Strain identifier

BacDive ID: 139940

Type strain: Yes

Species: Hallerella succinigenes

Strain Designation: UW S3, UWS3

Strain history: B. Abt; DSMZ, Germany; DSM 104698 (=UWS3) <-- A. Neumann; Univ. of Wisconsin, USA; UWS3.

NCBI tax ID(s): 1896222 (species)

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General

@ref: 42548

BacDive-ID: 139940

DSM-Number: 104698

keywords: genome sequence, 16S sequence, Bacteria, obligate anaerobe, mesophilic, rod-shaped

description: Hallerella succinigenes UW S3 is an obligate anaerobe, mesophilic, rod-shaped bacterium that was isolated from Pig cecum.

NCBI tax id

  • NCBI tax id: 1896222
  • Matching level: species

strain history

@refhistory
42548<- A. Neumann; Univ. of Wisconsin, Dept. of Bacteriology, Madison, Wisc., USA; UW S3 {2016}
67770B. Abt; DSMZ, Germany; DSM 104698 (=UWS3) <-- A. Neumann; Univ. of Wisconsin, USA; UWS3.

doi: 10.13145/bacdive139940.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/fibrobacterota
  • domain: Bacteria
  • phylum: Fibrobacterota
  • class: Fibrobacteria
  • order: Fibrobacterales
  • family: Fibrobacteraceae
  • genus: Hallerella
  • species: Hallerella succinigenes
  • full scientific name: Hallerella succinigenes Wylensek et al. 2021

@ref: 42548

domain: Bacteria

phylum: Fibrobacteres

class: Fibrobacteria

order: Fibrobacterales

family: Fibrobacteraceae

genus: Hallerella

species: Hallerella succinigenes

full scientific name: Hallerella succinigenes D. Wylensek

strain designation: UW S3, UWS3

type strain: yes

Morphology

cell morphology

  • @ref: 69645
  • cell length: 1-2 µm
  • cell shape: rod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
42548MDM (MODIFIED DEHORITY MEDIUM) (DSMZ Medium 1668)yeshttps://mediadive.dsmz.de/medium/1668Name: MDM (modified dehority medium) (DSMZ Medium 1668) Composition: L-Cysteine HCl 1.0 g/l Tryptone 1.0 g/l Yeast extract 1.0 g/l K2HPO4 0.013608 g/l NaHCO3 0.013442 g/l NaCl 0.00935 g/l NH4Cl 0.00321 g/l MgCl2 x 2 H2O 0.001942 g/l ZnCl2 0.000546 g/l NiCl2 x 6 H2O 0.000474 g/l CoCl2 0.000208 g/l MgCl2 0.00019 g/l CaCl2 0.000178 g/l Na2WO4 x 2 H2O 0.000132 g/l Na2 MoO4 x 2 H2O 9.6e-05 g/l Na2SeO3 7e-05 g/l FeSO4 x 7 H2O 5.6e-05 g/l Distilled water
69645Gifu Anaerobic Medium, modi?edyes
69645Wilkins-Chalgren Anaerobe brothyessupplemented with L-cysteine and DTT (0.05% and 0.02% (w/v), respectively)
69645modified YCFAyes

culture temp

@refgrowthtypetemperaturerange
42548positivegrowth37mesophilic
67770positivegrowth37mesophilic
69645positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 69645
  • oxygen tolerance: obligate anaerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836727082trehalose-builds acid from
6836762345L-rhamnose-builds acid from
6836730911sorbitol-builds acid from
6836716634raffinose-builds acid from
683676731melezitose-builds acid from
6836716024D-mannose-builds acid from
6836717057cellobiose-builds acid from
6836717754glycerol-builds acid from
683674853esculin-hydrolysis
683675291gelatin-hydrolysis
6836730849L-arabinose-builds acid from
6836765327D-xylose-builds acid from
6836717814salicin-builds acid from
6836717306maltose-builds acid from
6836717992sucrose-builds acid from
6836717716lactose-builds acid from
6836716899D-mannitol-builds acid from
6836717634D-glucose-builds acid from
6836716199urea-hydrolysis
6836727897tryptophan-energy source
6964517234glucose+assimilation
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate+degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
6836735581indoleno
6964530089acetateyes
6964515740formateyes
6964530031succinateyes
6838035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
6838035581indole-
6836735581indole-

enzymes

@refvalueactivityec
68380serine arylamidase-
68380glutamyl-glutamate 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
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
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
68367beta-glucosidase-3.2.1.21
68367gelatinase-
68367urease-3.5.1.5

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRE
42548--------------------

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
42548------+/---+/---+----+-----------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperatureisolation procedure
42548Pig cecumMadison, WIUSAUSANorth America
67770Cecum of a pig in MadisonWisconsinUSAUSANorth America
69645Pig caecumMadison, WisconsinUSAUSANorth AmericaModified Dehority Medium (DSMZ medium 1668)supplemented with 10 g cellobiose5 days37anaerobic

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Suidae (Pig,Swine)
#Host Body-Site#Gastrointestinal tract#Small intestine

Safety information

risk assessment

  • @ref: 42548
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 42548
  • description: Fibrobacter sp. DSM 104698 16S ribosomal RNA gene, partial sequence
  • accession: MN537467
  • length: 1521
  • database: ena
  • NCBI tax ID: 2652275

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Hallerella succinigenes UWS3GCA_002797675contigncbi1896222
66792Hallerella succinigenes UWS32747842507draftimg1896222

GC content

  • @ref: 67770
  • GC-content: 49.2
  • method: genome sequence analysis

External links

@ref: 42548

culture collection no.: DSM 104698, JCM 34256

straininfo link

  • @ref: 96370
  • straininfo: 405682

Reference

@idauthorstitledoi/urlcatalogue
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
42548Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-104698Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104698)
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68367Automatically annotated from API 20A
68380Automatically annotated from API rID32A
69645David Wylensek, Thomas C. A. Hitch, Thomas Riedel, Afrizal Afrizal, Neeraj Kumar, Esther Wortmann, Tianzhe Liu, Saravanan Devendran, Till R. Lesker, Sara B. Hernández, Viktoria Heine, Eva M. Buhl, Paul M. D'Agostino, Fabio Cumbo, Thomas Fischöder, Marzena Wyschkon, Torey Looft, Valeria R. Parreira, Birte Abt, Heidi L. Doden, Lindsey Ly, João M. P. Alves, Markus Reichlin, Krzysztof Flisikowski, Laura Navarro Suarez, Anthony P. Neumann, Garret Suen, Tomas de Wouters, Sascha Rohn, Ilias Lagkouvardos, Emma Allen-Vercoe, Cathrin Spröer, Boyke Bunk, Anja J. Taverne-Thiele, Marcel Giesbers, Jerry M. Wells, Klaus Neuhaus, Angelika Schnieke, Felipe Cava, Nicola Segata, Lothar Elling, Till Strowig, Jason M. Ridlon, Tobias A. M. Gulder, Jörg Overmann, Thomas ClavelA collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity10.1038/s41467-020-19929-w
96370Reimer, 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-ID405682.1