Strain identifier

BacDive ID: 470

Type strain: Yes

Species: Saccharophagus degradans

Strain Designation: 2-40

Strain history: <- R. M. Weiner <- G. Andrykovitch; 2-40. Strain shipped as an actively growing culture, but survives only 3 days in the post, making shipping outside of Europe problematic. Customers ordering from outside of Europe should inquire before ordering the strain

NCBI tax ID(s): 203122 (strain), 86304 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 6690

BacDive-ID: 470

DSM-Number: 17024

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

description: Saccharophagus degradans 2-40 is an aerobe, heterotroph, mesophilic bacterium that was isolated from decomposing marsh grass.

NCBI tax id

NCBI tax idMatching level
86304species
203122strain

strain history

  • @ref: 6690
  • history: <- R. M. Weiner <- G. Andrykovitch; 2-40. Strain shipped as an actively growing culture, but survives only 3 days in the post, making shipping outside of Europe problematic. Customers ordering from outside of Europe should inquire before ordering the strain

doi: 10.13145/bacdive470.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Cellvibrionales
  • family: Cellvibrionaceae
  • genus: Saccharophagus
  • species: Saccharophagus degradans
  • full scientific name: Saccharophagus degradans Ekborg et al. 2005

@ref: 6690

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Cellvibrionaceae, not assigned to order

family: Cellvibrionaceae

genus: Saccharophagus

species: Saccharophagus degradans

full scientific name: Saccharophagus degradans Ekborg et al. 2005

strain designation: 2-40

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangement
23294negative1.5-3.0 µm0.5 µmrod-shapedyesmonotrichous, polar
23294pleomorphic-shaped

colony morphology

  • @ref: 23294
  • colony color: cream

pigmentation

  • @ref: 23294
  • production: yes
  • color: Black
  • name: Eumelanin

Culture and growth conditions

culture medium

  • @ref: 6690
  • name: HALF STRENGTH BACTO MARINE BROTH (DSMZ Medium 514a)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514a
  • composition: Name: HALF STRENGTH BACTO MARINE BROTH (DSMZ Medium 514a) Composition: Agar 15.0 g/l NaCl 9.725 g/l MgCl2 2.95 g/l Bacto peptone 2.5 g/l Na2SO4 1.62 g/l CaCl2 0.9 g/l Yeast extract 0.5 g/l KCl 0.275 g/l NaHCO3 0.08 g/l Fe(III) citrate 0.05 g/l KBr 0.04 g/l SrCl2 0.017 g/l H3BO3 0.011 g/l Na2HPO4 0.004 g/l Na-silicate 0.002 g/l NaF 0.0012 g/l (NH4)NO3 0.0008 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
6690positivegrowth28mesophilic
23294positivegrowth4-37
23294positiveoptimum30mesophilic
63341positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
23294positiveoptimum7.5
23294positivegrowth4.5-10alkaliphile

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
6690aerobe
23294aerobe
63341aerobe

nutrition type

  • @ref: 23294
  • type: heterotroph

halophily

@refsaltgrowthtested relationconcentration
23294Sea Salts (S9883)nogrowth0 %
23294Sea Salts (S9883)positivegrowth1-10 %
23294Sea Salts (S9883)positiveoptimum3.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
232945291gelatin+assimilation
232942509agar+carbon source
2329458187alginate+carbon source
2329462968cellulose+carbon source
2329417029chitin+carbon source
232945181fucoidan+carbon source
232946364laminarin+carbon source
2329417309pectin+carbon source
2329427941pullulan+carbon source
2329428017starch+carbon source
2329437166xylan+carbon source
2329418186tyrosine+hydrolysis
2329417632nitrate+reduction

enzymes

@refvalueactivityec
23294catalase+1.11.1.6
23294cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6690decomposing marsh grassVA, Chesapeake BayUSAUSANorth America
23294surface of degrading salt marsh cord grass, Spartina alterniflora
63341Decomposing marsh grass

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Wetland (Swamp)
#Environmental#Terrestrial#Salt marsh
#Host#Plants#Decomposing plant
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_6445.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_235;96_3051;97_3748;98_4757;99_6445&stattab=map
  • Last taxonomy: Saccharophagus degradans subclade
  • 16S sequence: AF055269
  • Sequence Identity:
  • Total samples: 1102
  • soil counts: 62
  • aquatic counts: 962
  • animal counts: 56
  • plant counts: 22

Safety information

risk assessment

  • @ref: 6690
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bacterium 2-40 16S ribosomal RNA gene, partial sequenceAF063028519ena203122
6690Saccharophagus degradans 2-40 16S ribosomal RNA gene, partial sequenceAF0552691431ena203122

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Saccharophagus degradans 2-40GCA_000013665completencbi203122
66792Saccharophagus degradans 2-40203122.15completepatric203122
66792Saccharophagus degradans 2-40637000249completeimg86304

