Strain identifier

BacDive ID: 3773

Type strain: Yes

Species: Saccharicrinis fermentans

Strain history: CIP <- 2001, IFO <- IAM <- NCIMB <- ATCC <- H. Veldkamp

NCBI tax ID(s): 982 (species)

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General

@ref: 3636

BacDive-ID: 3773

DSM-Number: 9555

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

description: Saccharicrinis fermentans DSM 9555 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from marine mud.

NCBI tax id

  • NCBI tax id: 982
  • Matching level: species

strain history

@refhistory
3636<- ATCC <- H. Veldkamp
67770IAM 14302 <-- NCIMB 2218 <-- ATCC 19072 <-- H. Veldkamp.
119310CIP <- 2001, IFO <- IAM <- NCIMB <- ATCC <- H. Veldkamp

doi: 10.13145/bacdive3773.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Marinilabiliaceae
  • genus: Saccharicrinis
  • species: Saccharicrinis fermentans
  • full scientific name: Saccharicrinis fermentans (Bachmann 1955) Yang et al. 2014

  • synonyms

    • @ref: 20215
    • synonym: Cytophaga fermentans

@ref: 3636

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Cytophagales

family: Marinilabiliaceae

genus: Saccharicrinis

species: Saccharicrinis fermentans

full scientific name: Saccharicrinis fermentans (Bachmann 1955) Yang et al. 2014 emend. Liu et al. 2014

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative100
119310negativerod-shapedno

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_9555_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3636CYTOPHAGA MEDIUM (DSMZ Medium 669)yeshttps://mediadive.dsmz.de/medium/669Name: CYTOPHAGA MEDIUM (DSMZ Medium 669) Composition: NaCl 20.0 g/l Yeast extract 10.0 g/l Agar 3.0 g/l MgSO4 x 7 H2O 1.0 g/l NH4Cl 1.0 g/l K2HPO4 0.2 g/l FeCl3 0.001 g/l Tap water
35746MEDIUM 166 - for Cytophaga fermentansyesAgar (15.000 g);Yeast extract (1.000 g);Casitone (9.000 g);Syntheticsea solution - M0216 (1000.000 ml)
119310CIP Medium 166yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=166
119310CIP Medium 213yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=213

culture temp

@refgrowthtypetemperaturerange
3636positivegrowth30mesophilic
35746positivegrowth30mesophilic
67770positivegrowth30mesophilic
119310positivegrowth25-37mesophilic
119310nogrowth5psychrophilic
119310nogrowth15psychrophilic
119310nogrowth41thermophilic
119310nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119310
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.96

halophily

@refsaltgrowthtested relationconcentration
119310NaClpositivegrowth4 %
119310NaClnogrowth0 %
119310NaClnogrowth2 %
119310NaClnogrowth6 %
119310NaClnogrowth8 %
119310NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1193104853esculin-hydrolysis
119310606565hippurate-hydrolysis
11931017632nitrate-builds gas from
11931017632nitrate-reduction
11931016301nitrite-builds gas from
11931016301nitrite-reduction
11931017632nitrate+respiration

metabolite production

  • @ref: 119310
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11931015688acetoin-
11931017234glucose-

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
119310oxidase-
119310beta-galactosidase+3.2.1.23
119310alcohol dehydrogenase-1.1.1.1
119310gelatinase-
119310catalase-1.11.1.6
119310gamma-glutamyltransferase-2.3.2.2
119310lysine decarboxylase-4.1.1.18
119310ornithine decarboxylase-4.1.1.17
119310phenylalanine ammonia-lyase-4.3.1.24
119310tryptophan deaminase-
119310urease-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
119310-+++------++-+----+-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119310---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample type
3636marine mud
67770Marine mud
119310Environment, Marine mud

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Terrestrial#Mud (Sludge)
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_795.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16198;96_483;97_552;98_635;99_795&stattab=map
  • Last taxonomy: Saccharicrinis fermentans subclade
  • 16S sequence: AB517712
  • Sequence Identity:
  • Total samples: 2505
  • soil counts: 121
  • aquatic counts: 1715
  • animal counts: 641
  • plant counts: 28

