Strain identifier

BacDive ID: 14030

Type strain: Yes

Species: Alistipes finegoldii

Strain history: CIP <- 2003, CCUG <- M. Rautio and H. Jousimies-Somer, KTL, Helsinki, Finland: strain AHN 2437

NCBI tax ID(s): 679935 (strain), 214856 (species)

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General

@ref: 6849

BacDive-ID: 14030

DSM-Number: 17242

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

description: Alistipes finegoldii DSM 17242 is an anaerobe, mesophilic, rod-shaped human pathogen that was isolated from human, appendix tissue, 14-year-old boy.

NCBI tax id

NCBI tax idMatching level
214856species
679935strain

strain history

@refhistory
6849<- CCUG <- M. Rautio, Helsinki; strain AHN 2437
67770CCUG 46020 <-- M. Rautio AHN 2437.
67771<- CCUG <- M Rautio, Helsinki, strain AHN 2437
119353CIP <- 2003, CCUG <- M. Rautio and H. Jousimies-Somer, KTL, Helsinki, Finland: strain AHN 2437

doi: 10.13145/bacdive14030.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Rikenellaceae
  • genus: Alistipes
  • species: Alistipes finegoldii
  • full scientific name: Alistipes finegoldii Rautio et al. 2003

@ref: 6849

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Rikenellaceae

genus: Alistipes

species: Alistipes finegoldii

full scientific name: Alistipes finegoldii Rautio et al. 2003

type strain: yes

Morphology

cell morphology

@refcell shapegram stainconfidencemotility
67771rod-shaped
67771negative
69480negative99.868
119353rod-shapednegativeno

colony morphology

@reftype of hemolysisincubation periodhemolysis ability
6849gamma1-2 days
1193531

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_17242_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6849COLUMBIA 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
6849PYG 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
41769MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
119353CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
6849positivegrowth37mesophilic
41769positivegrowth37mesophilic
67770positivegrowth37mesophilic
67771positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
6849anaerobe
67771anaerobe
69480anaerobe99.245
119353anaerobe

spore formation

@refspore formationconfidence
67771no
69481no100
69480no99.999

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1193534853esculin-hydrolysis
11935317632nitrate-reduction
11935316301nitrite-reduction
11935317632nitrate+respiration
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838017632nitrate-reduction

metabolite production

  • @ref: 119353
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

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
68380alpha-fucosidase+3.2.1.51
68380N-acetyl-beta-glucosaminidase+3.2.1.52
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
119353oxidase-
119353beta-galactosidase-3.2.1.23
119353gelatinase+/-
119353amylase-
119353DNase+
119353caseinase-3.4.21.50
119353catalase-1.11.1.6
119353tween esterase+
119353lecithinase-
119353lipase-
119353protease-
119353urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase+3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119353-+++-+----++++-+-+-+

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
6849--++-++/---+--++--+--+----+--+-
6849--++-++/---+---+-++--+----+--+/--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
6849human, appendix tissue, 14-year-old boyHelsinkiFinlandFINEurope
57028Human appendix tissue,14-yr-old boyHelsinkiFinlandFINEurope1988
67770Human appendiceal tissue sample
67771From human appendix tissue, 14-yr-old boyHelsinkiFinlandFINEurope
119353Human, Appendix tissueFinlandFINEurope

isolation source categories

Cat1Cat2Cat3
#Host#Human#Male
#Host Body-Site#Gastrointestinal tract

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
6849yes, in single cases1Risk group (German classification)
1193531Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Alistipes finegoldii strain CIP 107999 sequence clone 3 16S ribosomal RNA gene, partial sequenceAY6430831446ena679935
20218Alistipes finegoldii strain CIP 107999 sequence clone 4 16S ribosomal RNA gene, partial sequenceAY6430841446ena679935
6849Bacteroides sp. ANH 2437 16S rRNA geneAJ5188741465ena679935
67770Alistipes finegoldii gene for 16S ribosomal RNA, partial sequence, strain: JCM 16770AB5542301487ena214856

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Alistipes finegoldii DSM 17242GCA_000265365completencbi679935
66792Alistipes finegoldii AHN 2437, DSM 172422509601035completeimg679935

GC content

@refGC-contentmethod
684957
6777056.6genome sequence analysis
6777057high performance liquid chromatography (HPLC)
6777157.0high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.09no
flagellatedno96.993no
gram-positiveno97.998yes
anaerobicyes98.192no
aerobicno97.573yes
halophileno83.985no
spore-formingno94.902no
thermophileno98.478yes
glucose-utilyes87.463no
glucose-fermentyes58.526no

External links

@ref: 6849

culture collection no.: DSM 17242, CCUG 46020, CIP 107999, KCTC 15236, AHN 2437, JCM 16770, VTT E-093113T

straininfo link

  • @ref: 83197
  • straininfo: 110568

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12866844Reclassification of Bacteroides putredinis (Weinberg et al., 1937) in a new genus Alistipes gen. nov., as Alistipes putredinis comb. nov., and description of Alistipes finegoldii sp. nov., from human sources.Rautio M, Eerola E, Vaisanen-Tunkelrott ML, Molitoris D, Lawson P, Collins MD, Jousimies-Somer HSyst Appl Microbiol10.1078/0723202033223460292003Appendicitis/*microbiology, Bacterial Typing Techniques, Bacteroides/chemistry/*classification/isolation & purification, Bile/microbiology, Child, DNA, Bacterial/genetics, Enterocolitis, Pseudomembranous/microbiology, Fatty Acids/analysis, Feces/microbiology, Gram-Negative Bacteria/*classification, Humans, Lactose Intolerance/microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Pigments, Biological/analysis, Porphyromonas/chemistry, Ribotyping, Species Specificity, *Terminology as TopicPathogenicity
Genetics23961309Complete genome sequence of the bile-resistant pigment-producing anaerobe Alistipes finegoldii type strain (AHN2437(T)).Mavromatis K, Stackebrandt E, Munk C, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mikhailova N, Huntemann M, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Rohde M, Gronow S, Goker M, Detter JC, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Woyke TStand Genomic Sci10.4056/sigs.35270322013
Phylogeny25563920Mucinivorans hirudinis gen. nov., sp. nov., an anaerobic, mucin-degrading bacterium isolated from the digestive tract of the medicinal leech Hirudo verbana.Nelson MC, Bomar L, Maltz M, Graf JInt J Syst Evol Microbiol10.1099/ijs.0.0000522015Animals, Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gastrointestinal Tract/*microbiology, Hirudo medicinalis/*microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6849Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17242)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17242
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
41769Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5571
57028Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 46020)https://www.ccug.se/strain?id=46020
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 life 35: 676-683 201728604660
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68380Automatically annotated from API rID32A
68382Automatically annotated from API zym
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
83197Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID110568.1StrainInfo: A central database for resolving microbial strain identifiers
119353Curators of the CIPCollection of Institut Pasteur (CIP 107999)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107999