GC content

  • @ref: 23294
  • GC-content: 45.8
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes90.715yes
flagellatedyes93.806yes
gram-positiveno98.898yes
anaerobicno99.091yes
halophileno60.306no
spore-formingno94.059no
thermophileno98.297no
glucose-utilyes90.527no
aerobicyes87.347no
glucose-fermentno83.909no

External links

@ref: 6690

culture collection no.: DSM 17024, ATCC 43961, CCUG 66513

straininfo link

  • @ref: 70149
  • straininfo: 87752

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16014479Saccharophagus degradans gen. nov., sp. nov., a versatile marine degrader of complex polysaccharides.Ekborg NA, Gonzalez JM, Howard MB, Taylor LE, Hutcheson SW, Weiner RMInt J Syst Evol Microbiol10.1099/ijs.0.63627-02005Alteromonadaceae/*classification/genetics/metabolism/physiology, Bacterial Typing Techniques, Biodegradation, Environmental, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Molecular Sequence Data, Phenotype, Polysaccharides/metabolism, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Species SpecificityMetabolism
Genetics16672483Genomic and proteomic analyses of the agarolytic system expressed by Saccharophagus degradans 2-40.Ekborg NA, Taylor LE, Longmire AG, Henrissat B, Weiner RM, Hutcheson SWAppl Environ Microbiol10.1128/AEM.72.5.3396-3405.20062006Alteromonadaceae/*enzymology/genetics/metabolism, Bacterial Proteins/genetics/*metabolism, Escherichia coli/enzymology/genetics, Gene Deletion, *Genome, Bacterial, Glycoside Hydrolases/*genetics/*metabolism, Molecular Sequence Data, Phylogeny, *Proteome, Sequence Analysis, DNAMetabolism
Metabolism16707677Complete cellulase system in the marine bacterium Saccharophagus degradans strain 2-40T.Taylor LE 2nd, Henrissat B, Coutinho PM, Ekborg NA, Hutcheson SW, Weiner RMJ Bacteriol10.1128/JB.01348-052006Bacterial Proteins/metabolism, Base Sequence, Cellulase/*metabolism, Gammaproteobacteria/*enzymology/genetics, Genome, Bacterial, Proteome, Restriction Mapping, Seawater/*microbiologyGenetics
Metabolism18193466Biosynthesis and characterization of polyhydroxyalkanoates in the polysaccharide-degrading marine bacterium Saccharophagus degradans ATCC 43961.Gonzalez-Garcia Y, Nungaray J, Cordova J, Gonzalez-Reynoso O, Koller M, Atlic A, Braunegg GJ Ind Microbiol Biotechnol10.1007/s10295-007-0299-02008Alteromonadaceae/chemistry/*metabolism, Calorimetry, Differential Scanning, Chromatography, Gel, Gas Chromatography-Mass Spectrometry, Molecular Weight, Polyhydroxyalkanoates/*biosynthesis/*chemistry, Polysaccharides/*metabolism
Metabolism18383127Utilization of cellulosic waste from tequila bagasse and production of polyhydroxyalkanoate (PHA) bioplastics by Saccharophagus degradans.Alva Munoz LE, Riley MRBiotechnol Bioeng10.1002/bit.218542008Agriculture/methods, Alcoholic Beverages/*microbiology, Biodegradation, Environmental, Cellulose/*metabolism, Gammaproteobacteria/*metabolism, Industrial Waste/*prevention & control, Plastics/metabolism, Polyhydroxyalkanoates/*metabolismBiotechnology
Genetics18516288Complete genome sequence of the complex carbohydrate-degrading marine bacterium, Saccharophagus degradans strain 2-40 T.Weiner RM, Taylor LE 2nd, Henrissat B, Hauser L, Land M, Coutinho PM, Rancurel C, Saunders EH, Longmire AG, Zhang H, Bayer EA, Gilbert HJ, Larimer F, Zhulin IB, Ekborg NA, Lamed R, Richardson PM, Borovok I, Hutcheson SPLoS Genet10.1371/journal.pgen.10000872008Alteromonadaceae/chemistry/enzymology/*genetics/metabolism, Bacterial Proteins/genetics/metabolism, Base Sequence, *Chromosome Mapping, *Genome, Bacterial, Glycoside Hydrolases/genetics/metabolism, Molecular Sequence Data, Polysaccharides/chemistry/genetics/*metabolism, Protein Transport, Seawater/*microbiology, Sequence Analysis, DNA, Signal Transduction, Substrate SpecificityMetabolism
Genetics18556790Insights into plant cell wall degradation from the genome sequence of the soil bacterium Cellvibrio japonicus.DeBoy RT, Mongodin EF, Fouts DE, Tailford LE, Khouri H, Emerson JB, Mohamoud Y, Watkins K, Henrissat B, Gilbert HJ, Nelson KEJ Bacteriol10.1128/JB.01701-072008Alteromonadaceae/genetics, Bacterial Proteins/*genetics, Cell Wall/*metabolism, Cellvibrio/*enzymology/*genetics, Esterases/genetics, *Genome, Bacterial, Genomics, Glycoside Hydrolases/genetics, Lyases/genetics, Molecular Sequence Data, Phylogeny, Plants/*metabolism, Sequence Analysis, DNA, Sequence Homology, Amino Acid, Soil Microbiology, SyntenyMetabolism
