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BacDive ID 132547
Type strain
Strain Designation BZ-SZ-XJ18
Culture col. no. DSM 29145 JCM 30195 BZ-SZ-XJ18
NCBI tax ID(s) 1548213
Links
For citation purpose refer to the digital object identifier (doi) of the current version.

Archive

version 10 (current version):
version 10 (current version)

General

@ref: 24336

BacDive-ID: 132547

DSM-Number: 29145

keywords: genome sequence, 16S sequence, obligate aerobe, slightly halophilic, Gram-positive, motile, rod-shaped, colony-forming

description: Alkalicoccus urumqiensis BZ-SZ-XJ18 is an obligate aerobe, slightly halophilic, Gram-positive prokaryote that forms circular colonies and was isolated from saline-alkaline lake, mixture of water and sediment .

NCBI tax id

  • NCBI tax id: 1548213
  • Matching level: species

strain history

@refhistory
24336<- B. Zhao, Graduate School, CAS, Beijing, China; BZ-SZ-XJ18 <- B. Zhao
67770B. Zhao; Grad. Sch. of Chin. Acad. of Agric. Sci., China; BZ-SZ-XJ18.

doi: 10.13145/bacdive132547.20251217.10

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: kingdom/bacillati
  • keyword: phylum/bacillota
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Alkalicoccus
  • species: Alkalicoccus urumqiensis
  • full scientific name: Alkalicoccus urumqiensis (Zhang et al. 2016) Gupta et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Bacillus urumqiensis

@ref: 24336

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Alkalicoccus

species: Alkalicoccus urumqiensis

full scientific name: Alkalicoccus urumqiensis (Zhang et al. 2016) Gupta et al. 2020

strain designation: BZ-SZ-XJ18

type strain: yes

Morphology

cell morphology

  • @ref: 43633
  • gram stain: positive
  • cell length: 1.2-2.1 µm
  • cell width: 0.6-0.7 µm
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 43633
  • colony size: 1-2 mm
  • colony color: Yellow
  • colony shape: circular
  • incubation period: 2-3 days
  • medium used: Modified solid medium plates

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43633Modified solid medium platesyes
24336BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514; with strain-specific modifications) Composition: NaCl 60.0 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@refgrowthtypetemperature
43633positivegrowth8-41
43633positiveoptimum37
24336positivegrowth35
67770positivegrowth35

culture pH

@refabilitytypepHPH range
43633positivegrowth6.5-10alkaliphile
43633positiveoptimum8.5-9.5

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
43633obligate aerobe
125439aerobe93.9

spore formation

@reftype of sporespore formationconfidence
43633endosporeno
125439yes91.4

halophily

@refhalophily levelsaltgrowthtested relationconcentration
43633slightly halophilicNaClpositivegrowth1.3-25.3 %(w/v)
43633moderately halophilicNaClpositiveoptimum6.3 %(w/v)

