Hymenobacter perfusus (CIP 110166, LMG 26000, UCCCB30)

Name: Hymenobacter perfusus (CIP 110166, LMG 26000, UCCCB30)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 137418

Type strain

Strain Designation A1-12

Culture col. no. CIP 110166 LMG 26000 UCCCB30 A1-12

NCBI tax ID(s) 1236770

Special Collections CIP UCCCB

History Chung A.P. University of Coimbra CIP <- 2010, P. Morais, IMAR Inst., Coimbra Univ., Coimbra, Portugal: strain A1-12

Links

Hymenobacter perfusus A1-12 is a facultative anaerobe, Gram-negative, rod-shaped bacterium of the family Hymenobacteraceae.

Gram-negative rod-shaped facultative anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 370069

LMG 25858,LMG 26000,CIP 110166,CCM 8560

@ref 20215

Last LPSN update 2026-02-09 11:32:53

Domain Bacteria

Phylum Bacteroidota

Class Cytophagia

Order Cytophagales

Family Hymenobacteraceae

Genus Hymenobacter

Species Hymenobacter perfusus

Full scientific name Hymenobacter perfusus Chung et al. 2011

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
125439	negative		98.2
125438	negative		93.905
37928	negative	rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Growth	Composition	Medium link
37928	MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromati		Distilled water make up to (1000.000 ml);R2A agar (18.200 g)
37928	CIP Medium 566			Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
37928	positive	growth	25
67772	positive	minimum	4
67772	positive	optimum	25

Culture pH

@ref	Ability	Type	PH
67772	positive	optimum	6.0-6.5

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
37928	facultative anaerobe
125439	obligate aerobe	93.7

Spore formation

@ref	Spore formation	Confidence
125439		98

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
37928	17632 ChEBI	nitrate	-	reduction
37928	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
37928	35581 ChEBI	indole

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
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
37928	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
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
37928	oxidase	-
68382	trypsin	-	3.4.21.4	from API zym
37928	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
37928	-	+	+	+	-	+	+	+	-	-	+	+	-	-	-	+	-	-	-	-

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
37928			Urgeirica	Portugal	PRT	Europe
67772	Acidic water (pH 6) that came directly from the mine into a water treatment plant	2008	Viseu, Urgeiriça	Portugal	PRT	Europe
37928	Mining, uranium		Urgeirica	Portugal	PRT	Europe	2008

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
67772	1
37928	1	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67772	ASM394476v1 assembly for Hymenobacter perfusus LMG 26000	contig	GCA_003944765	1236770.3	2898455262	1236770	74.53

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
67772	Hymenobacter perfusus strain A1-12 16S ribosomal RNA gene, partial sequence	HM032896	1492		1236770

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Hymenobacter perfusus LMG 26000
NCBI: GCA_003944765

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.00	no
125439	motility	BacteriaNetⓘ	yes	76.50	no
125439	gram_stain	BacteriaNetⓘ	negative	98.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	93.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Hymenobacter perfusus strain LMG 26000
PATRIC: 1236770.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	93.91	no
125438	anaerobic	anaerobicⓘ	no	98.40	yes
125438	spore-forming	spore-formingⓘ	no	84.38	no
125438	aerobic	aerobicⓘ	yes	84.19	yes
125438	thermophilic	thermophileⓘ	no	95.40	yes
125438	flagellated	motile2+ⓘ	no	87.03	no

Literature

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
#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 .
#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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Hymenobacter perfusus (CIP 110166, LMG 26000, UCCCB30)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Enzymes

API zym

Isolation, sampling and environmental information

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003944765

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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