Metabolism19568419The complete genome of Teredinibacter turnerae T7901: an intracellular endosymbiont of marine wood-boring bivalves (shipworms).Yang JC, Madupu R, Durkin AS, Ekborg NA, Pedamallu CS, Hostetler JB, Radune D, Toms BS, Henrissat B, Coutinho PM, Schwarz S, Field L, Trindade-Silva AE, Soares CA, Elshahawi S, Hanora A, Schmidt EW, Haygood MG, Posfai J, Benner J, Madinger C, Nove J, Anton B, Chaudhary K, Foster J, Holman A, Kumar S, Lessard PA, Luyten YA, Slatko B, Wood N, Wu B, Teplitski M, Mougous JD, Ward N, Eisen JA, Badger JH, Distel DLPLoS One10.1371/journal.pone.00060852009Animals, Bivalvia/metabolism/*microbiology, Computational Biology, *Genome, Bacterial, *Marine Biology, Nitrogen/metabolism, Phylogeny, Polysaccharides/metabolism, Proteobacteria/classification/enzymology/*genetics/physiology, Quorum Sensing, Spectrometry, Mass, Electrospray Ionization, *Symbiosis, Tandem Mass Spectrometry, *WoodPhylogeny
Metabolism19617364Processive endoglucanases mediate degradation of cellulose by Saccharophagus degradans.Watson BJ, Zhang H, Longmire AG, Moon YH, Hutcheson SWJ Bacteriol10.1128/JB.00481-092009Alteromonadaceae/*enzymology/genetics/growth & development/metabolism, *Bacterial Proteins/genetics/isolation & purification/metabolism, Cellobiose/metabolism, *Cellulase/genetics/isolation & purification/metabolism, Cellulose/chemistry/*metabolism, Cellulose 1,4-beta-Cellobiosidase/genetics/isolation & purification/metabolism, Cloning, Molecular, Computational Biology, Culture Media, PhylogenyEnzymology
Enzymology19646553Optimal production of a novel endo-acting beta-1,4-xylanase cloned from Saccharophagus degradans 2-40 into Escherichia coli BL21(DE3).Ko JK, Jung MW, Kim KH, Choi IGN Biotechnol10.1016/j.nbt.2009.07.0092009Alteromonadaceae/drug effects/*enzymology, Cell Proliferation/drug effects, Chromatography, High Pressure Liquid, Chromatography, Thin Layer, Cloning, Molecular, Electrophoresis, Polyacrylamide Gel, Endo-1,4-beta Xylanases/*biosynthesis/*genetics, Escherichia coli/cytology/drug effects/*metabolism, Fermentation/drug effects, Hydrolysis/drug effects, Isopropyl Thiogalactoside/pharmacology, Recombinant Proteins/biosynthesis, Temperature, Time Factors, Xylans/metabolismPathogenicity
Enzymology19802606Overexpression and molecular characterization of Aga50D from Saccharophagus degradans 2-40: an exo-type beta-agarase producing neoagarobiose.Kim HT, Lee S, Lee D, Kim HS, Bang WG, Kim KH, Choi IGAppl Microbiol Biotechnol10.1007/s00253-009-2256-52009Agar/metabolism, Alteromonadaceae/*enzymology/genetics, Cloning, Molecular, Disaccharides/*biosynthesis, *Glycoside Hydrolases/chemistry/genetics/isolation & purification/metabolism, Hydrogen-Ion Concentration, Kinetics, Magnetic Resonance Spectroscopy, Mass Spectrometry, Recombinant Proteins/chemistry/genetics/isolation & purification/metabolism, Temperature, Up-RegulationMetabolism
Metabolism19806675Global metabolic profiling of plant cell wall polysaccharide degradation by Saccharophagus degradans.Shin MH, Lee DY, Skogerson K, Wohlgemuth G, Choi IG, Fiehn O, Kim KHBiotechnol Bioeng10.1002/bit.225572010Alteromonadaceae/chemistry/enzymology/growth & development/*metabolism, Bacterial Proteins/analysis, Cell Wall/chemistry, Enzymes/analysis, Fatty Acids/analysis, Gas Chromatography-Mass Spectrometry, Glucuronic Acid/analysis, *Metabolomics, Nucleotides/analysis, Plants/chemistry, Polysaccharides/*metabolismEnzymology
Metabolism20023015Discovery and characterization of cadherin domains in Saccharophagus degradans 2-40.Fraiberg M, Borovok I, Weiner RM, Lamed RJ Bacteriol10.1128/JB.01236-092009Alteromonadaceae/*genetics/growth & development, Bacterial Proteins/*genetics/*metabolism, Betula/chemistry, Cadherins/*genetics/*metabolism, Calcium/metabolism, Pectins/isolation & purification/metabolism, Protein Binding, Protein Interaction Mapping, Protein Structure, Tertiary, Xylans/isolation & purification/metabolismEnzymology
