Strain identifier

BacDive ID: 12505

Type strain: Yes

Species: Porphyromonas asaccharolytica

Strain Designation: B440

Strain history: ATCC 25260 <-- W. E. C. Moore VPI 4198 <-- S. Finegold B440.

NCBI tax ID(s): 879243 (strain), 28123 (species)

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General

@ref: 8784

BacDive-ID: 12505

DSM-Number: 20707

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

description: Porphyromonas asaccharolytica B440 is an anaerobe, mesophilic, rod-shaped human pathogen that was isolated from empyema.

NCBI tax id

NCBI tax idMatching level
879243strain
28123species

strain history

@refhistory
8784<- ATCC <- W.E.C. Moore, VPI 4198 (Bacteroides melaninogenicus subsp. asaccharolyticus) <- S. Finegold, B440
67770ATCC 25260 <-- W. E. C. Moore VPI 4198 <-- S. Finegold B440.

doi: 10.13145/bacdive12505.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Porphyromonadaceae
  • genus: Porphyromonas
  • species: Porphyromonas asaccharolytica
  • full scientific name: Porphyromonas asaccharolytica (Holdeman and Moore 1970) Shah and Collins 1988

  • synonyms

    @refsynonym
    20215Bacteroides melaninogenicus subsp. asaccharolyticus
    20215Bacteroides asaccharolyticus

@ref: 8784

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Porphyromonadaceae

genus: Porphyromonas

species: Porphyromonas asaccharolytica

full scientific name: Porphyromonas asaccharolytica (Holdeman and Moore 1970) Shah and Collins 1988 emend. Hahnke et al. 2016

strain designation: B440

type strain: yes

Morphology

cell morphology

@refcell shapegram stainconfidence
68367rod-shaped
68367negative
125438negative94.104
125439negative91.9

colony morphology

  • @ref: 45041
  • incubation period: 3 days

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_20707_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8784COLUMBIA 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
8784CHOPPED 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

culture temp

@refgrowthtypetemperature
8784positivegrowth37
45041positivegrowth37
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
8784anaerobe
45041anaerobe
125438anaerobe92.362

spore formation

@refspore formationconfidence
68367no
125438no94.849
125439no99.2

observation

  • @ref: 67770
  • observation: quinones: MK-10, MK-11, MK-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838017632nitrate-reduction
6838027897tryptophan+energy source
6838029985L-glutamate-degradation
6838016199urea-hydrolysis
6838016024D-mannose-fermentation
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
683674853esculin-hydrolysis
683675291gelatin+hydrolysis
6836730849L-arabinose-builds acid from
6836765327D-xylose-builds acid from
6836717306maltose-builds acid from
6836717992sucrose-builds acid from
6836717716lactose-builds acid from
6836716899D-mannitol-builds acid from
6836716199urea-hydrolysis
6836727897tryptophan+energy source

metabolite production

@refChebi-IDmetaboliteproduction
6838035581indoleyes
6836735581indoleyes

metabolite tests

@refChebi-IDmetaboliteindole test
6838035581indole+
6836735581indole+

enzymes

@refvalueactivityec
68380alanine arylamidase+3.4.11.2
68380beta-glucosidase-3.2.1.21
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase-3.2.1.23
68380serine arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase+3.4.11.1
68380proline-arylamidase-3.4.11.5
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
68380alpha-glucosidase-3.2.1.20
68380alpha-galactosidase-3.2.1.22
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
8784+-+/-----+/---+-+/------------
8784+---------+-------------

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
8784-----------+-+-++--+---+/-+--+/--
8784-------------+-++--+-+/---+--+/--
8784-+-----------+-+++/--+-+--+--+-

Isolation, sampling and environmental information

isolation

@refsample type
8784empyema
45041Human empyema
67770Empyema

isolation source categories

  • Cat1: #Host Body Product
  • Cat2: #Fluids

taxonmaps

  • @ref: 69479
  • File name: preview.99_3456.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_391;96_1725;97_2066;98_2541;99_3456&stattab=map
  • Last taxonomy: Porphyromonas asaccharolytica
  • 16S sequence: NR_074588
  • Sequence Identity:
  • Total samples: 14984
  • soil counts: 179
  • aquatic counts: 178
  • animal counts: 14606
  • plant counts: 21

