Strain identifier

BacDive ID: 10465

Type strain: Yes

Species: Laribacter hongkongensis

Strain Designation: HKU1, HKUI

Strain history: CIP <- 2001, R. Leung, HKU Pasteur Research Centre, Hong Kong, China: strain HKUI

NCBI tax ID(s): 1122157 (strain), 168471 (species)

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General

@ref: 5653

BacDive-ID: 10465

DSM-Number: 14985

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped

description: Laribacter hongkongensis HKU1 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from blood of a patient with empyema.

NCBI tax id

NCBI tax idMatching level
1122157strain
168471species

strain history

@refhistory
5653<- K.-Y. Yuen
336332001, R. Leung, HKU Pasteur Research Centre, Hong kong, China: strain HKUI
119961CIP <- 2001, R. Leung, HKU Pasteur Research Centre, Hong Kong, China: strain HKUI

doi: 10.13145/bacdive10465.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Neisseriales
  • family: Chromobacteriaceae
  • genus: Laribacter
  • species: Laribacter hongkongensis
  • full scientific name: Laribacter hongkongensis Yuen et al. 2002

@ref: 5653

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Neisseriales

family: Chromobacteriaceae

genus: Laribacter

species: Laribacter hongkongensis

full scientific name: Laribacter hongkongensis Yuen et al. 2002

strain designation: HKU1, HKUI

type strain: yes

Morphology

cell morphology

  • @ref: 119961
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 119961

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_14985_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_14985_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_14985_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_14985_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_14985_5.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_14985_6.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5653BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
5653COLUMBIA BLOOD AGAR (DSMZ Medium 429)yeshttps://mediadive.dsmz.de/medium/429Name: COLUMBIA BLOOD AGAR (DSMZ Medium 429) Composition: Horse blood 40.0 g/l Columbia agar base
33633MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
119961CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
5653positivegrowth37mesophilic
33633positivegrowth37
56931positivegrowth37-42
119961positivegrowth30-41
119961nogrowth5psychrophilic
119961nogrowth10psychrophilic
119961nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
56931aerobe
119961facultative anaerobe

halophily

@refsaltgrowthtested relationconcentration
119961NaClpositivegrowth0-2 %
119961NaClnogrowth4 %
119961NaClnogrowth6 %
119961NaClnogrowth8 %
119961NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11996116947citrate-carbon source
11996117632nitrate+reduction
11996116301nitrite-reduction
11996115792malonate-assimilation
11996117632nitrate+respiration

antibiotic resistance

  • @ref: 119961
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 119961
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
119961oxidase+
119961alcohol dehydrogenase+1.1.1.1
119961amylase-
119961caseinase+3.4.21.50
119961catalase+1.11.1.6
119961tween esterase-
119961lecithinase-
119961lipase-
119961lysine decarboxylase-4.1.1.18
119961ornithine decarboxylase-4.1.1.17
119961protease-
119961urease+3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119961--++-+-----+--------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119961+++----+-++++------------------+-----------------+-------------------------+---++-------+-++----+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
5653blood of a patient with empyemaHongkongChinaCHNAsia
56931Human blood,bacteremia,empyema,cirrhotic patientHong KongChinaCHNAsia
119961Human, BloodHong KongChinaCHNAsia2001

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Fluids#Blood
#Infection#Disease
#Infection#Patient

taxonmaps

  • @ref: 69479
  • File name: preview.99_1476.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15355;96_48;97_931;98_1091;99_1476&stattab=map
  • Last taxonomy: Chromobacterium
  • 16S sequence: AB017489
  • Sequence Identity:
  • Total samples: 235
  • soil counts: 15
  • aquatic counts: 118
  • animal counts: 41
  • plant counts: 61

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
56532Risk group (German classification)
1199611Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5653
  • description: Beta proteobacterium MBIC3903 gene for 16S rRNA, partial sequence
  • accession: AB017489
  • length: 1474
  • database: ena
  • NCBI tax ID: 82200

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Laribacter hongkongensis DSM 14985GCA_000423285scaffoldncbi1122157
66792Laribacter hongkongensis DSM 149851122157.5wgspatric1122157
66792Laribacter hongkongensis DSM 149852524023164draftimg1122157

GC content

  • @ref: 5653
  • GC-content: 68±2.43

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes94.198no
flagellatedyes83.837no
gram-positiveno99.088no
anaerobicno85.3no
aerobicyes55.948yes
halophileno92.545no
spore-formingno95.295no
glucose-utilyes60.32no
thermophileno98.78yes
glucose-fermentno87.13no

External links

@ref: 5653

culture collection no.: DSM 14985, LMG 21516, CCUG 45813, CIP 107139

straininfo link

  • @ref: 79742
  • straininfo: 86622

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5653Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14985)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14985
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
33633Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4542
56931Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 45813)https://www.ccug.se/strain?id=45813
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
68382Automatically annotated from API zym
69479João 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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
79742Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID86622.1StrainInfo: A central database for resolving microbial strain identifiers
119961Curators of the CIPCollection of Institut Pasteur (CIP 107139)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107139