Strain identifier

BacDive ID: 133657

Type strain: Yes

Species: Agarivorans albus

Strain history: CIP <- 2004, M. Kurahashi, Tokyo Univ., Tokyo, Japan: strain MKT 106

NCBI tax ID(s): 1331007 (strain), 182262 (species)

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General

@ref: 29979

BacDive-ID: 133657

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

description: Agarivorans albus IAM 14998 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from Omphalius pfeifferi pfeifferi Banda.

NCBI tax id

NCBI tax idMatching level
182262species
1331007strain

strain history

@refhistory
326992004, M. Kurahashi, Tokyo Univ., Tokyo, Japan: strain MKT 106
67770IAM 14998 <-- M. Kurahashi MKT 106.
116196CIP <- 2004, M. Kurahashi, Tokyo Univ., Tokyo, Japan: strain MKT 106

doi: 10.13145/bacdive133657.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Alteromonadales
  • family: Alteromonadaceae
  • genus: Agarivorans
  • species: Agarivorans albus
  • full scientific name: Agarivorans albus Kurahashi and Yokota 2004

@ref: 29979

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Alteromonadaceae

genus: Agarivorans

species: Agarivorans albus

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29979negative1.7 µm0.8 µmrod-shapedyes
69480yes97.91
69480negative99.99
116196negativerod-shapedno

pigmentation

  • @ref: 29979
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
32699Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
116196CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
29979positiveoptimum37mesophilic
32699positivegrowth25mesophilic
67770positivegrowth25mesophilic
116196positivegrowth10-30
116196nogrowth5psychrophilic
116196nogrowth37mesophilic
116196nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29979aerobe
116196obligate aerobe

spore formation

@refspore formationconfidence
29979no
69481no100
69480no99.946

halophily

@refsaltgrowthtested relationconcentration
29979NaClpositivegrowth>0 %
116196NaClpositivegrowth0-8 %
116196NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2997917234glucose+carbon source
2997917306maltose+carbon source
2997929864mannitol+carbon source
2997918222xylose+carbon source
299794853esculin+hydrolysis
1161964853esculin-hydrolysis
11619617632nitrate-reduction
11619616301nitrite-reduction
116196132112sodium thiosulfate-builds gas from
11619617632nitrate-respiration

metabolite production

  • @ref: 116196
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
116196oxidase-
116196beta-galactosidase+3.2.1.23
116196alcohol dehydrogenase-1.1.1.1
116196gelatinase+
116196amylase-
116196DNase+
116196caseinase+3.4.21.50
116196catalase+1.11.1.6
116196tween esterase+
116196lecithinase+
116196lysine decarboxylase-4.1.1.18
116196ornithine decarboxylase-4.1.1.17
116196protease+
116196tryptophan deaminase-
116196urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase+3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase+3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116196-+++-+--+-++-++-+-+-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116196+++++----------++++-----+-+----+++--+------------++--++-+--+++---+------+-++-++++-----+--++-+++-++-

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
67770Omphalius pfeifferi pfeifferi BandaOmphalius pfeifferi pfeifferiTateyama, ChibaJapanJPNAsia
116196Mollusca, limpetTateyama chibaJapanJPNAsia1999

Safety information

risk assessment

  • @ref: 116196
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 29979
  • description: Agarivorans albus gene for 16S rRNA, partial sequene, strain:MKT106
  • accession: AB076561
  • length: 1454
  • database: nuccore
  • NCBI tax ID: 1331007

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Agarivorans albus JCM 21469GCA_019670105completencbi182262
66792Agarivorans albus strain JCM 21469182262.5completepatric182262
67770Agarivorans albus MKT 106GCA_000414175contigncbi1331007

GC content

@refGC-contentmethod
2997949.5
6777049.5high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes88.201no
gram-positiveno98.787no
anaerobicno96.097yes
aerobicyes84.744yes
halophileyes78.794no
spore-formingno95.709no
motileyes90.292yes
thermophileno99.7yes
glucose-utilyes88.333yes
glucose-fermentyes83.283no

External links

@ref: 29979

culture collection no.: IAM 14998, LMG 21761, MKT 106, JCM 21469, NBRC 102603, CIP 108457

straininfo link

  • @ref: 91546
  • straininfo: 93908

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15143010Agarivorans albus gen. nov., sp. nov., a gamma-proteobacterium isolated from marine animals.Kurahashi M, Yokota AInt J Syst Evol Microbiol10.1099/ijs.0.02778-02004Alteromonadaceae/*classification/genetics/*isolation & purification/metabolism, Animals, Base Composition, Chordata, Nonvertebrate/microbiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Marine Biology, Microscopy, Electron, Molecular Sequence Data, Mollusca/microbiology, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, SeawaterGenetics
Phylogeny20363930Agarivorans gilvus sp. nov. isolated from seaweed.Du ZJ, Lv GQ, Rooney AP, Miao TT, Xu QQ, Chen GJInt J Syst Evol Microbiol10.1099/ijs.0.019810-02010Alteromonadaceae/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Glycoside Hydrolases/metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Seaweed/*microbiology, Sequence Analysis, DNAGenetics
Genetics23868120Draft Genome Sequence of Agarivorans albus Strain MKT 106T, an Agarolytic Marine Bacterium.Yasuike M, Nakamura Y, Kai W, Fujiwara A, Fukui Y, Satomi M, Sano MGenome Announc10.1128/genomeA.00367-132013
Phylogeny25186952Agarivorans litoreus sp. nov., a novel gammaproteobacterium isolated from seawater and emended description of the genus Agarivorans.Park S, Park JM, Jung YT, Yoon JHAntonie Van Leeuwenhoek10.1007/s10482-014-0273-62014Aerobiosis, Alteromonadaceae/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Korea, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, TemperatureGenetics
Enzymology27743343Cloning, Expression, and Biochemical Characterization of a Novel Acidic GH16 beta-Agarase, AgaJ11, from Gayadomonas joobiniege G7.Jung S, Jeong BC, Hong SK, Lee CRAppl Biochem Biotechnol10.1007/s12010-016-2262-x2016*Alteromonadaceae/enzymology/genetics, *Bacterial Proteins/biosynthesis/chemistry/genetics, *Cloning, Molecular, *Gene Expression, *Glycoside Hydrolases/biosynthesis/chemistry/genetics

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
29979Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172634728776041
32699Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6081
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/
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
91546Reimer, 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-ID93908.1
116196Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108457Collection of Institut Pasteur (CIP 108457)