Strain identifier

BacDive ID: 138540

Type strain: Yes

Species: Rhodopseudomonas faecalis

Strain Designation: gc

Strain history: CIP <- 2004, JCM <- 2002, AS <- D. Zhang: strain gc

NCBI tax ID(s): 99655 (species)

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General

@ref: 39983

BacDive-ID: 138540

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

description: Rhodopseudomonas faecalis gc is a mesophilic, Gram-negative bacterium that was isolated from Effluent from an anaerobic reactor digesting chicken faeces.

NCBI tax id

  • NCBI tax id: 99655
  • Matching level: species

strain history

@refhistory
67770AS 1.2176 <-- D. Zhang strain gc.
39983CIP <- 2004, JCM <- 2002, AS <- D. Zhang: strain gc

doi: 10.13145/bacdive138540.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Nitrobacteraceae
  • genus: Rhodopseudomonas
  • species: Rhodopseudomonas faecalis
  • full scientific name: Rhodopseudomonas faecalis Zhang et al. 2002

@ref: 39983

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Hyphomicrobiales

family: Bradyrhizobiaceae

genus: Rhodopseudomonas

species: Rhodopseudomonas faecalis

strain designation: gc

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.995
39983negativerod-shapedyes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
39983MEDIUM 575 - for Rhodocista pekingensisyesDistilled water make up to (1000.000 ml);Sodium chloride (1.000 g);Magnesium chloride hexahydrate (0.500 g);Calcium chloride dihydrate (0.100 g);Yeast extract (0.500 g);Peptone (0.300 g);Potassium di-hydrogen phosphate (1.000 g);Ammonium chloride (1.000g)
39983CIP Medium 575yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=575

culture temp

@refgrowthtypetemperaturerange
39983positivegrowth30mesophilic
67770positivegrowth30mesophilic
39983positivegrowth22-37
39983nogrowth5psychrophilic
39983nogrowth15psychrophilic
39983nogrowth41thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.96

halophily

@refsaltgrowthtested relationconcentration
39983NaClpositivegrowth0 %
39983NaClnogrowth2 %
39983NaClnogrowth4 %
39983NaClnogrowth6 %
39983NaClnogrowth8 %
39983NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
39983citrate-carbon source16947
39983esculin-hydrolysis4853
39983glucose+fermentation17234
39983lactose+fermentation17716
39983nitrate-reduction17632
39983nitrite-reduction16301
39983sodium thiosulfate-builds gas from132112
39983glucose-degradation17234
39983nitrate+respiration17632

antibiotic resistance

  • @ref: 39983
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 39983
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
3998315688acetoin-
3998317234glucose-

enzymes

@refvalueactivityec
39983oxidase-
39983beta-galactosidase-3.2.1.23
39983alcohol dehydrogenase-1.1.1.1
39983gelatinase-
39983amylase-
39983DNase-
39983caseinase-3.4.21.50
39983catalase+1.11.1.6
39983tween esterase-
39983gamma-glutamyltransferase+2.3.2.2
39983lecithinase-
39983lipase-
39983lysine decarboxylase-4.1.1.18
39983ornithine decarboxylase-4.1.1.17
39983phenylalanine ammonia-lyase-4.3.1.24
39983tryptophan deaminase-
39983urease-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
39983--++-+--+-+-----+---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
39983----------+--------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
67770Effluent from an anaerobic reactor digesting chicken faecesShan Xi ProvinceChinaCHNAsia
39983Chicken, faeces

taxonmaps

  • @ref: 69479
  • File name: preview.99_529.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_86;96_297;97_329;98_429;99_529&stattab=map
  • Last taxonomy: Rhodopseudomonas
  • 16S sequence: AF123085
  • Sequence Identity:
  • Total samples: 9060
  • soil counts: 2768
  • aquatic counts: 2210
  • animal counts: 1747
  • plant counts: 2335

Safety information

risk assessment

  • @ref: 39983
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 67770
  • description: Rhodopseudomonas faecalis strain gc 16S ribosomal RNA gene, partial sequence
  • accession: AF123085
  • length: 1444
  • database: ena
  • NCBI tax ID: 99655

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhodopseudomonas faecalis strain JCM 1166899655.3wgspatric99655
66792Rhodopseudomonas faecalis JCM 116682740891854draftimg99655
67770Rhodopseudomonas faecalis JCM 11668GCA_003217325scaffoldncbi99655

GC content

  • @ref: 67770
  • GC-content: 63.6
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes88.694no
flagellatedno50no
gram-positiveno98.99no
anaerobicyes84.778no
halophileno96.981no
spore-formingno94.169no
thermophileno97.4no
glucose-utilyes66.164no
aerobicno80.796no
glucose-fermentno91.869no

External links

@ref: 39983

culture collection no.: CIP 108225, JCM 11668, AS 1.2176, BCRC 80540, CGMCC 1.2176

straininfo link

  • @ref: 95244
  • straininfo: 100909

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12508868Rhodopseudomonas faecalis sp. nov., a phototrophic bacterium isolated from an anaerobic reactor that digests chicken faeces.Zhang D, Yang H, Huang Z, Zhang W, Liu SJInt J Syst Evol Microbiol10.1099/00207713-52-6-20552002Animals, Base Composition, Bioreactors, Chickens, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Feces, Genes, Bacterial, Microscopy, Electron, Molecular Sequence Data, Photobiology, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rhodopseudomonas/*classification/genetics/*isolation & purification/metabolism, Species SpecificityGenetics
Phylogeny21986724Descriptions of Rhodopseudomonas parapalustris sp. nov., Rhodopseudomonas harwoodiae sp. nov. and Rhodopseudomonas pseudopalustris sp. nov., and emended description of Rhodopseudomonas palustris.Ramana VV, Chakravarthy SK, Raj PS, Kumar BV, Shobha E, Ramaprasad EVV, Sasikala C, Ramana CVInt J Syst Evol Microbiol10.1099/ijs.0.026815-02011Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fresh Water/microbiology, Geologic Sediments/microbiology, India, Lipids/analysis, Molecular Sequence Data, Phenotype, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodopseudomonas/*classification/genetics/isolation & purification, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Phylogeny32496176Genomic and genetic sequence information of strains assigned to the genus Rhodopseudomonas reveal the great heterogeneity of the group and identify strain Rhodopseudomonas palustris DSM 123(T) as the authentic type strain of this species.Imhoff JF, Meyer TE, Kyndt JInt J Syst Evol Microbiol10.1099/ijsem.0.0040772020Amino Acid Sequence, Bacterial Typing Techniques, DNA, Bacterial/genetics, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodopseudomonas/*classification, Sequence Analysis, DNATranscriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
39983Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108225Collection of Institut Pasteur (CIP 108225)
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
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
95244Reimer, 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-ID100909.1