Metabolism20054134Crystallization and preliminary X-ray analysis of neoagarobiose hydrolase from Saccharophagus degradans 2-40.Lee S, Lee JY, Ha SC, Jung J, Shin DH, Kim KH, Choi IGActa Crystallogr Sect F Struct Biol Cryst Commun10.1107/S174430910904603X2009Agar/metabolism, Alteromonadaceae/*enzymology/genetics, Base Sequence, Crystallization, Crystallography, X-Ray, DNA Primers/genetics, Disaccharidases/*chemistry/genetics/metabolism, Recombinant Proteins/chemistry/geneticsEnzymology
Metabolism20215059Global metabolite profiling of agarose degradation by Saccharophagus degradans 2-40.Shin MH, Lee DY, Wohlgemuth G, Choi IG, Fiehn O, Kim KHN Biotechnol10.1016/j.nbt.2010.02.0232010Alteromonadaceae/*metabolism, Bacterial Proteins/*metabolism, Gene Expression Profiling/*methods, Peptide Mapping/*methods, Proteome/*metabolism, Sepharose/*metabolismProteome
Enzymology20696711CAZymes Analysis Toolkit (CAT): web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database.Park BH, Karpinets TV, Syed MH, Leuze MR, Uberbacher ECGlycobiology10.1093/glycob/cwq1062010Alteromonadaceae/*enzymology/genetics, Bacterial Proteins/chemistry/*genetics/metabolism, *Carbohydrates, Clostridium thermocellum/*enzymology/genetics, *Databases, Protein, Enzymes/chemistry/classification/*genetics, Fungal Proteins/chemistry/*genetics/metabolism, Genome, Bacterial/physiology, Genome, Fungal/physiology, Molecular Sequence Annotation, Neurospora crassa/*enzymology/geneticsGenetics
Phylogeny20833889Pseudoteredinibacter isoporae gen. nov., sp. nov., a marine bacterium isolated from the reef-building coral Isopora palifera.Chen MH, Sheu SY, Arun AB, Young CC, Chen CA, Wang JT, Chen WMInt J Syst Evol Microbiol10.1099/ijs.0.024190-02010Animals, Anthozoa/*microbiology, DNA, Bacterial, DNA, Ribosomal/genetics, Fatty Acids/genetics/metabolism, Gammaproteobacteria, Gram-Negative Bacteria/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sodium Chloride/metabolismMetabolism
Metabolism21036994Cadherin domains in the polysaccharide-degrading marine bacterium Saccharophagus degradans 2-40 are carbohydrate-binding modules.Fraiberg M, Borovok I, Bayer EA, Weiner RM, Lamed RJ Bacteriol10.1128/JB.00842-102010Bacterial Proteins/genetics/metabolism, Cadherins/chemistry/genetics/*metabolism, Carbohydrate Metabolism, Gene Expression Regulation, Bacterial/physiology, Gram-Negative Aerobic Bacteria/genetics/*metabolism, Polysaccharides/*metabolism, Protein Binding, Protein Structure, Tertiary
Metabolism21327449Hydrolytic and phosphorolytic metabolism of cellobiose by the marine aerobic bacterium Saccharophagus degradans 2-40T.Zhang H, Moon YH, Watson BJ, Suvorov M, Santos E, Sinnott CA, Hutcheson SWJ Ind Microbiol Biotechnol10.1007/s10295-011-0945-42011Alteromonadaceae/genetics/*metabolism, Bacteria, Aerobic/metabolism, Cellobiose/*metabolism, Cellulose/metabolism, Cellulose 1,4-beta-Cellobiosidase/metabolism, Escherichia coli/genetics, Glucosyltransferases/genetics/metabolism, Hydrolysis, Phosphorylation, beta-Glucosidase/genetics/metabolism
Metabolism21731555Carbohydrase systems of Saccharophagus degradans degrading marine complex polysaccharides.Hutcheson SW, Zhang H, Suvorov MMar Drugs10.3390/md90406452011Alteromonadaceae/enzymology/*genetics, Bacterial Proteins/genetics/metabolism, Carbon/metabolism, *Genome, Bacterial, Glycoside Hydrolases/genetics/*metabolism, Polysaccharides/metabolismGenetics
Enzymology21810409Crystal structure of a key enzyme in the agarolytic pathway, alpha-neoagarobiose hydrolase from Saccharophagus degradans 2-40.Ha SC, Lee S, Lee J, Kim HT, Ko HJ, Kim KH, Choi IGBiochem Biophys Res Commun10.1016/j.bbrc.2011.07.0732011Agar/chemistry/metabolism, Alteromonadaceae/*enzymology, Cloning, Molecular, Cytosol/enzymology, Disaccharidases/*chemistry/genetics, Protein ConformationMetabolism
