Strain identifier

BacDive ID: 465

Type strain: Yes

Species: Microbulbifer hydrolyticus

Strain Designation: IRE-31

Strain history: CIP <- 1997, J. Gonzales, Georgia Univ., Athens, GA, USA: strain IRE-31

NCBI tax ID(s): 48074 (species)

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General

@ref: 4400

BacDive-ID: 465

DSM-Number: 11525

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

description: Microbulbifer hydrolyticus IRE-31 is a facultative aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from enrichment community growing on the high molecular weight fraction of a black liquor sample from the Federal Paper Board Company Inc..

NCBI tax id

  • NCBI tax id: 48074
  • Matching level: species

strain history

@refhistory
4400<- J. M. González, IRE-31
120004CIP <- 1997, J. Gonzales, Georgia Univ., Athens, GA, USA: strain IRE-31

doi: 10.13145/bacdive465.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Cellvibrionales
  • family: Microbulbiferaceae
  • genus: Microbulbifer
  • species: Microbulbifer hydrolyticus
  • full scientific name: Microbulbifer hydrolyticus González et al. 1997

@ref: 4400

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Microbulbiferaceae

genus: Microbulbifer

species: Microbulbifer hydrolyticus

full scientific name: Microbulbifer hydrolyticus González et al. 1997

strain designation: IRE-31

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
23292negative1.1-1.7 µm0.3-0.5 µmrod-shapedno
120004negativeoval-shapedno

colony morphology

  • @ref: 23292
  • colony size: 1 mm
  • colony color: cream
  • colony shape: circular
  • incubation period: 7 days
  • medium used: Marine agar 2216

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4400BACTO 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
36399Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
120004CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
4400positivegrowth28-37mesophilic
36399positivegrowth25mesophilic
120004positivegrowth10-41
120004nogrowth5psychrophilic

culture pH

@refabilitytypepHPH range
23292positiveoptimum7.5
23292positivegrowth6.5-8.5alkaliphile

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23292facultative aerobe
120004obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
23292NaClpositivegrowth0.1-1 M
23292NaClpositiveoptimum0.1-0.5 M
120004NaClpositivegrowth2-6 %
120004NaClnogrowth0 %
120004NaClnogrowth8 %
120004NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2329217234glucose-builds acid from
23292323734-coumarate-growth
23292178794-hydroxybenzoate-growth
2329216716benzene-growth
2329216150benzoate-growth
2329228885butanol-growth
2329223248cinnamate-growth
2329216947citrate-growth
2329216236ethanol-growth
2329215740formate-growth
2329228757fructose-growth
2329217754glycerol-growth
2329215428glycine-growth
2329217196L-asparagine-growth
2329229991L-aspartate-growth
2329217191L-isoleucine-growth
2329218019L-lysine-growth
2329216643L-methionine-growth
2329217295L-phenylalanine-growth
2329216828L-tryptophan-growth
2329216414L-valine-growth
2329217716lactose-growth
2329237684mannose-growth
2329217790methanol-growth
2329216830methylamine-growth
2329215882phenol-growth
2329228831propanol-growth
23292178242-propanol-growth
2329226546rhamnose-growth
2329230762salicylate-growth
2329217992sucrose-growth
232922509agar-hydrolysis
2329217632nitrate-reduction
2329229749ferulate+assimilation
2329216632vanillate+assimilation
2329230089acetate+growth
2329217968butyrate+growth
2329217057cellobiose+growth
23292370543-hydroxybutyrate+growth
2329229749ferulate+growth
2329217234glucose+growth
2329216977L-alanine+growth
2329216467L-arginine+growth
2329229985L-glutamate+growth
2329218050L-glutamine+growth
2329215971L-histidine+growth
2329215603L-leucine+growth
2329217203L-proline+growth
2329217115L-serine+growth
2329216857L-threonine+growth
2329225115malate+growth
23292506227N-acetylglucosamine+growth
2329217272propionate+growth
2329215361pyruvate+growth
2329230031succinate+growth
2329216632vanillate+growth
2329218222xylose+growth
2329262968cellulose+hydrolysis
2329217029chitin+hydrolysis
232925291gelatin+hydrolysis
2329228017starch+hydrolysis
2329253426tween 80+hydrolysis
1200044853esculin-hydrolysis
12000417632nitrate-reduction
12000416301nitrite-reduction
12000417632nitrate-respiration

