Strain identifier

BacDive ID: 12514

Type strain: Yes

Species: Proteiniphilum acetatigenes

Strain Designation: TB107

Strain history: S. Chen and X. Dong TB107.

NCBI tax ID(s): 1123008 (strain), 294710 (species)

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General

@ref: 7384

BacDive-ID: 12514

DSM-Number: 18083

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

description: Proteiniphilum acetatigenes TB107 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from granule sludge, UASB reactor treating brewery wastewater.

NCBI tax id

NCBI tax idMatching level
1123008strain
294710species

strain history

@refhistory
7384<- JCM <- S. Chen and X. Dong; TB107
67770S. Chen and X. Dong TB107.

doi: 10.13145/bacdive12514.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Dysgonomonadaceae
  • genus: Proteiniphilum
  • species: Proteiniphilum acetatigenes
  • full scientific name: Proteiniphilum acetatigenes Chen and Dong 2005

@ref: 7384

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Dysgonomonadaceae

genus: Proteiniphilum

species: Proteiniphilum acetatigenes

full scientific name: Proteiniphilum acetatigenes Chen and Dong 2005 emend. Hahnke et al. 2016

strain designation: TB107

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31558negative2.05 µm0.75 µmrod-shapedyes
69480negative99.992

colony morphology

  • @ref: 7384
  • incubation period: 1-2 days

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_18083_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_18083_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_18083_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_18083_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_18083_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

  • @ref: 7384
  • name: PYG MEDIUM (MODIFIED) (DSMZ Medium 104)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/104
  • composition: Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water

culture temp

@refgrowthtypetemperaturerange
7384positivegrowth37mesophilic
31558positivegrowth20-45
31558positiveoptimum37mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
31558positivegrowth6-9.7alkaliphile
31558positiveoptimum7.75

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
7384anaerobe
31558anaerobe
69480anaerobe97.961

spore formation

@refspore formationconfidence
31558no
69481no100
69480no99.981

halophily

@refsaltgrowthtested relationconcentration
31558NaClpositivegrowth0-5 %
31558NaClpositiveoptimum2.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3155830089acetate+carbon source
3155816449alanine+carbon source
3155829016arginine+carbon source
3155815428glycine+carbon source
3155817272propionate+carbon source
3155815361pyruvate+carbon source
3155817822serine+carbon source
3155826986threonine+carbon source
315584853esculin+hydrolysis
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68380serine arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase+3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase+3.4.11.1
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase-
68380alkaline phosphatase+3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase+3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380beta-glucosidase+3.2.1.21
68380alpha-glucosidase+3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase+3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
7384--++-+++-+++----+--+----+--+/--
7384--++-++--++/-+/-----+--+----+----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
7384granule sludge, UASB reactor treating brewery wastewaterChinaCHNAsia
60055Granule sludge,UASB reactor,brewery waistwater
67770Granule sludge of a UASB reactor treating brewery wastewater

isolation source categories

Cat1Cat2Cat3
#Engineered#Biodegradation#Anaerobic digestor
#Engineered#Waste#Industrial wastewater
#Engineered#Waste#Activated sludge

taxonmaps

  • @ref: 69479
  • File name: preview.99_8059.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_103;96_3654;97_4577;98_5872;99_8059&stattab=map
  • Last taxonomy: Proteiniphilum acetatigenes subclade
  • 16S sequence: AY742226
  • Sequence Identity:
  • Total samples: 1558
  • soil counts: 86
  • aquatic counts: 150
  • animal counts: 1236
  • plant counts: 86

Safety information

risk assessment

  • @ref: 7384
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7384
  • description: Proteiniphilum acetatigenes strain TB107 16S ribosomal RNA gene, complete sequence
  • accession: AY742226
  • length: 1523
  • database: ena
  • NCBI tax ID: 294710

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Proteiniphilum acetatigenes DSM 180831123008.3wgspatric1123008
66792Proteiniphilum acetatigenes DSM 180832518645612draftimg1123008
67770Proteiniphilum acetatigenes DSM 18083GCA_000380985scaffoldncbi1123008

GC content

@refGC-contentmethod
738446.6
738443.1sequence analysis
6777038thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno80.007yes
flagellatedno97.689no
gram-positiveno95.201yes
anaerobicyes61.243no
aerobicno90.773yes
halophileno83.225no
spore-formingno91.772yes
glucose-utilyes88.467no
thermophileno99.137no
glucose-fermentyes57.928no

External links

@ref: 7384

culture collection no.: DSM 18083, CGMCC 1.5024, JCM 12891, CCUG 53886

straininfo link

  • @ref: 81733
  • straininfo: 281464

literature

  • topic: Phylogeny
  • Pubmed-ID: 16280479
  • title: Proteiniphilum acetatigenes gen. nov., sp. nov., from a UASB reactor treating brewery wastewater.
  • authors: Chen S, Dong X
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63807-0
  • year: 2005
  • mesh: Anaerobiosis, Bacteroidetes/*classification/cytology/isolation & purification, Base Composition, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fermentation, Hydrogen-Ion Concentration, Molecular Sequence Data, Phylogeny, Sewage/*microbiology, Temperature, *Water Microbiology
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7384Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18083)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18083
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
31558Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2784828776041
60055Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53886)https://www.ccug.se/strain?id=53886
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 life28604660 35: 676-683 2017
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68380Automatically annotated from API rID32A
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
81733Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID281464.1StrainInfo: A central database for resolving microbial strain identifiers