Strain identifier

BacDive ID: 159448

Type strain: Yes

Species: Berryella intestinalis

Strain Designation: 68-1-3

Strain history: B. Abt; DSMZ, Germany; DSM 104960 (=68-1-3) <-- T. Looft; ARS, USDA, USA.

NCBI tax ID(s): 1531429 (species)

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General

@ref: 66271

BacDive-ID: 159448

DSM-Number: 104960

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Berryella intestinalis 68-1-3 is a mesophilic bacterium that was isolated from intestinal tract of a three month-old healthy pig.

NCBI tax id

  • NCBI tax id: 1531429
  • Matching level: species

strain history

@refhistory
66271<- T. Looft, USDA-ARS-NADC; 68-1-3
67770B. Abt; DSMZ, Germany; DSM 104960 (=68-1-3) <-- T. Looft; ARS, USDA, USA.

doi: 10.13145/bacdive159448.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Coriobacteriia
  • order: Eggerthellales
  • family: Eggerthellaceae
  • genus: Berryella
  • species: Berryella intestinalis
  • full scientific name: Berryella intestinalis Wylensek et al. 2021

@ref: 66271

domain: Bacteria

phylum: Actinobacteria

class: Coriobacteriia

order: Eggerthellales

family: Eggerthellaceae

genus: Berryella

species: Berryella intestinalis

full scientific name: Berryella intestinalis

strain designation: 68-1-3

type strain: yes

Morphology

cell morphology

@refgram stainconfidencemotility
125439negative98.2
12543891no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
66271CHOPPED MEAT MEDIUM (DSMZ Medium 78)yeshttps://mediadive.dsmz.de/medium/78Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water
66271COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base

culture temp

@refgrowthtypetemperature
66271positivegrowth37
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

  • @ref: 125439
  • oxygen tolerance: obligate anaerobe
  • confidence: 95.2

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 99.5

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838029985L-glutamate-degradation
6838016634raffinose-fermentation
6838016024D-mannose-fermentation
6838029016arginine-hydrolysis
6838016199urea-hydrolysis
6838027897tryptophan-energy source
6838017632nitrate-reduction

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+
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase+
68380glycin arylamidase+
68380alanine arylamidase-3.4.11.2
68380leucine arylamidase+3.4.11.1
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase-3.4.11.1
68380L-arginine arylamidase+
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
68380alpha-arabinosidase-3.2.1.55
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
68380urease-3.5.1.5
68380tyrosine arylamidase+
68380pyrrolidonyl arylamidase-3.4.19.3
68380proline-arylamidase-3.4.11.5
68380alkaline phosphatase-3.1.3.1
68380arginine dihydrolase-3.5.3.6

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
66271-----------------+---+-+-++-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
66271intestinal tract (ileal lumen) of a three month-old healthy pigAmes, IowaUSAUSANorth America42.0308-93.6318
67770Ileal content of a pig in AmesIowaUSAUSANorth America

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_3893.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15800;96_1994;97_2397;98_2961;99_3893&stattab=map
  • Last taxonomy: Berryella intestinalis subclade
  • 16S sequence: MN537474
  • Sequence Identity:
  • Total samples: 8696
  • soil counts: 269
  • aquatic counts: 105
  • animal counts: 8287
  • plant counts: 35

Sequence information

16S sequences

  • @ref: 66271
  • description: Berryella intestinalis strain 68-1-3 16S ribosomal RNA gene, partial sequence
  • accession: MN537474
  • length: 1389
  • database: nuccore
  • NCBI tax ID: 2652296

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Berryella intestinalis 68-1-3GCA_000814825completencbi1531429
66792Berryella intestinalis 68-1-32634166451completeimg1531429

GC content

  • @ref: 67770
  • GC-content: 63.6
  • method: genome sequence analysis

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes81.798no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes88.427no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no93.626no
125438spore-formingspore-formingAbility to form endo- or exosporesno82.552no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno87.412yes
125438motile2+flagellatedAbility to perform flagellated movementno91no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno99.5
125439BacteriaNetmotilityAbility to perform movementyes78
125439BacteriaNetgram_stainReaction to gram-stainingnegative98.2
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate anaerobe95.2

External links

@ref: 66271

culture collection no.: DSM 104960, JCM 34389

straininfo link

  • @ref: 111942
  • straininfo: 401089

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
66271Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-104960Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104960)
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/
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
111942Reimer, 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-ID401089.1
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG