Strain identifier

BacDive ID: 99

Type strain: Yes

Species: Acidaminococcus intestini

Strain history: CIP <- 2004, H. Marchandin, Montpellier Hosp., Montpellier, France: strain ADV 255.99

NCBI tax ID(s): 1120921 (strain), 187327 (species)

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General

@ref: 15684

BacDive-ID: 99

DSM-Number: 21505

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, coccus-shaped, colony-forming

description: Acidaminococcus intestini DSM 21505 is an anaerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from Human peritoneal fluid.

NCBI tax id

NCBI tax idMatching level
187327species
1120921strain

strain history

@refhistory
15684<- CCUG <- CIP <- H. Marchandin, Montpellier Hosp., Montpellier, France; ADV 255.99
420182004, H. Marchandin, Montpellier Hosp., Montpellier, France: strain ADV 255.99
67771<- CCUG <- C Bizet, CIP, Paris, France <- H Marchandin, Montpellier, France
120258CIP <- 2004, H. Marchandin, Montpellier Hosp., Montpellier, France: strain ADV 255.99

doi: 10.13145/bacdive99.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Negativicutes
  • order: Acidaminococcales
  • family: Acidaminococcaceae
  • genus: Acidaminococcus
  • species: Acidaminococcus intestini
  • full scientific name: Acidaminococcus intestini Jumas-Bilak et al. 2007

@ref: 15684

domain: Bacteria

phylum: Firmicutes

class: Negativicutes

order: Selenomonadales

family: Acidaminococcaceae

genus: Acidaminococcus

species: Acidaminococcus intestini

full scientific name: Acidaminococcus intestini Jumas-Bilak et al. 2007

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapemotility
22965negative0.5-0.6 µmcoccus-shapedno
67771coccus-shaped
67771negative
120258negativecoccus-shapedno

colony morphology

@reftype of hemolysiscolony sizecolony colorcolony shapeincubation periodmedium used
22965gamma0.3-0.5 mmwhitishcircular2 daysColumbia sheep blood agar
120258

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15684COLUMBIA 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
15684PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: 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
22965Columbia sheep blood agaryes
42018MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
120258CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
15684positivegrowth37mesophilic
42018positivegrowth37mesophilic
67771positivegrowth37mesophilic
120258positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
15684anaerobe
22965obligate anaerobe
67771anaerobe

spore formation

@refspore formation
22965no
67771no

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2296524996lactate-growth
2296517632nitrate-reduction
2296529985L-glutamate+fermentation
12025817108D-arabinose-degradation
12025815824D-fructose-degradation
12025817634D-glucose-degradation
12025865327D-xylose-degradation
12025817057cellobiose-degradation
12025817716lactose-degradation
12025817306maltose-degradation
12025817814salicin-degradation
12025817992sucrose+degradation
1202584853esculin-hydrolysis
12025817632nitrate-reduction
12025816301nitrite-reduction
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
2296517272propionateyes
2296517968butyrateyes
2296530089acetateyes
12025835581indoleno
6838035581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
22965catalase-1.11.1.6
22965cytochrome oxidase-1.9.3.1
22965gelatinase-
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase-3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase+
68380glycin arylamidase+
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase-
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 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
120258oxidase-
120258beta-galactosidase-3.2.1.23
120258gelatinase-
120258amylase-
120258DNase-
120258caseinase-3.4.21.50
120258catalase-1.11.1.6
120258tween esterase-
120258lecithinase-
120258lipase-
120258protease-
120258urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120258--+-------++--------

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
15684-----------------+---+/-+/---++--
15684-----------------+---+---++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture durationenrichment culture temperaturesampling dateisolation date
15684Human peritoneal fluidUniversity Hospital Arnaud de Villeneuve, MontpellierFranceFRAEurope
22965gastro-intestinal tract of humansColumbia sheep blood agar2-5 days37.0
59050Human peritoneal fluid,45-yr-old manMontpellierFranceFRAEurope1999-06-01
67771From human peritoneal fluid, 45-yr-old manUniversity Hospital Arnaud de Villeneuve, MontpellierFranceFRAEurope
120258Human, Peritoneal liquidMontpellierFranceFRAEurope1999

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Host#Human
#Host Body Product#Fluids
#Host Body-Site#Other#Abdomen

taxonmaps

  • @ref: 69479
  • File name: preview.99_2644.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_220;96_1410;97_1683;98_2049;99_2644&stattab=map
  • Last taxonomy: Acidaminococcus intestini subclade
  • 16S sequence: NR_041894
  • Sequence Identity:
  • Total samples: 87963
  • soil counts: 822
  • aquatic counts: 4666
  • animal counts: 82055
  • plant counts: 420

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
156842Risk group (German classification)
1202581Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
15684Acidaminococcus intestini strain ADV 255.99 16S ribosomal RNA gene, partial sequenceAF4738351439ena187327
15684Acidaminococcus intestini strain ADV 255.99 16S ribosomal RNA, partial sequenceNR_0418941439nuccore187327

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Acidaminococcus intestini DSM 215051120921.3wgspatric1120921
66792Acidaminococcus intestini DSM 215052524614855draftimg1120921
67771Acidaminococcus intestini DSM 21505GCA_000425045scaffoldncbi1120921

GC content

@refGC-contentmethod
1568449.3
2296549.3high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno92.051yes
flagellatedno95.523yes
gram-positiveno95.505yes
anaerobicyes99.539yes
aerobicno98.689yes
halophileno64.111no
spore-formingno90.198no
thermophileno98.62yes
glucose-utilyes57.023no
glucose-fermentno50no

External links

@ref: 15684

culture collection no.: DSM 21505, CCUG 50930, CIP 108586, KCTC 15229, ADV 255.99, AIP 283.01

straininfo link

  • @ref: 69782
  • straininfo: 310986

literature

  • topic: Phylogeny
  • Pubmed-ID: 17911303
  • title: Acidaminococcus intestini sp. nov., isolated from human clinical samples.
  • authors: Jumas-Bilak E, Carlier JP, Jean-Pierre H, Mory F, Teyssier C, Gay B, Campos J, Marchandin H
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64883-0
  • year: 2007
  • mesh: Acidaminococcus/*classification/cytology/*isolation & purification/physiology, Adolescent, Adult, Aged, Aged, 80 and over, Anaerobiosis/physiology, Bacterial Proteins/metabolism, Bacterial Typing Techniques, Base Composition, Chromosomes, Bacterial/genetics, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Enzymes/metabolism, Female, France, Genes, rRNA, Gram-Negative Bacterial Infections/*microbiology, Humans, Male, Middle Aged, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
15684Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21505)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21505
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
22965Estelle Jumas-Bilak,Jean-Philippe Carlier,Hélène Jean-Pierre,Francine Mory,Corinne Teyssier,Bernard Gay,Josiane Campos,Hélène Marchandin10.1099/ijs.0.64883-0Acidaminococcus intestini sp. nov., isolated from human clinical samplesIJSEM 57: 2314-2319 200717911303
42018Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6231
59050Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 50930)https://www.ccug.se/strain?id=50930
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)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68380Automatically annotated from API rID32A
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69782Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID310986.1StrainInfo: A central database for resolving microbial strain identifiers
120258Curators of the CIPCollection of Institut Pasteur (CIP 108586)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108586