Hymenobacter profundi (CCTCC AB 2017185, KCTC 62120, M2)

Name: Hymenobacter profundi (CCTCC AB 2017185, KCTC 62120, M2)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 158732

Type strain

Strain Designation M2

Culture col. no. CCTCC AB 2017185 KCTC 62120 M2

NCBI tax ID(s) 1982110

Special Collections KCTC Literature strains

Links

Hymenobacter profundi M2 is an aerobe, Gram-negative, rod-shaped prokaryote that forms circular colonies and has a red pigmentation.

Gram-negative rod-shaped colony-forming pigmented aerobe genome sequence 16S sequence

Name and taxonomic classification

SI-ID 288184

KCTC 62120

@ref 20215

Last LPSN update 2025-12-16 10:08:05

Domain Pseudomonadati

Phylum Bacteroidota

Class Cytophagia

Order Cytophagales

Family Hymenobacteraceae

Genus Hymenobacter

Species Hymenobacter profundi

Full scientific name Hymenobacter profundi Sun et al. 2018

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
65482	negative	1.2-2.2 µm	0.6-1 µm	rod-shaped
67771				rod-shaped
67771	negative
125438	negative				97.482

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
65482	1-2 mm	red	circular	3 days	Reasoner's 2A agar

Pigmentation

@ref	Production	Color
65482		red

Culture and growth conditions

Culture medium

@ref	Name	Growth
65482	Reasoner's 2A agar
65482	Nutrient agar (NA)
65482	trypticase soy agar
65482	LB (Luria-Bertani) MEDIUM
65482	brain-heart infusion agar
65482	2216E agar

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
65482	positive	growth	4-33
65482	positive	optimum	25	mesophilic
67771	positive	growth	25	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
65482	positive	optimum	7
65482	positive	growth	6-9	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
65482	aerobe
67771	aerobe

Halophily

@ref	Salt	Growth	Tested relation	Concentration
65482	NaCl	positive	growth	0-4 %(w/v)
65482	NaCl	positive	optimum	1 %(w/v)

Observation

@ref	Observation
65482	major isoprenoid quinone and polar lipid are MK-7 and phosphatidylethanolamine
65482	major polyamine of strain M2 is sym-homospermidine
67771	quinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
65482	17234 ChEBI	glucose	+	fermentation
65482	17716 ChEBI	lactose	+	fermentation
65482	15792 ChEBI	malonate	+	assimilation
65482	37684 ChEBI	mannose	-	fermentation
65482	17632 ChEBI	nitrate	+	reduction
65482	16634 ChEBI	raffinose	+	fermentation
65482	53424 ChEBI	tween 20	-	hydrolysis

Antibiotic resistance

@ref	ChEBI	Group ID	Metabolite	Sensitivity conc.	Resistance conc.
65482	2637		amikacin	16000 µg/mL
65482	2676	11	amoxicillin	8000 µg/mL
65482	2676		amoxicillin	8000 µg/mL
65482	28971		ampicillin	8000 µg/mL
65482	161680		aztreonam		4000 µg/mL
65482	124991		cefalotin	8000 µg/mL
65482	474053		cefazolin		2000 µg/mL
65482	478164		cefepime
65482	472657		cefixime		1000 µg/mL
65482	204928		cefotaxime		1000 µg/mL
65482	209807		cefoxitin	8000 µg/mL
65482	3508		ceftazidime		4000 µg/mL
65482	100241		ciprofloxacin	1000-2000 µg/mL
65482	48947	11	clavulanic acid	4000 µg/mL
65482	17833		gentamicin	4000 µg/mL
65482	471744		imipenem	1000 µg/mL
65482	63598		levofloxacin	2000 µg/mL
65482	43968		meropenem	1000 µg/mL
65482	100147		nalidixic acid	16000 µg/mL
65482	7731		ofloxacin	2000 µg/mL
65482	8232		piperacillin	16000 µg/mL
65482	27902		tetracycline	4000 µg/mL
65482	9587		ticarcillin	16000 µg/mL
65482	28864		tobramycin		4000 µg/mL

