Strain identifier

BacDive ID: 141098

Type strain: Yes

Species: Gemmobacter straminiformis

Strain Designation: CAM-8

Strain history: K. Y. Jhang; Chungbuk Natl. Univ., South Korea; CAM-8.

NCBI tax ID(s): 2045119 (species)

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General

@ref: 44007

BacDive-ID: 141098

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

description: Gemmobacter straminiformis CAM-8 is a facultative anaerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and builds pairs, chains.

NCBI tax id

  • NCBI tax id: 2045119
  • Matching level: species

strain history

  • @ref: 67770
  • history: K. Y. Jhang; Chungbuk Natl. Univ., South Korea; CAM-8.

doi: 10.13145/bacdive141098.20230509.8.1

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 straminiformis
  • full scientific name: Gemmobacter straminiformis Kang et al. 2017

@ref: 44007

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Gemmobacter

species: Gemmobacter straminiformis

strain designation: CAM-8

type strain: yes

Morphology

cell morphology

  • @ref: 44007
  • gram stain: negative
  • cell length: 4.5-6.5 µm
  • cell width: 0.6-0.8 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 44007
  • colony size: 1 mm
  • colony color: beige-coloured containing brown in the centre of the colonies
  • colony shape: circular
  • incubation period: 3 days
  • medium used: Reasoners 2A agar

multicellular morphology

  • @ref: 44007
  • forms multicellular complex: yes
  • complex name: pairs, chains

Culture and growth conditions

culture medium

  • @ref: 44007
  • name: Reasoners 2A agar
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
44007positivegrowth20-37
44007positiveoptimum25mesophilic
67770positivegrowth25mesophilic

culture pH

@refabilitytypepH
44007positivegrowth5.5-7.0
44007positiveoptimum6

Physiology and metabolism

oxygen tolerance

  • @ref: 44007
  • oxygen tolerance: facultative anaerobe

spore formation

  • @ref: 44007
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
44007NaClpositivegrowth0-2 %
44007NaClpositiveoptimum0 %

observation

@refobservation
44007V-shaped tip and sometimes a bulb shape
44007grows well on Reasoners 2A agar medium and slightly on nutrient agar medium
44007the main respiratory quinone is ubiquinone Q-10
67770quinones: Q-10

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
44007casein-hydrolysis
44007cellulose-hydrolysis62968
44007dna-hydrolysis16991
44007gelatin-hydrolysis5291
44007starch-hydrolysis28017
44007urea-hydrolysis16199
44007nitrate-reduction17632
44007(R)-lactate+assimilation16004
44007(S)-lactate+assimilation16651
440072-oxopentanoate+assimilation28644
44007beta-hydroxybutyrate+assimilation8295
44007D-fructose+assimilation15824
44007methyl pyruvate+assimilation51850
44007monomethyl succinate+assimilation75146
44007xylitol+assimilation17151
44007esculin+hydrolysis4853

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
4400728971ampicillinyesyes10 µg (disc)
4400717698chloramphenicolyesyes30 µg (disc)
4400750845doxycyclineyesyes30 µg (disc)
4400748923erythromycinyesyes15 µg (disc)
440076104kanamycinyesyes30 µg (disc)
4400728368novobiocinyesyes5 µg (disc)
4400728077rifampicinyesyes30 µg (disc)
4400717076streptomycinyesyes30 µg (disc)
4400717076streptomycinyesyes10 µg (disc)
4400727902tetracyclineyesyes30 µg (disc)
4400728001vancomycinyesyes30 µg (disc)
440078309polymyxin byesyes100 Unit

metabolite production

  • @ref: 44007
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
44007cytochrome oxidase+1.9.3.1
44007catalase+1.11.1.6
44007leucine arylamidase+3.4.11.1
44007valine arylamidase+
44007acid phosphatase+3.1.3.2
44007alpha-glucosidase+3.2.1.20

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    44007C10:0 3OH1.7
    44007C16:01.5
    44007C18:01
    44007C18:0 3OH2.1
    44007C18:0iso6.5
    4400711-methyl C18:1ω7c3.1
    44007C18:1ω7c and/or C18:1ω6c78.8
    44007C19:1ω7c and/or C19:1ω6c2.2
  • type of FA analysis: whole cell analysis
  • incubation medium: Reasoners 2A agar
  • agar/liquid: agar
  • incubation temperature: 25
  • software version: Sherlock 6.1
  • library/peak naming table: RTSBA6
  • system: MIS MIDI
  • method/protocol: Minnikin, 1984
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
44007freshwater of an artificial fountainRepublic of KoreaKORAsia
67770Artificial fountain at Chonbuk National UniversityRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment#Water reservoir (Aquarium/pool)
#Environmental#Aquatic#Freshwater

taxonmaps

  • @ref: 69479
  • File name: preview.99_80853.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_926;97_8084;98_56250;99_80853&stattab=map
  • Last taxonomy: Gemmobacter straminiformis subclade
  • 16S sequence: KX832992
  • Sequence Identity:
  • Total samples: 547
  • soil counts: 25
  • aquatic counts: 483
  • animal counts: 23
  • plant counts: 16

Sequence information

16S sequences

  • @ref: 44007
  • description: 16S rRNA gene sequence
  • accession: KX832992
  • database: nuccore

Genome sequences

  • @ref: 66792
  • description: Gemmobacter straminiformis CAM-8
  • accession: GCA_014243445
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 2045119

GC content

  • @ref: 44007
  • GC-content: 65.9
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno85.757no
gram-positiveno98.254yes
anaerobicno97.83yes
aerobicyes73.911yes
halophileno81.848no
spore-formingno96.014no
glucose-utilyes79.183no
thermophileno97.259yes
motileno60.122no
glucose-fermentno84.12no

External links

@ref: 44007

culture collection no.: KACC 19224, JCM 31905

literature

  • topic: Phylogeny
  • Pubmed-ID: 29022543
  • title: Gemmobacter straminiformis sp. nov., isolated from an artificial fountain.
  • authors: Kang JY, Kim MJ, Chun J, Son KP, Jahng KY
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002403
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Ubiquinone/chemistry, *Water Microbiology
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournalpubmed
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
44007Ji Young Kang, Mi-Jung Kim, Jeesun Chun, Kyung Pyo Son, Kwang Yeop JahngGemmobacter straminiformis sp. nov., isolated from an artificial fountain10.1099/ijsem.0.002403IJSEM 67: 5019-5025 201729022543
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
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/