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantresistance conc.is sensitivesensitivity conc.
2329218208penicillin gyesyes10 Unit
2329217076streptomycinyesyes10 µg
2329228001vancomycinyesyes30 µg
2329228971ampicillinyesyes10 µg
2329217698chloramphenicolyesyes30 µg
232926104kanamycinyesyes30 µg
2329227902tetracyclineyesyes30 µg
1200040129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)yesnoyes

metabolite production

@refChebi-IDmetaboliteproduction
2329253388polyhydroxybutyrateno
12000435581indoleno

enzymes

@refvalueactivityec
23292amylase+
23292catalase+1.11.1.6
23292cellulase+3.2.1.4
23292chitinase+3.2.1.14
23292cytochrome oxidase+1.9.3.1
23292endo-1,4-beta-xylanase+3.2.1.8
23292gelatinase+
23292lipase (Tween 80)+
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
120004oxidase+
120004beta-galactosidase+3.2.1.23
120004alcohol dehydrogenase-1.1.1.1
120004gelatinase+
120004amylase-
120004DNase+
120004caseinase+3.4.21.50
120004catalase+1.11.1.6
120004lecithinase+
120004lipase-
120004lysine decarboxylase-4.1.1.18
120004ornithine decarboxylase-4.1.1.17
120004protease+
120004tryptophan deaminase-
120004urease-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
120004-+++-+----++---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
4400enrichment community growing on the high molecular weight fraction of a black liquor sample from the Federal Paper Board Company Inc.Georgia, AugustaUSAUSANorth America
120004Environment, Coastal seawaterGeorgiaUnited States of AmericaUSANorth America1994

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial#Industrial production
#Engineered#Laboratory#Lab enrichment
#Environmental#Microbial community

taxonmaps

  • @ref: 69479
  • File name: preview.99_56258.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_1255;97_1489;98_4840;99_56258&stattab=map
  • Last taxonomy: Microbulbifer
  • 16S sequence: AJ608704
  • Sequence Identity:
  • Total samples: 30
  • soil counts: 5
  • aquatic counts: 25

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
44001Risk group (German classification)
1200041Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Microbulbifer hydrolyticus 16S rRNA gene, type strain DSM 11525TAJ6087041503ena48074
4400Microbulbifer hydrolyticus 16S ribosomal RNA gene, partial sequenceU583381393ena48074

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbulbifer hydrolyticus DSM 11525GCA_014202835contigncbi48074
66792Microbulbifer hydrolyticus strain DSM 1152548074.4wgspatric48074
66792Microbulbifer hydrolyticus DSM 115252861623431draftimg48074

GC content

  • @ref: 23292
  • GC-content: 57.7
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno98.967yes
anaerobicno98.712yes
halophileyes73.016no
spore-formingno96.178no
glucose-utilyes90.68yes
aerobicyes85.913yes
thermophileno98.849yes
motileno84.153yes
flagellatedno88.274yes
glucose-fermentno88.688no

External links

@ref: 4400

culture collection no.: DSM 11525, ATCC 700072, IRE 31, CIP 105235

straininfo link

  • @ref: 70144
  • straininfo: 43755

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9103623Microbulbifer hydrolyticus gen. nov., sp. nov., and Marinobacterium georgiense gen. nov., sp. nov., two marine bacteria from a lignin-rich pulp mill waste enrichment community.Gonzalez JM, Mayer F, Moran MA, Hodson RE, Whitman WBInt J Syst Bacteriol10.1099/00207713-47-2-3691997Base Composition, Base Sequence, Biodegradation, Environmental, DNA Primers/genetics, DNA, Bacterial/chemistry/genetics, Fatty Acids/analysis, Gram-Negative Aerobic Bacteria/classification/genetics/*metabolism, Lignin/*metabolism, Marine Biology, Microscopy, Electron, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Terminology as Topic, Water MicrobiologyMetabolism
Phylogeny12656152Microbulbifer salipaludis sp. nov., a moderate halophile isolated from a Korean salt marsh.Yoon JH, Kim IG, Shin DY, Kang KH, Park YHInt J Syst Evol Microbiol10.1099/ijs.0.02342-02003Alteromonadaceae/*classification/genetics/*isolation & purification/metabolism, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Fresh Water/microbiology, Korea, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/microbiologyGenetics
Phylogeny28141501Microbulbifer aestuariivivens sp. nov., isolated from a tidal flat.Park S, Yoon SY, Ha MJ, Yoon JHInt J Syst Evol Microbiol10.1099/ijsem.0.0018312017Alteromonadaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Glycolipids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Metabolism30680703Effect of Different Carbon Sources on Cellulase Production by Marine Strain Microbulbifer hydrolyticus IRE-31-192.Liu H, Zeng L, Jin Y, Nie K, Deng L, Wang FAppl Biochem Biotechnol10.1007/s12010-018-02948-12019Aquatic Organisms/*enzymology, Biomass, Carbon/*metabolism, Cellulase/*biosynthesis/metabolism, Culture Media, Fermentation, Gammaproteobacteria/*enzymology/genetics/growth & development, Glucose/metabolism, Mutation, Seawater/*microbiology, Substrate Specificity, Xylose/metabolismEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4400Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11525)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11525
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
23292J. M. GONZáLEZ, F. MAYER, M. A. MORAN, R. E. HODSON, W. B. WHITMAN10.1099/00207713-47-2-369Microbulbifer hydrolyticus gen. nov., sp. nov., and Marinobacterium georgiense gen. nov., sp. nov., Two Marine Bacteria from a Lignin-Rich Pulp Mill Waste Enrichment CommunityIJSEM 47: 369-376 19979103623
36399Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17232
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)
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
70144Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID43755.1StrainInfo: A central database for resolving microbial strain identifiers
120004Curators of the CIPCollection of Institut Pasteur (CIP 105235)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105235