Enzymology22281843Depolymerization of alginate into a monomeric sugar acid using Alg17C, an exo-oligoalginate lyase cloned from Saccharophagus degradans 2-40.Kim HT, Chung JH, Wang D, Lee J, Woo HC, Choi IG, Kim KHAppl Microbiol Biotechnol10.1007/s00253-012-3882-x2012Alginates/*metabolism, Alteromonadaceae/*enzymology/genetics, Cloning, Molecular, Enzyme Stability, Escherichia coli/genetics, Gene Expression, Hydrogen-Ion Concentration, Kinetics, Polysaccharide-Lyases/chemistry/genetics/isolation & purification/*metabolism, Recombinant Proteins/chemistry/genetics/isolation & purification/metabolism, Substrate Specificity, Sugar Acids/*metabolism, TemperatureMetabolism
Enzymology22344647Functional cell surface display and controlled secretion of diverse Agarolytic enzymes by Escherichia coli with a novel ligation-independent cloning vector based on the autotransporter YfaL.Ko HJ, Park E, Song J, Yang TH, Lee HJ, Kim KH, Choi IGAppl Environ Microbiol10.1128/AEM.07004-112012Alteromonadaceae/enzymology/genetics, Escherichia coli/*enzymology/*genetics, Escherichia coli Proteins/*genetics/*metabolism, Genes, Reporter, Genetic Engineering/methods, *Genetic Vectors, Genetics, Microbial/methods, Glycoside Hydrolases/chemistry/*genetics/*metabolism, Luminescent Proteins/analysis/genetics, Membrane Transport Proteins/*genetics/*metabolism, Molecular Weight, Recombinant Proteins/chemistry/genetics/metabolismMetabolism
Enzymology22526785Agar degradation by microorganisms and agar-degrading enzymes.Chi WJ, Chang YK, Hong SKAppl Microbiol Biotechnol10.1007/s00253-012-4023-22012Agar/*metabolism, Alteromonadaceae/enzymology, Geologic Sediments/microbiology, Glycoside Hydrolases/chemistry/genetics/*metabolism, Hydrolysis, Protein Conformation, Seawater/microbiology, Streptomyces coelicolor/enzymologyMetabolism
Enzymology22814498Cloning of agarase gene from non-marine agarolytic bacterium Cellvibrio sp.Ariga O, Inoue T, Kubo H, Minami K, Nakamura M, Iwai M, Moriyama H, Yanagisawa M, Nakasaki KJ Microbiol Biotechnol10.4014/jmb.1202.020202012Amino Acid Sequence, Bacterial Proteins/chemistry/*genetics/isolation & purification/metabolism, Base Sequence, Cellvibrio/*enzymology/genetics, Cloning, Molecular, Disaccharides/analysis/metabolism, Enzyme Stability, Escherichia coli/enzymology/genetics, Galactosides/analysis/metabolism, Glycoside Hydrolases/chemistry/*genetics/isolation & purification/metabolism, Hydrogen-Ion Concentration, Hydrolysis, Molecular Sequence Data, Oligosaccharides/analysis/metabolism, Recombinant Proteins/chemistry/genetics/isolation & purification/metabolism, Sepharose/analysis/metabolism, TemperatureMetabolism
Metabolism22843394Bacterial cadherin domains as carbohydrate binding modules: determination of affinity constants to insoluble complex polysaccharides.Fraiberg M, Borovok I, Weiner RM, Lamed R, Bayer EAMethods Mol Biol10.1007/978-1-61779-956-3_112012Adsorption, Alteromonadaceae/*metabolism, Bacterial Proteins/*metabolism, Cadherins/classification/*metabolism, Calcium/metabolism, Chemistry Techniques, Analytical, Electrophoresis, Polyacrylamide Gel/methods, Kinetics, Polysaccharides, Bacterial/*metabolism, Protein Structure, TertiaryEnzymology
Phylogeny22950007Isolation of a novel Saccharophagus species (Myt-1) capable of degrading a variety of seaweeds and polysaccharides.Sakatoku A, Wakabayashi M, Tanaka Y, Tanaka D, Nakamura SMicrobiologyopen10.1002/mbo3.102012
Phylogeny23291764Identification and characterization of cellobiose 2-epimerases from various aerobes.Ojima T, Saburi W, Yamamoto T, Mori H, Matsui HBiosci Biotechnol Biochem10.1271/bbb.1207422013Aerobiosis, Bacteria, Aerobic/chemistry/*enzymology, Bacterial Proteins/classification/*isolation & purification/*metabolism, Carbohydrate Epimerases/classification/*isolation & purification/*metabolism, Cellobiose/*metabolism, Enzyme Assays, Enzyme Stability, Escherichia coli/genetics, Glucose/metabolism, Hydrogen-Ion Concentration, Isoenzymes/classification/isolation & purification/metabolism, Kinetics, Lactose/metabolism, Mannose/metabolism, Phylogeny, Recombinant Proteins/classification/isolation & purification/metabolism, Species Specificity, Stereoisomerism, Substrate Specificity, TemperatureEnzymology
