Strain identifier

BacDive ID: 134036

Type strain: Yes

Species: Gemmobacter lanyuensis

Strain Designation: Orc-4

NCBI tax ID(s): 1054497 (species)

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General

@ref: 31111

BacDive-ID: 134036

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

description: Gemmobacter lanyuensis Orc-4 is a facultative anaerobe, Gram-negative, rod-shaped bacterium that was isolated from freshwater .

NCBI tax id

  • NCBI tax id: 1054497
  • Matching level: species

doi: 10.13145/bacdive134036.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Paracoccaceae
  • genus: Gemmobacter
  • species: Gemmobacter lanyuensis
  • full scientific name: Gemmobacter lanyuensis Sheu et al. 2013

@ref: 31111

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Gemmobacter

species: Gemmobacter lanyuensis

strain designation: Orc-4

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31111negative2 µm0.45 µmrod-shapedno
125438negative98.5
125439negative93.2

pigmentation

  • @ref: 31111
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperature
31111positivegrowth15-40
31111positiveoptimum27.5

culture pH

@refabilitytypepHPH range
31111positivegrowth6.0-9.0alkaliphile
31111positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
31111facultative anaerobe
125439obligate aerobe93.2

spore formation

  • @ref: 31111
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31111NaClpositivegrowth0-1 %
31111NaClpositiveoptimum0.25 %

observation

  • @ref: 31111
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3111117754glycerol+carbon source
3111124996lactate+carbon source
3111129864mannitol+carbon source
3111137684mannose+carbon source
3111151850methyl pyruvate+carbon source
311114853esculin+hydrolysis
3111117632nitrate+reduction

enzymes

@refvalueactivityec
31111acid phosphatase+3.1.3.2
31111alkaline phosphatase+3.1.3.1
31111catalase+1.11.1.6
31111cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 31111
  • sample type: freshwater (river, lake, pond)

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Freshwater
#Environmental#Aquatic#Lake (large)
#Environmental#Aquatic#Pond (small)
#Environmental#Aquatic#River (Creek)

taxonmaps

  • @ref: 69479
  • File name: preview.99_117552.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_926;97_3623;98_15523;99_117552&stattab=map
  • Last taxonomy: Gemmobacter lanyuensis
  • 16S sequence: JN104393
  • Sequence Identity:
  • Total samples: 181
  • soil counts: 1
  • aquatic counts: 159
  • animal counts: 21

Sequence information

16S sequences

  • @ref: 31111
  • description: Gemmobacter lanyuensis strain Orc-4 16S ribosomal RNA gene, partial sequence
  • accession: JN104393
  • length: 1404
  • database: nuccore
  • NCBI tax ID: 1054497

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Gemmobacter lanyuensis KCTC 23714GCA_014652355scaffoldncbi1054497
66792Gemmobacter lanyuensis strain KCTC 237141054497.3wgspatric1054497

GC content

  • @ref: 31111
  • GC-content: 63.5

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe93.2
125439BacteriaNetgram_stainReaction to gram-stainingnegative93.2
125439BacteriaNetmotilityAbility to perform movementyes53.4
125439BacteriaNetspore_formationAbility to form endo- or exosporesno89.3
125438gram-positivegram-positivePositive reaction to Gram-stainingno98.5yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no87.992no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes67.898yes
125438spore-formingspore-formingAbility to form endo- or exosporesno87.185no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96.6yes
125438motile2+flagellatedAbility to perform flagellated movementyes70.606no

External links

@ref: 31111

culture collection no.: BCRC 80378, LMG 26667, KCTC 23714

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23728371Gemmobacter lanyuensis sp. nov., isolated from a freshwater spring.Sheu SY, Shiau YW, Wei YT, Chen WMInt J Syst Evol Microbiol10.1099/ijs.0.052399-02013Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Hydroxybutyrates, Molecular Sequence Data, Natural Springs/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Polyesters, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Taiwan, Ubiquinone/analogs & derivatives/chemistryGenetics
Phylogeny32553048Gemmobacter serpentinus sp. nov., isolated from conserved forages.Lim K, Kannan AD, Shobnam N, Mahmood M, Lee J, Im JInt J Syst Evol Microbiol10.1099/ijsem.0.0042762020Animal Feed/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Kansas, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/isolation & purification, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urlID_cross_referencepubmed
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
31111Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172744028776041
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
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