Strain identifier

BacDive ID: 158732

Type strain: Yes

Species: Hymenobacter profundi

Strain Designation: M2

Strain history: <- Jingjing Sun, Yellow Sea Fisheries Research Institute

NCBI tax ID(s): 1982110 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9.1 (current version):
version 9:
version 8.1:
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 9.1 (current version)

General

@ref: 65482

BacDive-ID: 158732

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped, colony-forming, pigmented

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

NCBI tax id

  • NCBI tax id: 1982110
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Jingjing Sun, Yellow Sea Fisheries Research Institute

doi: 10.13145/bacdive158732.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Hymenobacteraceae
  • genus: Hymenobacter
  • species: Hymenobacter profundi
  • full scientific name: Hymenobacter profundi Sun et al. 2018

@ref: 65482

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Hymenobacteraceae

genus: Hymenobacter

species: Hymenobacter profundi

strain designation: M2

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
65482negative1.2-2.2 µm0.6-1 µmrod-shapedno
67771rod-shapedno
67771negative
69480negative97.482

colony morphology

  • @ref: 65482
  • colony size: 1-2 mm
  • colony color: red
  • colony shape: circular
  • incubation period: 3 days
  • medium used: Reasoner's 2A agar

pigmentation

  • @ref: 65482
  • production: yes
  • color: red

Culture and growth conditions

culture medium

@refnamegrowth
65482Reasoner's 2A agaryes
65482Nutrient agar (NA)yes
65482trypticase soy agaryes
65482LB (Luria-Bertani) MEDIUMyes
65482brain-heart infusion agaryes
654822216E agaryes

culture temp

@refgrowthtypetemperature
65482positivegrowth4-33
65482positiveoptimum25
67771positivegrowth25

culture pH

@refabilitytypepHPH range
65482positivegrowth6-9alkaliphile
65482positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
65482aerobe
67771aerobe

halophily

@refsaltgrowthtested relationconcentration
65482NaClpositivegrowth0-4 %(w/v)
65482NaClpositiveoptimum1 %(w/v)

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6548217234glucose+fermentation
6548217716lactose+fermentation
6548215792malonate+assimilation
6548237684mannose-fermentation
6548217632nitrate+reduction
6548216634raffinose+fermentation
6548253424tween 20-hydrolysis

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.group IDis resistantresistance conc.
65482471744imipenemyesyes1000 µg/mL
6548243968meropenemyesyes1000 µg/mL
654827731ofloxacinyesyes2000 µg/mL
6548263598levofloxacinyesyes2000 µg/mL
654822676amoxicillinyesyes8000 µg/mL11
6548248947clavulanic acidyesyes4000 µg/mL11
6548227902tetracyclineyesyes4000 µg/mL
6548217833gentamicinyesyes4000 µg/mL
6548228971ampicillinyesyes8000 µg/mL
654822676amoxicillinyesyes8000 µg/mL
65482124991cefalotinyesyes8000 µg/mL
65482209807cefoxitinyesyes8000 µg/mL
654829587ticarcillinyesyes16000 µg/mL
654828232piperacillinyesyes16000 µg/mL
654822637amikacinyesyes16000 µg/mL
65482100147nalidixic acidyesyes16000 µg/mL
65482100241ciprofloxacinyesyes1000-2000 µg/mL
65482478164cefepimeyesyes
65482472657cefiximeyesyes1000 µg/mL
65482204928cefotaximeyesyes1000 µg/mL
65482474053cefazolinyesyes2000 µg/mL
65482161680aztreonamyesyes4000 µg/mL
654823508ceftazidimeyesyes4000 µg/mL
6548228864tobramycinyesyes4000 µg/mL

metabolite production

@refChebi-IDmetaboliteproduction
6548216136hydrogen sulfideno
6548235581indoleno

enzymes

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

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationlatitudelongitudeenrichment culture durationenrichment culture temperatureisolation dateisolation procedurecountry
65482a deep-sea water sample of the Mariana Trench (salinity 34.536 ‰ (w/v); temperature 4.794°C) at a depth of 1000 mwestern Pacific Ocean10.9369143.0287 days25September 20was 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.
67771From a deep-sea waterthe Mariana Trench, the western Pacific OceanPacific Ocean

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

Sequence information

16S sequences

  • @ref: 65482
  • description: Hymenobacter profundi strain M2 16S ribosomal RNA gene, partial sequence
  • accession: KY988565
  • database: nuccore

Genome sequences

  • @ref: 66792
  • description: Hymenobacter profundi M2
  • accession: GCA_019334315
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 1982110

GC content

@refGC-contentmethod
6548259.98high performance liquid chromatography (HPLC)
6777159.98

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingno97.482yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.638no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes89.263yes
69480spore-formingspore-formingAbility to form endo- or exosporesno88.167no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno95.225no
69480flagellatedmotile2+Ability to perform flagellated movementno89.25no

External links

@ref: 65482

culture collection no.: CCTCC AB 2017185, KCTC 62120

literature

  • topic: Phylogeny
  • Pubmed-ID: 29458543
  • title: Hymenobacter profundi sp. nov., isolated from deep-sea water.
  • authors: Sun J, Xing M, Wang W, Dai F, Liu J, Hao J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002621
  • year: 2018

Reference

@idauthorstitledoi/urljournalpubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
65482Jingjing Sun, Mengxin Xing, Wei Wang, Fangqun Dai, Junzhong Liu, Jianhua HaoHymenobacter profundi sp. nov., isolated from deep-sea water10.1099/ijsem.0.002621IJSEM 68: 947-950 201829458543
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes