Strain identifier

BacDive ID: 5481

Type strain: Yes

Species: Arenibacter latericius

Strain history: CIP <- 2000, E. Ivanova, Russian Academy Sci., Vladivostok, Russia <- O.I. Nedashkovskaya

NCBI tax ID(s): 1121012 (strain), 86104 (species)

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General

@ref: 6180

BacDive-ID: 5481

DSM-Number: 15913

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

description: Arenibacter latericius DSM 15913 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sandy sediment samples.

NCBI tax id

NCBI tax idMatching level
1121012strain
86104species

strain history

@refhistory
6180<- E. P. Ivanova, Swinburne Univ. Technol., IRIS, Hawthorn, Australia; KMM 426 <- O. I. Nedashkovskaya, Pacific Inst. Bioorg. Chem., RAS, Vladivostok
67770KMM 426 <-- O. I. Nedashkovskaya.
120568CIP <- 2000, E. Ivanova, Russian Academy Sci., Vladivostok, Russia <- O.I. Nedashkovskaya

doi: 10.13145/bacdive5481.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Arenibacter
  • species: Arenibacter latericius
  • full scientific name: Arenibacter latericius Ivanova et al. 2001

@ref: 6180

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Arenibacter

species: Arenibacter latericius

full scientific name: Arenibacter latericius Ivanova et al. 2001 emend. Nedashkovskaya et al. 2006 emend. Hahnke et al. 2016

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.948
120568negativerod-shapedno

pigmentation

  • @ref: 120568
  • production: no
  • name: Flexirubin

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_15913_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_15913_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_15913_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_15913_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_15913_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6180BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
39596Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
120568CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
6180positivegrowth28mesophilic
39596positivegrowth30mesophilic
56790positivegrowth25-37mesophilic
67770positivegrowth25mesophilic
120568positivegrowth15-41
120568nogrowth5psychrophilic
120568nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
56790aerobe
120568obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.977

halophily

@refsaltgrowthtested relationconcentration
120568NaClnogrowth0 %
120568NaClnogrowth2 %
120568NaClnogrowth4 %
120568NaClnogrowth6 %
120568NaClnogrowth8 %
120568NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1205684853esculin+hydrolysis
120568606565hippurate+hydrolysis
12056817632nitrate+reduction
12056816301nitrite-reduction
12056815792malonate-assimilation
12056817632nitrate-respiration

antibiotic resistance

  • @ref: 120568
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 120568
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12056815688acetoin-
12056817234glucose+

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase+3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase+3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
120568oxidase+
120568beta-galactosidase+3.2.1.23
120568alcohol dehydrogenase-1.1.1.1
120568gelatinase+/-
120568amylase-
120568DNase+
120568caseinase-3.4.21.50
120568catalase+1.11.1.6
120568tween esterase-
120568gamma-glutamyltransferase+2.3.2.2
120568lecithinase-
120568lipase-
120568lysine decarboxylase-4.1.1.18
120568ornithine decarboxylase-4.1.1.17
120568phenylalanine ammonia-lyase-4.3.1.24
120568tryptophan deaminase-
120568urease+3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120568-+++-+++--++----+++-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120568+++++-+++-++++-++++--+++-------+-+-+-----+-----------------+--+--+--------------------+--+++-------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcontinentcountryorigin.countryisolation date
6180sandy sediment samplesSouth China Sea in the Indian OceanAsia
56790Sandy sediments,holothurian,brown alga
67770Sandy sediment samples
120568Environment, Sandy sedimentsCu Lao Re Island, Indian OceanAsiaVietnamVNM1988

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Sandy
#Environmental#Terrestrial#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_16915.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_102;96_8695;97_10454;98_12812;99_16915&stattab=map
  • Last taxonomy: Arenibacter
  • 16S sequence: AF052742
  • Sequence Identity:
  • Total samples: 175
  • soil counts: 4
  • aquatic counts: 132
  • animal counts: 38
  • plant counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
61801Risk group (German classification)
1205681Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6180
  • description: Arenibacter latericius strain KMM 426 16S ribosomal RNA gene, partial sequence
  • accession: AF052742
  • length: 1444
  • database: ena
  • NCBI tax ID: 86104

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Arenibacter latericius DSM 159131121012.3wgspatric1121012
66792Arenibacter latericius DSM 159132524614597draftimg1121012
67770Arenibacter latericius DSM 15913GCA_000424985scaffoldncbi1121012

GC content

@refGC-contentmethod
618036.8sequence analysis
6777037.5thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno90.2no
flagellatedno96.057no
gram-positiveno97.507no
anaerobicno99.447no
aerobicyes89.566no
halophileno57.715no
spore-formingno95.991no
thermophileno99.512yes
glucose-utilyes90.101no
glucose-fermentno88.139no

External links

@ref: 6180

culture collection no.: DSM 15913, CCUG 45454, CIP 106861, JCM 13508, KMM 426, LMG 19693, VKM B-2137D, LMG 19694

straininfo link

  • @ref: 74968
  • straininfo: 264388

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11760939Arenibacter gen. nov., new genus of the family flavobacteriaceae and description of a new species, Arenibacter latericius sp. nov.Ivanova EP, Nedashkovskaya OI, Chun J, Lysenko AM, Frolova GM, Svetashev VI, Vysotskii MV, Mikhailov VV, Huq A, Colwell RRInt J Syst Evol Microbiol10.1099/00207713-51-6-19872001Animals, Base Composition, DNA, Ribosomal/genetics, Fatty Acids/analysis, Geologic Sediments/microbiology, Gram-Negative Aerobic Rods and Cocci/*classification/*genetics/isolation & purification, Molecular Sequence Data, Phaeophyta/microbiology, Phenotype, Phylogeny, Pigments, Biological/metabolism, RNA, Ribosomal, 16S, Sea Cucumbers/microbiology, Seawater/microbiologyGenetics
Enzymology12126478Alpha-N-acetylgalactosaminidase from marine bacterium Arenibacter latericius KMM 426T removing blood type specificity of A-erythrocytes.Bakunina IY, Kuhlmann RA, Likhosherstov LM, Martynova MD, Nedashkovskaya OI, Mikhailov VV, Elyakova LABiochemistry (Mosc)10.1023/a:10161066236552002ABO Blood-Group System/*immunology, Bacterial Proteins/*metabolism, Carbohydrate Sequence, Erythrocytes/*immunology, Gram-Negative Aerobic Rods and Cocci/*enzymology, Hexosaminidases/isolation & purification/*metabolism, Kinetics, Molecular Sequence Data, alpha-N-AcetylgalactosaminidaseMetabolism
25927009Recombinant alpha-NAcetylgalactosaminidase from Marine Bacterium-Modifying A Erythrocyte Antigens.Balabanova LA, Golotin VA, Bakunina IY, Slepchenko LV, Isakov VV, Podvolotskaya AB, Rasskazov VAActa Naturae2015
Phylogeny28945544Arenibacter antarcticus sp. nov., isolated from marine sediment.Li AZ, Lin LZ, Zhang MX, Zhu HHInt J Syst Evol Microbiol10.1099/ijsem.0.0023402017Antarctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Geologic Sediments/*microbiology, Phospholipids/analysis, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Metabolism30609674Effect of Pentacyclic Guanidine Alkaloids from the Sponge Monanchora pulchra on Activity of alpha-Glycosidases from Marine Bacteria.Bakunina I, Likhatskaya G, Slepchenko L, Balabanova L, Tekutyeva L, Son O, Shubina L, Makarieva TMar Drugs10.3390/md170100222019Alkaloids/*pharmacology, Animals, Glycoside Hydrolases/*metabolism, Guanidine/*analogs & derivatives/metabolism, Guanidines/*pharmacology, Porifera/*metabolism, Pseudoalteromonas/*drug effectsPathogenicity
Phylogeny32955652Arenibacter lacus sp. nov., Isolated from Chilika Lagoon, India.Kumar D, Smita N, Kumar G, Suresh G, Jagadeeshwari U, Sasikala C, Ramana CVCurr Microbiol10.1007/s00284-020-02205-x2020Bacterial Typing Techniques, DNA, Bacterial/genetics, *Ecosystem, Fatty Acids/analysis, Flavobacteriaceae, India, Nucleic Acid Hybridization, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, *Seawater, Sequence Analysis, DNA, Vitamin K 2Transcriptome
Phylogeny33502300Arenibacter amylolyticus sp. nov., an amylase-producing bacterium of the family Flavobacteriaceae isolated from marine water in India.Sidhu C, Saini MK, Srinivas Tanuku NR, Pinnaka AKInt J Syst Evol Microbiol10.1099/ijsem.0.0046642021

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6180Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15913)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15913
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
39596Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19038
56790Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 45454)https://www.ccug.se/strain?id=45454
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
74968Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID264388.1StrainInfo: A central database for resolving microbial strain identifiers
120568Curators of the CIPCollection of Institut Pasteur (CIP 106861)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106861