Metabolism23627584Biochemical characterization of 4-alpha-glucanotransferase from Saccharophagus degradans 2-40 and its potential role in glycogen degradation.Hwang S, Choi KH, Kim J, Cha JFEMS Microbiol Lett10.1111/1574-6968.121672013Alteromonadaceae/*enzymology/genetics/metabolism, Amino Acid Sequence, Bacterial Proteins/*chemistry/genetics/*metabolism, Enzyme Stability, Glycogen/*metabolism, Glycogen Debranching Enzyme System/*chemistry/genetics/*metabolism, Hydrogen-Ion Concentration, Molecular Sequence Data, Molecular Weight, Sequence AlignmentEnzymology
Enzymology23990129Feasibility test of utilizing Saccharophagus degradans 2-40(T) as the source of crude enzyme for the saccharification of lignocellulose.Jung YH, Kim HK, Song DS, Choi IG, Yang TH, Lee HJ, Seung D, Kim KHBioprocess Biosyst Eng10.1007/s00449-013-1040-12013Alteromonadaceae/*enzymology, Bacterial Proteins/*chemistry, Cellulase/*chemistry, Endo-1,4-beta Xylanases/*chemistry, Lignin/*chemistry
Metabolism24140897An expansin from the marine bacterium Hahella chejuensis acts synergistically with xylanase and enhances xylan hydrolysis.Lee HJ, Kim IJ, Kim JF, Choi IG, Kim KHBioresour Technol10.1016/j.biortech.2013.09.0862013Bacterial Proteins/*metabolism, Endo-1,4-beta Xylanases/*metabolism, Gammaproteobacteria/*metabolism, Hydrogen-Ion Concentration, Hydrolysis, Seawater/*microbiology, Temperature, Xylans/*metabolism
Enzymology24395600Gene cloning, expression and characterisation of a new beta-agarase, AgWH50C, producing neoagarobiose from Agarivorans gilvus WH0801.Liu N, Mao X, Yang M, Mu B, Wei DWorld J Microbiol Biotechnol10.1007/s11274-013-1591-y2014Alteromonadaceae/chemistry/*enzymology/genetics, Amino Acid Sequence, Bacterial Proteins/*chemistry/genetics/metabolism, *Cloning, Molecular, Disaccharides/*metabolism, Enzyme Stability, Gene Expression, Glycoside Hydrolases/*chemistry/genetics/metabolism, Hydrogen-Ion Concentration, Kinetics, Molecular Sequence Data, Sequence AlignmentMetabolism
Phylogeny25085545A laboratory case study of efficient polyhydoxyalkonates production by Bacillus cereus, a contaminant in Saccharophagus degradans ATCC 43961 in minimal sea salt media.Sawant SS, Salunke BK, Kim BSCurr Microbiol10.1007/s00284-014-0664-y2014Bacillus cereus/growth & development/*isolation & purification/*metabolism, Culture Media/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Gas Chromatography-Mass Spectrometry, Molecular Sequence Data, Polyhydroxyalkanoates/*metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spectroscopy, Fourier Transform Infrared, Sudan, Time FactorsMetabolism
Metabolism25846336Comparative study of MnO2 nanoparticle synthesis by marine bacterium Saccharophagus degradans and yeast Saccharomyces cerevisiae.Salunke BK, Sawant SS, Lee SI, Kim BSAppl Microbiol Biotechnol10.1007/s00253-015-6559-42015Culture Media/chemistry, Filtration, Gammaproteobacteria/*metabolism, Manganese Compounds/*metabolism, Microscopy, Electron, Transmission, Nanoparticles/*metabolism, Oxides/*metabolism, Potassium Permanganate/metabolism, Saccharomyces cerevisiae/*metabolism, Spectrum AnalysisCultivation
Metabolism26138394A rapid, sensitive, simple plate assay for detection of microbial alginate lyase activity.Sawant SS, Salunke BK, Kim BSEnzyme Microb Technol10.1016/j.enzmictec.2015.05.0032015Alginates/metabolism, Bacillus cereus/enzymology/growth & development, Bacterial Proteins/*analysis/metabolism, Bacteriological Techniques, Gammaproteobacteria/enzymology/growth & development, Glucuronic Acid/metabolism, Hexuronic Acids/metabolism, Hydrolysis, Iodine, Paracoccus/enzymology/growth & development, Polysaccharide-Lyases/*analysis/metabolism, Ponds/microbiology, Soil Microbiology, Species SpecificityEnzymology
Metabolism26458373Putative Alginate Assimilation Process of the Marine Bacterium Saccharophagus degradans 2-40 Based on Quantitative Proteomic Analysis.Takagi T, Morisaka H, Aburaya S, Tatsukami Y, Kuroda K, Ueda MMar Biotechnol (NY)10.1007/s10126-015-9667-32015Alginates/*metabolism, Aquatic Organisms/*metabolism, Bacterial Proteins/*chemistry/*metabolism, Gammaproteobacteria/*metabolism, Glucuronic Acid/metabolism, Hexuronic Acids/metabolism, Proteome/*metabolism, Signal Transduction/physiologyProteome
