Strain identifier

BacDive ID: 24768

Type strain: Yes

Species: Christensenella hongkongensis

Strain Designation: HKU 16, HKU16

Strain history: S. K. P. Lau HKU16.

NCBI tax ID(s): 270498 (species)

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General

@ref: 19060

BacDive-ID: 24768

DSM-Number: 18959

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive

description: Christensenella hongkongensis HKU 16 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from patient with intestinal obstruction and secondary sepsis.

NCBI tax id

  • NCBI tax id: 270498
  • Matching level: species

strain history

@refhistory
19060<- S. K. P. Lau, Queen Mary Hospital; HKU 16
67770S. K. P. Lau HKU16.

doi: 10.13145/bacdive24768.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Christensenellaceae
  • genus: Christensenella
  • species: Christensenella hongkongensis
  • full scientific name: Christensenella hongkongensis (Lau et al. 2014) Liu et al. 2021

  • synonyms

    • @ref: 20215
    • synonym: Catabacter hongkongensis

@ref: 19060

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Eubacteriales

family: Christensenellaceae

genus: Christensenella

species: Christensenella hongkongensis

full scientific name: Christensenella hongkongensis (Lau et al. 2014) Liu et al. 2021

strain designation: HKU 16, HKU16

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 99.415

colony morphology

@refincubation period
190602-3 days
601123 days

Culture and growth conditions

culture medium

  • @ref: 19060
  • name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/110
  • composition: Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water

culture temp

@refgrowthtypetemperaturerange
19060positivegrowth37mesophilic
60112positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
19060anaerobe
60112anaerobe
69480anaerobe99.998

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.984

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate+degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase-
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase+4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase-3.2.1.21
68380alpha-glucosidase-3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase-3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
19060------------+----------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
19060patient with intestinal obstruction and secondary sepsisChinaCHNAsia
60112Human blood,48-yr-old man,intestinal obstructionChinaCHNAsiaHongkong
67770Blood cultures of patients with acute gastrointestinal compromises or with acute sepsis

isolation source categories

Cat1Cat2
#Infection#Disease
#Infection#Patient
#Host Body-Site#Gastrointestinal tract

taxonmaps

  • @ref: 69479
  • File name: preview.99_2199.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_294;96_1147;97_1410;98_1716;99_2199&stattab=map
  • Last taxonomy: Catabacter hongkongensis subclade
  • 16S sequence: AY574991
  • Sequence Identity:
  • Total samples: 42934
  • soil counts: 376
  • aquatic counts: 1000
  • animal counts: 41354
  • plant counts: 204

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
19060Catabacter hongkongensis 16S ribosomal RNA gene, partial sequenceAY5749911453ena270498
67770Catabacter hongkongensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 17853AB6717631497ena270498

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Christensenella hongkongensis DSM 18959GCA_004342745scaffoldncbi270498
66792Catabacter hongkongensis strain DSM 18959270498.28wgspatric270498
66792Catabacter honkongensis DSM 189592795385462draftimg270498
67770Christensenella hongkongensis HKU16GCA_000981035contigncbi270498

GC content

@refGC-contentmethod
1906040.2thermal denaturation, midpoint method (Tm)
6777048.53genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno51no
motileyes75.652no
flagellatedno77.096no
gram-positiveyes58.742no
anaerobicyes99.376no
aerobicno97.423yes
halophileno96.745no
spore-formingno71.294no
glucose-utilyes90.451no
thermophileno76.688yes
glucose-fermentyes62.231no

External links

@ref: 19060

culture collection no.: DSM 18959, CCUG 54229, JCM 17853, KCTC 15500

straininfo link

  • @ref: 88594
  • straininfo: 303645

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17122022Catabacter hongkongensis gen. nov., sp. nov., isolated from blood cultures of patients from Hong Kong and Canada.Lau SK, McNabb A, Woo GK, Hoang L, Fung AM, Chung LM, Woo PC, Yuen KYJ Clin Microbiol10.1128/JCM.01831-062006Adult, Aged, Anaerobiosis, Bacteremia/*epidemiology/microbiology, Bacterial Typing Techniques, Base Composition, Blood/microbiology, Canada/epidemiology, Culture Media, Female, Gram-Positive Bacteria/*classification/genetics/*isolation & purification, Gram-Positive Bacterial Infections/*epidemiology/microbiology, Hong Kong/epidemiology, Humans, Male, Middle Aged, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNACultivation
Phylogeny19648349Caldicoprobacter oshimai gen. nov., sp. nov., an anaerobic, xylanolytic, extremely thermophilic bacterium isolated from sheep faeces, and proposal of Caldicoprobacteraceae fam. nov.Yokoyama H, Wagner ID, Wiegel JInt J Syst Evol Microbiol10.1099/ijs.0.011379-02009Anaerobiosis, Animals, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Feces/*microbiology, Gram-Positive Bacteria/*classification/genetics/*isolation & purification/metabolism, Hot Temperature, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sheep, Xylose/metabolismMetabolism
Genetics25999561Draft Genome Sequence of Catabacter hongkongensis Type Strain HKU16T, Isolated from a Patient with Bacteremia and Intestinal Obstruction.Lau SK, Teng JL, Huang Y, Curreem SO, Tsui SK, Woo PCGenome Announc10.1128/genomeA.00531-152015Phylogeny
27830080First case of human bacteraemia by Catabacter hongkongensis in Scandinavia.Kaden R, Thelander M, Engstrand L, Herrmann BNew Microbes New Infect10.1016/j.nmni.2016.09.0152016

Reference

@idauthorscataloguedoi/urltitle
19060Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18959)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18959
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
60112Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 54229)https://www.ccug.se/strain?id=54229
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68380Automatically annotated from API rID32A
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
88594Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID303645.1StrainInfo: A central database for resolving microbial strain identifiers