Strain identifier

BacDive ID: 12562

Type strain: Yes

Species: Prevotella amnii

Strain history: CCUG 53648 <-- S. Kawash.

NCBI tax ID(s): 1122979 (strain), 419005 (species)

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General

@ref: 16819

BacDive-ID: 12562

DSM-Number: 23384

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, Gram-negative, rod-shaped, human pathogen

description: Prevotella amnii DSM 23384 is an anaerobe, Gram-negative, rod-shaped human pathogen that was isolated from amniotic fluid of a 29-year-old female.

NCBI tax id

NCBI tax idMatching level
419005species
1122979strain

strain history

@refhistory
16819<- JCM/RIKEN <- CCUG <- S. Kawash
67770CCUG 53648 <-- S. Kawash.

doi: 10.13145/bacdive12562.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Prevotellaceae
  • genus: Prevotella
  • species: Prevotella amnii
  • full scientific name: Prevotella amnii Lawson et al. 2008

@ref: 16819

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Prevotellaceae

genus: Prevotella

species: Prevotella amnii

full scientific name: Prevotella amnii Lawson et al. 2008 emend. Hahnke et al. 2016

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32204negative1.9 µm1 µmrod-shapedno
68367rod-shaped
68367negative
69480no90.5
69480negative95.734

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16819COLUMBIA 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
16819CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)yeshttps://mediadive.dsmz.de/medium/110Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water
16819FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a)yeshttps://mediadive.dsmz.de/medium/1203aName: FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a) Composition: Fastidious Anaerobe Basal Broth 35.4 g/l Distilled water
16819YCFA-MEDIUM (MODIFIED) (DSMZ Medium 1611)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1611.pdf

culture temp

@refgrowthtypetemperature
16819positivegrowth37
32204positivegrowth37
59961positivegrowth37
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
16819anaerobe
32204anaerobe
59961anaerobe

spore formation

@refspore formationconfidence
32204no
68367no
69480no92.33
69481no100

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3220417234glucose+carbon source
3220417716lactose+carbon source
3220417306maltose+carbon source
322044853esculin+hydrolysis
6836727082trehalose-builds acid from
6836762345L-rhamnose-builds acid from
6836730911sorbitol-builds acid from
6836716634raffinose-builds acid from
683676731melezitose-builds acid from
6836717057cellobiose-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
6836716199urea-hydrolysis
6836727897tryptophan-energy source
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
6836735581indoleno
6838035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
6838035581indole-
6836735581indole-

enzymes

@refvalueactivityec
16819catalase-1.11.1.6
16819cytochrome-c oxidase-1.9.3.1
32204acid phosphatase+3.1.3.2
32204alkaline phosphatase+3.1.3.1
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
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase-3.2.1.21
68380alpha-glucosidase+3.2.1.20
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5
68367catalase-1.11.1.6
68367beta-glucosidase-3.2.1.21
68367gelatinase-
68367urease-3.5.1.5

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRECATSPORGRAMCOCC
16819---+/-+/-+/-------+/------------
16819--+/--+/----------+/-------

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
16819---++/-+---+------+--+----+--+-
16819---+++---+------+--+--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
16819amniotic fluid of a 29-year-old femaleGöteborgSwedenSWEEurope
59961Human amniotic fluid,turbid and ill smellingGöteborgSwedenSWEEurope2006-10-23
67770Human amniotic fluid

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Host Body Product#Fluids
#Host#Human#Female

taxonmaps

  • @ref: 69479
  • File name: preview.99_1412.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_44;96_817;97_951;98_1118;99_1412&stattab=map
  • Last taxonomy: Prevotella amnii subclade
  • 16S sequence: AM422125
  • Sequence Identity:
  • Total samples: 41878
  • soil counts: 340
  • aquatic counts: 589
  • animal counts: 40800
  • plant counts: 149

Safety information

risk assessment

  • @ref: 16819
  • pathogenicity human: yes, in single cases
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Prevotella amnii gene for 16S ribosomal RNA, partial sequence, strain: JCM 14753AB5476701491nuccore419005
16819Prevotella amniotica partial 16S rRNA gene, type strain CCUG 53648AM4221251474nuccore419005

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Prevotella amnii DSM 233841122979.3wgspatric1122979
66792Prevotella amnii JCM 147531236496.3wgspatric1122979
66792Prevotella amnii JCM 147532585427892draftimg1122979
66792Prevotella amnii DSM 233842518645615draftimg1122979
67770Prevotella amnii DSM 23384 = JCM 14753GCA_000378745scaffoldncbi1122979
67770Prevotella amnii DSM 23384 = JCM 14753GCA_000613765contigncbi1122979

GC content

  • @ref: 16819
  • GC-content: 36.6
  • method: sequence analysis

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno95.734yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes88.281yes
69480spore-formingspore-formingAbility to form endo- or exosporesno92.33no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no96.58yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno93.083yes
69480flagellatedmotile2+Ability to perform flagellated movementno90.5no

External links

@ref: 16819

culture collection no.: DSM 23384, CCUG 53648, JCM 14753, KCTC 15072

straininfo link

  • @ref: 81776
  • straininfo: 303425

literature

  • topic: Phylogeny
  • Pubmed-ID: 18175689
  • title: Prevotella amnii sp. nov., isolated from human amniotic fluid.
  • authors: Lawson PA, Moore E, Falsen E
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65118-0
  • year: 2008
  • mesh: Adult, Amniotic Fluid/*microbiology, Bacterial Typing Techniques, Bacteroidaceae Infections/*microbiology, DNA, Bacterial/analysis, Fatty Acids/analysis, Female, Genes, rRNA, Humans, Molecular Sequence Data, Phenotype, Phylogeny, Prevotella/chemistry/*classification/genetics/*isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
16819Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23384)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23384
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
32204Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128446
59961Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53648)https://www.ccug.se/strain?id=53648
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68367Automatically annotated from API 20A
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
81776Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID303425.1StrainInfo: A central database for resolving microbial strain identifiers