Enzymology26809714Characterization of the biochemical properties of recombinant Xyn10C from a marine bacterium, Saccharophagus degradans 2-40.Ko JK, Ko H, Kim KH, Choi IGBioprocess Biosyst Eng10.1007/s00449-016-1548-22016Aquatic Organisms/*enzymology/genetics, Bacterial Proteins/*chemistry/genetics, Glycoside Hydrolases/*chemistry/genetics, Gram-Negative Aerobic Rods and Cocci/*enzymology/genetics, Hot Temperature, Hydrogen-Ion Concentration, Recombinant Proteins/chemistry/genetics, Xylans/*chemistryStress
Enzymology27129264Biochemical and Structural Characterization of a Five-domain GH115 alpha-Glucuronidase from the Marine Bacterium Saccharophagus degradans 2-40T.Wang W, Yan R, Nocek BP, Vuong TV, Di Leo R, Xu X, Cui H, Gatenholm P, Toriz G, Tenkanen M, Savchenko A, Master ERJ Biol Chem10.1074/jbc.M115.7029442016Amino Acid Sequence, Circular Dichroism, Gammaproteobacteria/*enzymology, Glycoside Hydrolases/chemistry/*metabolism, Marine Biology, Models, Molecular, Protein Conformation, Sequence Homology, Amino AcidMetabolism
Metabolism27208098A Novel Glycoside Hydrolase Family 5 beta-1,3-1,6-Endoglucanase from Saccharophagus degradans 2-40T and Its Transglycosylase Activity.Wang D, Kim DH, Seo N, Yun EJ, An HJ, Kim JH, Kim KHAppl Environ Microbiol10.1128/AEM.00635-162016Cellulase/*genetics/*metabolism, Chromatography, High Pressure Liquid, Chromatography, Thin Layer, Cloning, Molecular, Escherichia coli/genetics/metabolism, Gammaproteobacteria/*enzymology/genetics, Gene Expression, Glucans/metabolism, Hydrolysis, Polysaccharides/metabolism, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Substrate SpecificityEnzymology
Enzymology27521023The first bacterial beta-1,6-endoglucanase from Saccharophagus degradans 2-40(T) for the hydrolysis of pustulan and laminarin.Wang D, Kim DH, Yun EJ, Park YC, Seo JH, Kim KHAppl Microbiol Biotechnol10.1007/s00253-016-7753-82016Cellulase/genetics/*isolation & purification/*metabolism, Cloning, Molecular, Disaccharides/metabolism, Escherichia coli/genetics/metabolism, Gammaproteobacteria/*enzymology/genetics, Gene Expression, Glucans/*metabolism, Glucose/metabolism, Hydrogen-Ion Concentration, Hydrolysis, Kinetics, Phaeophyta, Polysaccharides/*metabolism, Recombinant Proteins/genetics/isolation & purification/metabolism, TemperatureMetabolism
Enzymology27664160Enzymatic liquefaction of agarose above the sol-gel transition temperature using a thermostable endo-type beta-agarase, Aga16B.Kim JH, Yun EJ, Seo N, Yu S, Kim DH, Cho KM, An HJ, Kim JH, Choi IG, Kim KHAppl Microbiol Biotechnol10.1007/s00253-016-7831-y2016Cloning, Molecular, Enzyme Stability, Gammaproteobacteria/enzymology, Glycoside Hydrolases/genetics/isolation & purification/*metabolism, Kinetics, Phase Transition, Recombinant Proteins/metabolism, Seaweed/chemistry, Sepharose/*chemistry/*metabolism, Transition TemperatureMetabolism
Metabolism28216576Identification of 2-keto-3-deoxy-d-Gluconate Kinase and 2-keto-3-deoxy-d-Phosphogluconate Aldolase in an Alginate-Assimilating Bacterium, Flavobacterium sp. Strain UMI-01.Nishiyama R, Inoue A, Ojima TMar Drugs10.3390/md150200372017Aldehyde-Lyases/*metabolism, Alginates/*metabolism, Amino Acid Sequence, Bacteroidetes/metabolism, Escherichia coli/metabolism, Flavobacterium/*metabolism, Gluconates/*metabolism, Glucuronic Acid/metabolism, Hexuronic Acids/metabolism, Oxidoreductases/*metabolism, Phosphotransferases (Alcohol Group Acceptor)/*metabolism, Phylogeny, Proteobacteria/metabolism, Sequence Alignment, Uronic Acids/metabolismPhylogeny
Metabolism29154880Consolidated bioprocessing for production of polyhydroxyalkanotes from red algae Gelidium amansii.Sawant SS, Salunke BK, Kim BSInt J Biol Macromol10.1016/j.ijbiomac.2017.11.0842017Carbon/metabolism, *Fermentation, Polyhydroxyalkanoates/*biosynthesis/*chemistry, Rhodophyta/growth & development/*metabolism, Spectroscopy, Fourier Transform InfraredBiotechnology
29563967A novel beta-glucosidase from Saccharophagus degradans 2-40(T) for the efficient hydrolysis of laminarin from brown macroalgae.Kim DH, Kim DH, Lee SH, Kim KHBiotechnol Biofuels10.1186/s13068-018-1059-22018
