Strain identifier

BacDive ID: 132678

Type strain: Yes

Species: Wukongibacter baidiensis

Strain Designation: DY30321

Strain history: <- G. Li, Third Inst. Oceanography, State Oceanic Administration, Xiamen, China; DY30321 <- X. Zhang and G. Li {2014}

NCBI tax ID(s): 1723361 (species)

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General

@ref: 24467

BacDive-ID: 132678

DSM-Number: 103478

keywords: 16S sequence, Bacteria, anaerobe, spore-forming, Gram-positive, rod-shaped

description: Wukongibacter baidiensis DY30321 is an anaerobe, spore-forming, Gram-positive bacterium that was isolated from mixture of sulfides , grey sediment and black magmatic rock glass at a water depth of 2327 m.

NCBI tax id

  • NCBI tax id: 1723361
  • Matching level: species

strain history

  • @ref: 24467
  • history: <- G. Li, Third Inst. Oceanography, State Oceanic Administration, Xiamen, China; DY30321 <- X. Zhang and G. Li {2014}

doi: 10.13145/bacdive132678.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Peptostreptococcaceae
  • genus: Wukongibacter
  • species: Wukongibacter baidiensis
  • full scientific name: Wukongibacter baidiensis Li et al. 2016

@ref: 24467

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Peptostreptococcaceae

genus: Wukongibacter

species: Wukongibacter baidiensis

full scientific name: Wukongibacter baidiensis Li et al. 2016

strain designation: DY30321

type strain: yes

Morphology

cell morphology

  • @ref: 25020
  • gram stain: positive
  • cell length: 1.6-10.5 µm
  • cell width: 0.4-0.6 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 25020
  • colony size: 5 mm
  • colony color: creamy
  • incubation period: 2 days
  • medium used: YTG agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
25020YTG agaryes
24467PARAMALEDIVIBACTER MEDIUM (DSMZ Medium 986)yeshttps://mediadive.dsmz.de/medium/986Name: PARAMALEDIVIBACTER MEDIUM (DSMZ Medium 986) Composition: Sea Salt 29.97 g/l D-Glucose 3.996 g/l NaHCO3 1.998 g/l NH4Cl 0.999001 g/l Peptone 0.499501 g/l Yeast extract 0.499501 g/l KH2PO4 0.2997 g/l K2HPO4 0.2997 g/l L-Cysteine HCl x H2O 0.24975 g/l Na2S x 9 H2O 0.24975 g/l Sodium resazurin 0.0004995 g/l Pyridoxine hydrochloride 9.99001e-05 g/l Calcium D-(+)-pantothenate 4.995e-05 g/l Thiamine HCl 4.995e-05 g/l Riboflavin 4.995e-05 g/l Nicotinic acid 4.995e-05 g/l (DL)-alpha-Lipoic acid 4.995e-05 g/l p-Aminobenzoic acid 4.995e-05 g/l Folic acid 1.998e-05 g/l Biotin 1.998e-05 g/l Vitamin B12 9.99001e-07 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
25020positivegrowth10-45
25020positiveoptimum30mesophilic
24467positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
25020positivegrowth2.0-10.0alkaliphile
25020positiveoptimum8

Physiology and metabolism

oxygen tolerance

  • @ref: 25020
  • oxygen tolerance: anaerobe

spore formation

  • @ref: 25020
  • spore description: terminal end
  • type of spore: endospore
  • spore formation: yes

