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/bacdive141098.20250331.9.3

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

  • synonyms

    • @ref: 20215
    • synonym: Paragemmobacter straminiformis

@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

@refgram staincell lengthcell widthcell shapemotilityconfidence
44007negative4.5-6.5 µm0.6-0.8 µmrod-shapedno
125438negative98
125439negative99.5

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

@refgrowthtypetemperature
44007positivegrowth20-37
44007positiveoptimum25
67770positivegrowth25

culture pH

@refabilitytypepH
44007positivegrowth5.5-7.0
44007positiveoptimum6

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
44007facultative anaerobe
125439obligate aerobe91.9

spore formation

@refspore formationconfidence
44007no
125438no90.021

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: Gemmobacter straminiformis strain CAM-8 16S ribosomal RNA gene, partial 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

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno98yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no94.776yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes83.394no
125438spore-formingspore-formingAbility to form endo- or exosporesno90.021yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97.416no
125438motile2+flagellatedAbility to perform flagellated movementyes60.34no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno75.3
125439BacteriaNetmotilityAbility to perform movementyes70.1
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.5
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe91.9

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/
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