Biotechnology29896965Model-Based Complete Enzymatic Production of 3,6-Anhydro-l-galactose from Red Algal Biomass.Pathiraja D, Lee S, Choi IGJ Agric Food Chem10.1021/acs.jafc.8b017922018Agar/*chemistry, Bacterial Proteins/*chemistry, Biocatalysis, Galactose/*analogs & derivatives/chemistry, Gammaproteobacteria/*enzymology, Glycoside Hydrolases/*chemistry, Hydrolysis, Rhodophyta/*chemistryEnzymology
Enzymology30128580Identification and biochemical characterization of a novel cold-adapted 1,3-alpha-3,6-anhydro-L-galactosidase, Ahg786, from Gayadomonas joobiniege G7.Asghar S, Lee CR, Park JS, Chi WJ, Kang DK, Hong SKAppl Microbiol Biotechnol10.1007/s00253-018-9277-x2018Alteromonadaceae/chemistry/*enzymology/genetics, Amino Acid Sequence, Bacterial Proteins/*chemistry/genetics/metabolism, Enzyme Stability, Galactosidases/*chemistry/genetics/metabolism, Hydrogen-Ion Concentration, Molecular Sequence Data, Protein Sorting Signals, Sequence Alignment, TemperatureMetabolism
Metabolism30788710Molecular Cloning and Characterization of a Novel Cold-Adapted Alkaline 1,3-alpha-3,6-Anhydro-L-galactosidase, Ahg558, from Gayadomonas joobiniege G7.Asghar S, Lee CR, Chi WJ, Kang DK, Hong SKAppl Biochem Biotechnol10.1007/s12010-019-02963-w2019Chromatography, Thin Layer, Cloning, Molecular, Disaccharides/metabolism, Galactosidases/*metabolism, Galactosides/metabolism, Hydrogen-Ion Concentration, Mass Spectrometry, Oligosaccharides/metabolismEnzymology
Phylogeny31793854Thalassocella blandensis gen. nov., sp. nov., a novel member of the family Cellvibrionaceae.Lucena T, Arahal DR, Sanz-Saez I, Acinas SG, Sanchez O, Aznar R, Pedros-Alio C, Pujalte MJInt J Syst Evol Microbiol10.1099/ijsem.0.0039062020Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Mediterranean Sea, Phospholipids/chemistry, Phyllobacteriaceae/*classification/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Enzymology33278947Specific hydrolysis of curdlan with a novel glycoside hydrolase family 128 beta-1,3-endoglucanase containing a carbohydrate-binding module.Jia X, Wang C, Du X, Peng H, Liu L, Xiao Y, He CCarbohydr Polym10.1016/j.carbpol.2020.1172762020Biocatalysis, Cellulase/*chemistry, Cloning, Molecular/methods, Escherichia coli/enzymology/genetics, Gammaproteobacteria/*enzymology/genetics, Glycoside Hydrolases/*chemistry, Hydrogen-Ion Concentration, Hydrolysis, Oligosaccharides/biosynthesis, Polysaccharides, Bacterial/*chemistry, Substrate Specificity, Temperature, beta-Glucans/*chemistry
Metabolism33527231Enhanced glycolic acid yield through xylose and cellobiose utilization by metabolically engineered Escherichia coli.Cabulong RB, Banares AB, Nisola GM, Lee WK, Chung WJBioprocess Biosyst Eng10.1007/s00449-020-02502-62021Cellobiose/genetics/*metabolism, *Escherichia coli/genetics/metabolism, Glycolates/*metabolism, *Metabolic Engineering, *Microorganisms, Genetically-Modified/genetics/metabolism, Xylose/genetics/*metabolismBiotechnology
34335544Carbohydrate-Binding Module and Linker Allow Cold Adaptation and Salt Tolerance of Maltopentaose-Forming Amylase From Marine Bacterium Saccharophagus degradans 2-40 (T).Ding N, Zhao B, Ban X, Li C, Venkataram Prasad BV, Gu Z, Li ZFront Microbiol10.3389/fmicb.2021.7084802021

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6690Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17024)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17024
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
23294Nathan A. Ekborg, Jose M. Gonzalez, Michael B. Howard, Larry E. Taylor, Steven W. Hutcheson, Ronald M. Weiner10.1099/ijs.0.63627-0Saccharophagus degradans gen. nov., sp. nov., a versatile marine degrader of complex polysaccharidesIJSEM 55: 1545-1549 200516014479
63341Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 66513)https://www.ccug.se/strain?id=66513
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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
70149Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID87752.1StrainInfo: A central database for resolving microbial strain identifiers