observation

  • @ref: 67770
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4363312936D-galactose-builds acid from
4363330849L-arabinose-builds acid from
4363362345L-rhamnose-builds acid from
4363330849L-arabinose-carbon source
4363363154N-acetyl-beta-D-mannosamine-carbon source
4363328037N-acetylgalactosamine-carbon source
43633506227N-acetylglucosamine-carbon source
4363318186tyrosine-degradation
4363330849L-arabinose-energy source
4363363154N-acetyl-beta-D-mannosamine-energy source
4363328037N-acetylgalactosamine-energy source
43633506227N-acetylglucosamine-energy source
4363317234glucose-fermentation
4363329806fumarate-growth
43633manganese dioxide-growth
4363363005sodium nitrate-growth
4363378870sodium nitrite-growth
43633132112sodium thiosulfate-growth
43633606565hippurate-hydrolysis
4363353424tween 20-hydrolysis
4363353426tween 80-hydrolysis
4363363154N-acetyl-beta-D-mannosamine-nitrogen source
4363328037N-acetylgalactosamine-nitrogen source
43633506227N-acetylglucosamine-nitrogen source
4363317632nitrate-reduction
4363316301nitrite-reduction
4363317925alpha-D-glucose+builds acid from
4363336219alpha-lactose+builds acid from
4363317057cellobiose+builds acid from
4363315824D-fructose+builds acid from
4363328847D-fucose+builds acid from
4363317306maltose+builds acid from
4363316024D-mannose+builds acid from
436336731melezitose+builds acid from
4363316634raffinose+builds acid from
4363316988D-ribose+builds acid from
4363365327D-xylose+builds acid from
4363317992sucrose+builds acid from
4363317925alpha-D-glucose+carbon source
4363336219alpha-lactose+carbon source
4363317057cellobiose+carbon source
4363315824D-fructose+carbon source
4363328847D-fucose+carbon source
4363312936D-galactose+carbon source
4363317306maltose+carbon source
4363316024D-mannose+carbon source
436336731melezitose+carbon source
4363316634raffinose+carbon source
4363316988D-ribose+carbon source
4363316523D-serine+carbon source
4363365327D-xylose+carbon source
4363316865gamma-aminobutyric acid+carbon source
4363332323glucuronamide+carbon source
4363370744glycine-proline+carbon source
4363316977L-alanine+carbon source
4363316467L-arginine+carbon source
4363329991L-aspartate+carbon source
4363329985L-glutamate+carbon source
4363315971L-histidine+carbon source
4363318183L-pyroglutamic acid+carbon source
4363362345L-rhamnose+carbon source
4363317115L-serine+carbon source
4363317992sucrose+carbon source
4363317925alpha-D-glucose+energy source
4363336219alpha-lactose+energy source
4363317057cellobiose+energy source
4363315824D-fructose+energy source
4363328847D-fucose+energy source
4363312936D-galactose+energy source
4363317306maltose+energy source
4363316024D-mannose+energy source
436336731melezitose+energy source
4363316634raffinose+energy source
4363316988D-ribose+energy source
4363316523D-serine+energy source
4363365327D-xylose+energy source
4363316865gamma-aminobutyric acid+energy source
4363332323glucuronamide+energy source
4363370744glycine-proline+energy source
4363316977L-alanine+energy source
4363316467L-arginine+energy source
4363329991L-aspartate+energy source
4363329985L-glutamate+energy source
4363315971L-histidine+energy source
4363318183L-pyroglutamic acid+energy source
4363362345L-rhamnose+energy source
4363317115L-serine+energy source
4363317992sucrose+energy source
43633casein+hydrolysis
436335291gelatin+hydrolysis
4363328017starch+hydrolysis
4363316523D-serine+nitrogen source
4363316865gamma-aminobutyric acid+nitrogen source
4363332323glucuronamide+nitrogen source
4363370744glycine-proline+nitrogen source
4363316977L-alanine+nitrogen source
4363316467L-arginine+nitrogen source
4363329991L-aspartate+nitrogen source
4363329985L-glutamate+nitrogen source
4363315971L-histidine+nitrogen source
4363318183L-pyroglutamic acid+nitrogen source
4363317115L-serine+nitrogen source

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
43633124991cefalotinyesyes30 µg (disc)
43633209807cefoxitinyesyes30 µg (disc)
4363317698chloramphenicolyesyes30 µg (disc)
436333732clarithromycinyesyes15 µg (disc)
436333745clindamycinyesyes2 µg (disc)
4363348923erythromycinyesyes15 µg (disc)
4363328077rifampicinyesyes30 µg (disc)
436339332sulfamethoxazoleyesyes300 µg (disc)
4363328001vancomycinyesyes30 µg (disc)
436338309polymyxin byesyes300 Unit (disc)
436332676amoxicillinyesyes10 µg (disc)
4363328971ampicillinyesyes50 µg (disc)
436333393carbenicillinyesyes100 µg (disc)
43633204928cefotaximeyesyes30 µg (disc)
4363317833gentamicinyesyes10 µg (disc)
436336104kanamycinyesyes50 µg (disc)
43633100147nalidixic acidyesyes30 µg (disc)
436337507neomycinyesyes30 µg (disc)
4363317076streptomycinyesyes300 µg (disc)
4363327902tetracyclineyesyes30 µg (disc)
4363317334penicillinyesyes10 Unit (disc)

metabolite production

@refChebi-IDmetaboliteproduction
4363316136hydrogen sulfideno
4363335581indoleno
4363315688acetoinyes

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-test
4363317234glucose-
4363315688acetoin+

enzymes

@refvalueactivityec
43633catalase+1.11.1.6
43633cytochrome oxidase+1.9.3.1
43633lysine decarboxylase+4.1.1.18
43633ornithine decarboxylase+4.1.1.17
43633arginine decarboxylase-4.1.1.19

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
24336saline-alkaline lake, mixture of water and sediment (43° 24' 35'' N, 88° 6' 39'' E, 1072 m elevation)Xinjiang Uyghur Autonomous Region, close to Urumqi cityChinaCHNAsia43.409788.1108
43633a mixture of water and sediment of a saline-alkaline lake close to Urumqi CityUrumqi City, Xinjiang Uyghur Autonomous Region of ChinaChinaCHNAsia43.40988.11
67770Mixed water and sediment of a saline-alkaline lakeXinjiang Uyghur Autonomous RegionChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Sediment
#Condition#Alkaline
#Condition#Saline
#Environmental#Aquatic#Lake (large)
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_44063.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_7678;97_25222;98_31979;99_44063&stattab=map
  • Last taxonomy: Bacillaceae
  • 16S sequence: KM066107
  • Sequence Identity:
  • Total samples: 46
  • soil counts: 2
  • aquatic counts: 11
  • animal counts: 33

Interaction and safety

risk assessment

  • @ref: 24336
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

Genome sequences

  • @ref: 67770
  • description: ASM299333v1 assembly for Alkalicoccus urumqiensis BZ-SZ-XJ18
  • assembly level: scaffold
  • INSDC accession: GCA_002993335
  • BV-BRC accession: 1548213.3
  • IMG accession: 8022824719
  • NCBI tax ID: 1548213
  • score: 70.79

16S sequences

  • @ref: 24336
  • description: Alkalicoccus urumqiensis strain BZ-SZ-XJ18 16S ribosomal RNA gene, partial sequence
  • accession: KM066107
  • length: 1530
  • database: nuccore
  • NCBI tax ID: 1548213

GC content

@refGC-contentmethod
4363341.4thermal denaturation, midpoint method (Tm)
2433642.3high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes81.009yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.61yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes80.547yes
125438spore-formingspore-formingAbility to form endo- or exosporesyes54.432yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno89.701no
125438motile2+flagellatedAbility to perform flagellated movementyes81.786no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes91.4
125439BacteriaNetmotilityAbility to perform movementyes89.5
125439BacteriaNetgram_stainReaction to gram-stainingvariable89.6
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe93.9

Literature

@ref: 24336

culture collection no.: DSM 29145, JCM 30195

straininfo link

  • @ref: 126262
  • straininfo: 404443

literature

  • topic: Genetics
  • Pubmed-ID: 29853504
  • title: Draft Genome Sequence of Bacillus urumqiensis BZ-SZ-XJ18(T), a Moderately Haloalkaliphilic Bacterium Isolated from a Saline-Alkaline Lake.
  • authors: Liao Z, Ren C, Guo X, Yan Y, Li J, Zhao B
  • journal: Genome Announc
  • DOI: 10.1128/genomeA.00460-18
  • year: 2018
  • topic2: Phylogeny

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
24336Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29145Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29145)
43633Shanshan Zhang, Zhaojun Li, Yanchun Yan, Chuanlun Zhang, Jun Li, Baisuo ZhaoBacillus urumqiensis sp. nov., a moderately haloalkaliphilic bacterium isolated from a salt lake10.1099/ijsem.0.001028IJSEM 66: 2305-2312 201626978771
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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/
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG
126262A. 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. ReimerStrainInfo—the central database for linked microbial strain identifiers10.1093/database/baaf059

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