Safety information

risk assessment

  • @ref: 8784
  • pathogenicity human: yes
  • pathogenicity animal: yes
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Porphyromonas asaccharolytica strain ATCC 25260 16S-23S ribosomal RNA intergenic spacer and 23S ribosomal RNA gene, partial sequenceAF386069672nuccore879243
20218Porphyromonas asaccharolytica strain ATCC 25260 16S-23S ribosomal RNA intergenic spacer, partial sequenceAY546484858nuccore879243
20218Porphyromonas asaccharolytica strain ATCC 25260 16S ribosomal RNA gene, partial sequenceFJ7925371368nuccore879243
20218Porphyromonas asaccharolytica DSM 20707 strain ATCC 25260 16S ribosomal RNA gene, partial sequenceL164901478nuccore879243
8784Porphyromonas asaccharolytica DSM 20707 16S ribosomal RNA, partial sequenceNR_0745881517nuccore879243
67770Porphyromonas asaccharolytica gene for 16S ribosomal RNA, partial sequence, strain: JCM 6326AB5476531479nuccore879243

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Porphyromonas asaccharolytica DSM 20707GCA_000212375completencbi879243
66792Porphyromonas asaccharolytica DSM 20707879243.3completepatric879243
66792Porphyromonas asaccharolytica VPI 4198, DSM 207072504756018completeimg879243

GC content

@refGC-contentmethod
878452.1
878452.5sequence analysis
6777053thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno94.104yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes92.362yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no97.571no
125438spore-formingspore-formingAbility to form endo- or exosporesno94.849yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno90.443yes
125438motile2+flagellatedAbility to perform flagellated movementno89no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno99.2
125439BacteriaNetmotilityAbility to perform movementyes69.4
125439BacteriaNetgram_stainReaction to gram-stainingnegative91.9
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthanaerobe74.4

External links

@ref: 8784

culture collection no.: CCUG 7834, CCUG 14451, JCM 6326, DSM 20707, ATCC 25260, VPI 4198, BCRC 10618, LMG 13178

straininfo link

  • @ref: 81724
  • straininfo: 13933

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny7981094Porphyromonas gingivicanis sp. nov. and Porphyromonas crevioricanis sp. nov., isolated from beagles.Hirasawa M, Takada KInt J Syst Bacteriol10.1099/00207713-44-4-6371994Animals, DNA, Bacterial/analysis, Dogs/*microbiology, Gingiva/microbiology, Porphyromonas/genetics/*isolation & purification/metabolismEnzymology
Phylogeny8186085Porphyromonas canoris sp. nov., an asaccharolytic, black-pigmented species from the gingival sulcus of dogs.Love DN, Karjalainen J, Kanervo A, Forsblom B, Sarkiala E, Bailey GD, Wigney DI, Jousimies-Somer HInt J Syst Bacteriol10.1099/00207713-44-2-2041994Animals, Bacterial Typing Techniques, Carbohydrate Metabolism, DNA, Bacterial, Dental Plaque/*microbiology, Dogs, Fatty Acids/analysis, Gingiva/*microbiology, Gingival Diseases/microbiology/*veterinary, Nucleic Acid Hybridization, Pigments, Biological, Porphyromonas/*classification/isolation & purificationMetabolism
9871324Phospholipid molecular species distribution of Porphyromonas asaccharolytica ATCC 25260T: effects of temperature, culture age and pH.Tavana AM, Drucker DB, Boote VJ Appl Microbiol10.1111/j.1365-2672.1998.tb05268.x1998Hydrogen-Ion Concentration, Phospholipids/*analysis, Porphyromonas/*chemistry, Temperature
Phylogeny1577463216S-23S rRNA gene internal transcribed spacer sequences for analysis of the phylogenetic relationships among species of the genus Porphyromonas.Conrads G, Citron DM, Tyrrell KL, Horz HP, Goldstein EJCInt J Syst Evol Microbiol10.1099/ijs.0.63234-02005Bacterial Typing Techniques, DNA, Ribosomal Spacer/*analysis, Genes, rRNA, Humans, Molecular Sequence Data, *Phylogeny, Porphyromonas/*classification/genetics, RNA, Ribosomal, 16S/*genetics, RNA, Ribosomal, 23S/*genetics, Sequence Analysis, DNA, Species SpecificityTranscriptome
35618163Chalcones with potential antibacterial and antibiofilm activities against periodontopathogenic bacteria.Satokata AAC, Souza JH, Silva LLO, Santiago MB, Ramos SB, Assis LR, Theodoro RDS, Oliveira LRE, Regasini LO, Martins CHGAnaerobe10.1016/j.anaerobe.2022.1025882022

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8784Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20707)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20707
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
45041Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 7834)https://www.ccug.se/strain?id=7834
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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
81724Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13933.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1