Strain identifier

BacDive ID: 133643

Type strain: Yes

Species: Altericroceibacterium xinjiangense

Strain Designation: S3-63

Strain history: CIP <- 2010, CCTCC <- Q. Xue <- K. Zhang, China: strain S3-63

NCBI tax ID(s): 762261 (species)

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General

@ref: 29902

BacDive-ID: 133643

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

description: Altericroceibacterium xinjiangense S3-63 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from Environment, Soil, sand sample.

NCBI tax id

  • NCBI tax id: 762261
  • Matching level: species

strain history

  • @ref: 123981
  • history: CIP <- 2010, CCTCC <- Q. Xue <- K. Zhang, China: strain S3-63

doi: 10.13145/bacdive133643.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Erythrobacteraceae
  • genus: Altericroceibacterium
  • species: Altericroceibacterium xinjiangense
  • full scientific name: Altericroceibacterium xinjiangense (Xue et al. 2012) Xu et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Altererythrobacter xinjiangensis

@ref: 29902

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Erythrobacteraceae

genus: Altererythrobacter

species: Altererythrobacter xinjiangensis

strain designation: S3-63

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29902negative1.3-1.6 µm1.1-1.2 µmrod-shapedno
125439negative99.3
125438negative94.833
123981negativeoval-shapedno

pigmentation

  • @ref: 29902
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
42197Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
123981CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperature
29902positivegrowth20-37
29902positiveoptimum30
42197positivegrowth30

culture pH

@refabilitytypepHPH range
29902positivegrowth07-09alkaliphile
29902positiveoptimum8

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
29902aerobe
125439obligate aerobe98.3

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 97

halophily

@refsaltgrowthtested relationconcentration
29902NaClpositivegrowth0-3 %
29902NaClpositiveoptimum1 %

observation

  • @ref: 29902
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2990230089acetate+carbon source
2990222653asparagine+carbon source
2990223652dextrin+carbon source
2990228757fructose+carbon source
2990228087glycogen+carbon source
2990218257ornithine+carbon source
2990251850methyl pyruvate+carbon source
2990216634raffinose+carbon source
2990253423tween 40+carbon source
12398117632nitrate+reduction
12398116301nitrite+reduction

metabolite production

  • @ref: 123981
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
29902acid phosphatase+3.1.3.2
29902alkaline phosphatase+3.1.3.1
29902catalase+1.11.1.6
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase+3.2.1.23
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin+3.4.21.1
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
123981oxidase-
123981catalase+1.11.1.6
123981urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123981-+++-++--+++-+-++---

Isolation, sampling and environmental information

isolation

  • @ref: 123981
  • sample type: Environment, Soil, sand sample
  • geographic location: Xinjiang
  • country: China
  • origin.country: CHN
  • continent: Asia
  • isolation date: 2007

Safety information

risk assessment

  • @ref: 123981
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 29902
  • description: Altererythrobacter xinjiangensis strain S3-63 16S ribosomal RNA gene, partial sequence
  • accession: HM028673
  • length: 1444
  • database: nuccore
  • NCBI tax ID: 762261

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Altericroceibacterium xinjiangense CCTCC AB 207166GCA_003958635contigncbi762261
66792Altererythrobacter xinjiangensis strain CCTCC AB 207166762261.3wgspatric762261
66792Altererythrobacter xinjiangensis CCTCC AB 2071662894831738draftimg762261

GC content

  • @ref: 29902
  • GC-content: 64.6

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno94.833yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no92.232yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes79.869no
125438spore-formingspore-formingAbility to form endo- or exosporesno89.204no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno95.941yes
125438motile2+flagellatedAbility to perform flagellated movementno57.49no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno97
125439BacteriaNetmotilityAbility to perform movementno54.4
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.3
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe98.3

External links

@ref: 29902

culture collection no.: CCTCC AB 207166, CIP 110125

straininfo link

  • @ref: 91540
  • straininfo: 379026

Reference

@idauthorstitledoi/urlID_cross_referencepubmedcatalogue
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
29902Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172627428776041
42197Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7949
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
68382Automatically annotated from API zym
91540Reimer, 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-ID379026.1
123981Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110125Collection of Institut Pasteur (CIP 110125)
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