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
36361Risk group (German classification)
1193101Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Cytophaga fermentans gene for 16S ribosomal RNA, partial sequence, strain: NBRC 15936AB5177121448ena982
20218Cytophaga fermentans gene for 16S ribosomal RNA, partial sequenceD126611257ena869213
3636Cytophaga fermentans strain ATCC 19072 16S ribosomal RNA gene, partial sequenceM587661474ena982

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cytophaga fermentans DSM 9555869213.4wgspatric869213
66792Cytophaga fermentans JCM 211421236536.3wgspatric869213
66792Saccharicrinis fermentans JCM 211422576861787draftimg869213
66792Saccharicrinis fermentans DSM 95552509601038draftimg869213
67770Saccharicrinis fermentans DSM 9555 = JCM 21142GCA_000517085scaffoldncbi869213
67770Saccharicrinis fermentans DSM 9555 = JCM 21142GCA_000583675contigncbi869213

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno74.204no
flagellatedno94.227no
gram-positiveno97.047no
anaerobicno62.758no
halophileno76.371no
spore-formingno90.289no
thermophileno97.999no
glucose-utilyes89.851no
aerobicno82.782no
glucose-fermentno56.176no

External links

@ref: 3636

culture collection no.: DSM 9555, ATCC 19072, IAM 14302, NCIMB 2218, JCM 21142, CECT 7602, CIP 104805, IFO 15936, LMG 1338, NBRC 15936

straininfo link

  • @ref: 73285
  • straininfo: 2146

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19620374Marinifilum fragile gen. nov., sp. nov., isolated from tidal flat sediment.Na H, Kim S, Moon EY, Chun JInt J Syst Evol Microbiol10.1099/ijs.0.009027-02009Bacterial Typing Techniques, Bacteroidetes/chemistry/*classification/genetics/*isolation & purification, Cluster Analysis, Cytophaga/genetics, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Humans, Korea, Microscopy, Electron, Scanning, Microscopy, Electron, Transmission, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysisPathogenicity
Phylogeny24436065Carboxylicivirga gen. nov. in the family Marinilabiliaceae with two novel species, Carboxylicivirga mesophila sp. nov. and Carboxylicivirga taeanensis sp. nov., and reclassification of Cytophaga fermentans as Saccharicrinis fermentans gen. nov., comb. nov.Yang SH, Seo HS, Woo JH, Oh HM, Jang H, Lee JH, Kim SJ, Kwon KKInt J Syst Evol Microbiol10.1099/ijs.0.053462-02014Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, Cytophaga/*classification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Genetics24675859Draft Genome Sequence of Cytophaga fermentans JCM 21142T, a Facultative Anaerobe Isolated from Marine Mud.Starns D, Oshima K, Suda W, Iino T, Yuki M, Inoue J, Kitamura K, Iida T, Darby A, Hattori M, Ohkuma MGenome Announc10.1128/genomeA.00206-142014Phylogeny
Phylogeny24695056Saccharicrinis carchari sp. nov., isolated from a shark, and emended descriptions of the genus Saccharicrinis and Saccharicrinis fermentans.Liu QQ, Wang Y, Li J, Du ZJ, Chen GJInt J Syst Evol Microbiol10.1099/ijs.0.061986-02014Animals, Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gills/microbiology, Molecular Sequence Data, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sharks/*microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny26297337Saccharicrinis marinus sp. nov., isolated from marine sediment.Liu QQ, Li J, Xiao D, Lu JX, Chen GJ, Du ZJInt J Syst Evol Microbiol10.1099/ijsem.0.0004362015Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3636Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 9555)https://www.dsmz.de/collection/catalogue/details/culture/DSM-9555
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
35746Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16753
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
73285Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID2146.1StrainInfo: A central database for resolving microbial strain identifiers
119310Curators of the CIPCollection of Institut Pasteur (CIP 104805)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104805