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2502022599arabinose-builds acid from
2502022599arabinose-carbon source
2502017057cellobiose-builds acid from
2502017057cellobiose-carbon source
2502015824D-fructose-carbon source
2502016899D-mannitol-carbon source
2502016024D-mannose-carbon source
25020esculin ferric citrate-carbon source
2502017234glucose-builds acid from
2502017754glycerol-builds acid from
2502015978glycerol 3-phosphate-carbon source
2502016857L-threonine-carbon source
2502017716lactose-builds acid from
2502017306maltose-builds acid from
2502029864mannitol-builds acid from
2502037684mannose-builds acid from
250206731melezitose-carbon source
2502028037N-acetylgalactosamine-respiration
2502017814salicin-builds acid from
2502017992sucrose-builds acid from
2502017992sucrose-carbon source
2502027082trehalose-carbon source
2502018222xylose-builds acid from
25020645522-hydroxybutyrate+respiration
25020167632-oxobutanoate+carbon source
25020370543-hydroxybutyrate+respiration
25020370543-hydroxybutyrate+carbon source
2502018024D-galacturonic acid+respiration
2502016024D-mannose+respiration
2502017992sucrose+respiration
250205291gelatin+carbon source
2502017234glucose+builds acid from
2502017234glucose+carbon source
2502018287L-fucose+respiration
2502018287L-fucose+carbon source
2502029985L-glutamate+respiration
2502018050L-glutamine+carbon source
2502062345L-rhamnose+respiration
2502062345L-rhamnose+carbon source
2502051850methyl pyruvate+respiration
2502051850methyl pyruvate+carbon source
2502018394palatinose+respiration
2502018394palatinose+carbon source
2502015361pyruvate+respiration
2502015361pyruvate+carbon source
2502027897tryptophan+energy source

metabolite production

  • @ref: 25020
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

  • @ref: 25020
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
25020beta-glucosidase-3.2.1.21
25020catalase-1.11.1.6
25020gelatinase+
25020tryptophan deaminase+4.1.99.1
25020urease-3.5.1.5

Isolation, sampling and environmental information

isolation

  • @ref: 24467
  • sample type: mixture of sulfides (about 30 %, v/v), grey sediment and black magmatic rock glass at a water depth of 2327 m
  • geographic location: Southwest Indian Ridge, Baidi hydrothermal field
  • country: International waters
  • latitude: -38
  • longitude: 48.15

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Volcanic
#Condition#Sulfuric

taxonmaps

  • @ref: 69479
  • File name: preview.99_66243.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15791;96_25629;97_32147;98_41216;99_66243&stattab=map
  • Last taxonomy: Wukongibacter baidiensis subclade
  • 16S sequence: KT783480
  • Sequence Identity:
  • Total samples: 45
  • soil counts: 1
  • aquatic counts: 44

Safety information

risk assessment

  • @ref: 24467
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24467
  • description: Wukongibacter baidiensis strain DY30321 16S ribosomal RNA gene, partial sequence
  • accession: KT783480
  • length: 1455
  • database: ena
  • NCBI tax ID: 1723361

GC content

@refGC-contentmethod
2502033.4genome sequence analysis
2446733.4sequence analysis

External links

@ref: 24467

culture collection no.: DSM 103478, KCTC 15549, MCCC 1A01532

straininfo link

  • @ref: 90986
  • straininfo: 397428

literature

  • topic: Phylogeny
  • Pubmed-ID: 27473553
  • title: Wukongibacter baidiensis gen. nov., sp. nov., an anaerobic bacterium isolated from hydrothermal sulfides, and proposal for the reclassification of the closely related Clostridium halophilum and Clostridium caminithermale within Maledivibacter gen. nov. and Paramaledivibacter gen. nov., respectively.
  • authors: Li G, Zeng X, Liu X, Zhang X, Shao Z
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001355
  • year: 2016
  • mesh: Bacterial Typing Techniques, Base Composition, Clostridiales/*classification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hydrothermal Vents/*microbiology, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sulfides
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
24467Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103478Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103478)
25020G. Z. Li, X.,Liu, X.,Zhang, X.,Shao, Z.Wukongibacter baidiensis gen. nov., sp. nov., an anaerobic bacterium isolated from hydrothermal sulfides, and proposal for the reclassification of the closely related Clostridium halophilum and Clostridium caminithermale within Maledivibacter gen. nov. and Paramaledivibacter gen. nov., respectively10.1099/ijsem.0.001355IJSEM 66: 4355-4361 201627473553
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
90986Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID397428.1