Metabolite production

@ref	Chebi-ID	Metabolite	Production
65482	16136 ChEBI	hydrogen sulfide
65482	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
65482	acid phosphatase	+	3.1.3.2
65482	alkaline phosphatase	+	3.1.3.1
65482	alpha-chymotrypsin	-	3.4.21.1
65482	alpha-fucosidase	-	3.2.1.51
65482	alpha-galactosidase	+	3.2.1.22
65482	alpha-glucosidase	+	3.2.1.20
65482	alpha-mannosidase	+	3.2.1.24
65482	beta-galactosidase	+	3.2.1.23
65482	beta-glucosidase	+	3.2.1.21
65482	beta-glucuronidase	-	3.2.1.31
65482	catalase	+	1.11.1.6
65482	cystine arylamidase	+	3.4.11.3
65482	cytochrome oxidase	-	1.9.3.1
65482	esterase (C 4)	+
65482	esterase Lipase (C 8)	+
65482	leucine arylamidase	+	3.4.11.1
65482	lipase (C 14)	-
65482	lysine decarboxylase	+	4.1.1.18
65482	N-acetyl-beta-glucosaminidase	+	3.2.1.52
65482	naphthol-AS-BI-phosphohydrolase	+
65482	ornithine decarboxylase	-	4.1.1.17
65482	trypsin	-	3.4.21.4
65482	valine arylamidase	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Geographic location	Latitude	Longitude	Enrichment culture duration	Enrichment culture temperature	Isolation date	Isolation procedure	Country
65482	a deep-sea water sample of the Mariana Trench (salinity 34.536 ‰ (w/v); temperature 4.794°C) at a depth of 1000 m	western Pacific Ocean	10.9369	143.028 10.9369/143.028	7 days	25	September 20	was isolated by the standard dilution-plating method on R2A agar (Difco) aerobically at 25°C for 7 days. The purification procedure was repeated three times.
67771	From a deep-sea water	the Mariana Trench, the western Pacific Ocean							Pacific Ocean

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1933431v1 assembly for Hymenobacter profundi M2	contig	GCA_019334315	1982110.3	8068743237	1982110	28.63

16S sequences

@ref	Description	Accession	Database
65482	Hymenobacter profundi strain M2 16S ribosomal RNA gene, partial sequence	KY988565

GC content

@ref	GC-content (mol%)	Method
65482	59.98	high performance liquid chromatography (HPLC)
67771	59.98

Genome-based predictions

Predictions

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Hymenobacter profundi M2
NCBI: GCA_019334315.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.48	yes
125438	anaerobic	anaerobicⓘ	no	96.64	no
125438	aerobic	aerobicⓘ	yes	89.26	yes
125438	spore-forming	spore-formingⓘ	no	88.17	no
125438	thermophilic	thermophileⓘ	no	95.23	no
125438	flagellated	motile2+ⓘ	no	89.25	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Hymenobacter citatus sp. nov., isolated from soil in South Korea.	Park Y, Chang Y, Kim MK.	Arch Microbiol	10.1007/s00203-021-02298-3	2021
Phylogeny	Hymenobacter profundi sp. nov., isolated from deep-sea water.	Sun J, Xing M, Wang W, Dai F, Liu J, Hao J	Int J Syst Evol Microbiol	10.1099/ijsem.0.002621	2018

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 )
#65482	Jingjing Sun, Mengxin Xing, Wei Wang, Fangqun Dai, Junzhong Liu, Jianhua Hao: Hymenobacter profundi sp. nov., isolated from deep-sea water. IJSEM 68: 947 - 950 2018 ( DOI 10.1099/ijsem.0.002621 , PubMed 29458543 )
#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) .
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 )
#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 profundi (CCTCC AB 2017185, KCTC 62120, M2)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Halophily

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_019334315

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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