter perfusus A1-12
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 137418

Type strain:

Species: Hymenobacter perfusus

Strain Designation: A1-12

Culture col. no.: CIP 110166, LMG 26000, UCCCB30

Strain history: CIP <- 2010, P. Morais, IMAR Inst., Coimbra Univ., Coimbra, Portugal: strain A1-12

NCBI tax ID(s): 1236770 (species)

SI-ID 370069

LMG 25858, LMG 26000, CIP 110166, CCM 8560

Section

Hymenobacter perfusus A1-12 is a facultative anaerobe, mesophilic bacterium of the family Hymenobacteraceae.

facultative anaerobe
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	*Bacteroidota*
	Class	*Cytophagia*
	Order	*Cytophagales*
	Family	*Hymenobacteraceae*
	Genus	*Hymenobacter*
	Species	**Hymenobacter perfusus**
	Full Scientific Name (LPSN)	Hymenobacter perfusus Chung et al. 2011

Information on morphological and physiological properties Morphology

[Ref.: #37928]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.979

[Ref.: #37928]	Cell shape	rod-shaped

[Ref.: #37928]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %93.719

Information on culture and growth conditions Culture and growth conditions

[Ref.: #37928]

Culture medium

MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromati

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Culture medium growth

[Ref.: #37928]

Culture medium composition

expand / minimize

[Ref.: #37928]

Culture medium

CIP Medium 566

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Culture medium growth

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Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #37928]	growth	25 °C
[Ref.: #67772]	minimum	4 °C
[Ref.: #67772]	optimum	25 °C

[Ref.: #37928]	Temperature range	mesophilic
[Ref.: #67772]	Temperature range	psychrophilic
[Ref.: #67772]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #67772]			optimum	6.0-6.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #37928]

Oxygen tolerance

facultative anaerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.998

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #37928]		nitrate ChEBI	-	reduction
[Ref.: #37928]		nitrite ChEBI	-	reduction

	Metabolite production	Metabolite	Production
[Ref.: #37928]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[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.: #37928]	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.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #37928]	oxidase	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #37928]	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.: #37928]	12405	-	+	+	+	-	+	+	+	-	-	+	+	-	-	-	+	-	-	-	-

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

[Ref.: #67772]	Sample type/isolated from	Acidic water (pH 6) that came directly from the mine into a water treatment plant
[Ref.: #67772]	Sampling date	2008
[Ref.: #67772]	Geographic location (country and/or sea, region)	Viseu, Urgeiriça
[Ref.: #67772]	Country	Portugal
[Ref.: #67772]	Country ISO 3 Code	PRT
[Ref.: #67772]	Continent	Europe

[Ref.: #37928]	Sample type/isolated from	Mining, uranium
[Ref.: #37928]	Geographic location (country and/or sea, region)	Urgeirica
[Ref.: #37928]	Country	Portugal
[Ref.: #37928]	Country ISO 3 Code	PRT
[Ref.: #37928]	Continent	Europe
[Ref.: #37928]	Isolation date	2008

[Ref.: #37928]	Geographic location (country and/or sea, region)	Urgeirica
[Ref.: #37928]	Country	Portugal
[Ref.: #37928]	Country ISO 3 Code	PRT
[Ref.: #37928]	Continent	Europe
* marker position based on {}

[Ref.: #69479]

Global distribution of 16S sequence HM032896 (>99% sequence identity) for Hymenobacter from Microbeatlas

Aquatic Samples	66
Soil Samples	50
Animal Samples	184
Plant Samples	60
Total Samples	360

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

[Ref.: #67772]	Biosafety level	1
[Ref.: #37928]	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.: #67772]	Hymenobacter perfusus strain A1-12 16S ribosomal RNA gene, partial sequence	HM032896	1492	ENA	1236770 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67772]	Hymenobacter perfusus LMG 26000	GCA_003944765	contig	GenBank	1236770 tax ID
[Ref.: #66792]	Hymenobacter perfusus strain LMG 26000	1236770.3	wgs	PATRIC	1236770 tax ID	*
[Ref.: #66792]	Hymenobacter perfusus LMG 26000	2898455262	draft	JGI IMG/M	1236770 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: Hymenobacter perfusus strain LMG 26000 PATRIC: 1236770.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Hymenobacter perfusus strain LMG 26000 PATRIC: 1236770.3
[Ref.: #69480]	motile	no	93.048	no
[Ref.: #69480]	gram-positive	no	96.974	no
[Ref.: #69480]	anaerobic	no	99.382	no
[Ref.: #69480]	aerobic	yes	91.065	no
[Ref.: #69480]	halophile	no	94.627	no
[Ref.: #69480]	spore-forming	no	93.503	no
[Ref.: #69480]	glucose-util	yes	79.506	no
[Ref.: #69480]	flagellated	no	97.334	no
[Ref.: #69480]	thermophile	no	97.364	yes
[Ref.: #69480]	glucose-ferment	no	88.271	no

Availability in culture collections External links

[Ref.: #37928]

Culture collection no.

CIP 110166, LMG 26000, UCCCB30

[Ref.: #94319]

SI-ID 370069

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Hymenobacter translucens sp. nov. and Hymenobacter pini sp. nov. isolated from soil.	Bang M, Kim MK, Jung HY	Arch Microbiol	10.1007/s00203-022-02991-x	2022	*
Phylogeny	Hymenobacter telluris sp. nov., isolated from soil in South Korea.	Damdintogtokh T, Park Y, Maeng S, Oh HJ, Bang M, Lee YK, Oh J, Bai J, Kim MK	Arch Microbiol	10.1007/s00203-021-02692-x	2022	*
Phylogeny	Hymenobacter guriensis sp. nov., and Hymenobacter duratus sp. nov., Radiation-Resistant Species Isolated from Soil in South Korea.	Damdintogtokh T, Cha IT, Kim MK	Curr Microbiol	10.1007/s00284-021-02517-6	2021	*
Phylogeny	Hymenobacter metallilatus sp. nov., isolated from abandoned lead-zinc ore.	Feng GD, Zhang J, Zhang XJ, Wang SN, Xiong X, Zhang YL, Huang HR, Zhu HH	Int J Syst Evol Microbiol	10.1099/ijsem.0.003450	2019	*
Phylogeny	Hymenobacter tenuis sp. nov., isolated from wastewater of an acidic water neutralization facility.	Kang JW, Lee JH, Choe HN, Seong CN	Int J Syst Evol Microbiol	10.1099/ijsem.0.001918	2017	*
Phylogeny	Hymenobacter swuensis sp. nov., a gamma-radiation-resistant bacteria isolated from mountain soil.	Lee JJ, Srinivasan S, Lim S, Joe M, Lee SH, Kwon SA, Kwon YJ, Lee J, Choi JJ, Lee HM, Auh YK, Kim MK	Curr Microbiol	10.1007/s00284-013-0478-3	2013	*
Phylogeny	Hymenobacter perfusus sp. nov., Hymenobacter flocculans sp. nov. and Hymenobacter metalli sp. nov. three new species isolated from an uranium mine waste water treatment system.	Chung AP, Lopes A, Nobre MF, Morais PV	Syst Appl Microbiol	10.1016/j.syapm.2010.09.002	2010	*

References

#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 )

#37928 Collection of Institut Pasteur ; Curators of the CIP; CIP 110166

#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) .

#67772 The University of Coimbra Bacteria Culture Collection (UCCCB) ; Curators of the UCCCB;

#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 )

#94319

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-ID370069.1 )

* These data were automatically processed and therefore are not curated

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Hymenobacter perfusus strain LMG 26000

Hymenobacter perfusus strain LMG 26000

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