Strain identifier

BacDive ID: 2250

Type strain: Yes

Species: Atopococcus tabaci

Strain history: CIP <- 2004, CCUG <- Karlsson Ingela, SIK, Göteborg, Sweden <- A. Wiernik, Swedish Match, Sweden

NCBI tax ID(s): 1121024 (strain), 269774 (species)

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General

@ref: 7051

BacDive-ID: 2250

DSM-Number: 17538

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, coccus-shaped

description: Atopococcus tabaci DSM 17538 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from moist snuff, industry.

NCBI tax id

NCBI tax idMatching level
1121024strain
269774species

strain history

@refhistory
7051<- CIP <- CCUG <- Karlsson Ingela <- A. Wiernik
123405CIP <- 2004, CCUG <- Karlsson Ingela, SIK, Göteborg, Sweden <- A. Wiernik, Swedish Match, Sweden

doi: 10.13145/bacdive2250.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Carnobacteriaceae
  • genus: Atopococcus
  • species: Atopococcus tabaci
  • full scientific name: Atopococcus tabaci Collins et al. 2005

@ref: 7051

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Carnobacteriaceae

genus: Atopococcus

species: Atopococcus tabaci

full scientific name: Atopococcus tabaci Collins et al. 2005

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
31461positivecoccus-shapedno
69480positive100
123405positivecoccus-shapedno

colony morphology

@refincubation periodhemolysis ability
580552 days
1234051

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_17538_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_17538_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_17538_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_17538_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_17538_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7051COLUMBIA 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
40008MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
123405CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
7051positivegrowth28mesophilic
31461positiveoptimum30mesophilic
40008positivegrowth30mesophilic
58055positivegrowth30mesophilic
123405positivegrowth25-45
123405nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31461aerobe
58055aerobe

spore formation

@refspore formationconfidence
31461no
69480no99.621

halophily

@refsaltgrowthtested relationconcentration
31461NaClpositivegrowth08-09 %
123405NaClpositivegrowth6.5 %

observation

  • @ref: 31461
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3146117234glucose+carbon source
3146117716lactose+carbon source
3146125017leucine+carbon source
3146117306maltose+carbon source
3146133942ribose+carbon source
3146117992sucrose+carbon source
3146127082trehalose+carbon source
314614853esculin+hydrolysis
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837117992sucrose+builds acid from
6837117716lactose+builds acid from
6837117306maltose+builds acid from
6837117814salicin+builds acid from
6837118305arbutin-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
6837028087glycogen-builds acid from
6837028017starch+builds acid from
6837016634raffinose+builds acid from
6837015443inulin-builds acid from
6837027082trehalose+builds acid from
6837017716lactose+builds acid from
6837017924D-sorbitol-builds acid from
6837016899D-mannitol-builds acid from
6837030849L-arabinose-builds acid from
6837016988D-ribose-builds acid from
6837029016arginine+hydrolysis
683704853esculin+hydrolysis
68370606565hippurate+hydrolysis
6836830849L-arabinose-fermentation
6836827613amygdalin-fermentation
6836828053melibiose-fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol-fermentation
6836817634D-glucose-fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
1234054853esculin-hydrolysis
123405606565hippurate+hydrolysis
12340517632nitrate-reduction
12340516301nitrite-reduction
6837917632nitrate-reduction
683794853esculin+hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose+fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose+fermentation
6837917716lactose+fermentation
6837917992sucrose+fermentation
6837928087glycogen-fermentation
6838129016arginine-hydrolysis
6838116988D-ribose+builds acid from
6838116899D-mannitol-builds acid from
6838130911sorbitol-builds acid from
6838117716lactose+builds acid from
6838116634raffinose-builds acid from
6838117992sucrose+builds acid from
6838130849L-arabinose-builds acid from
6838118333D-arabitol-builds acid from
6838140585alpha-cyclodextrin-builds acid from
6838128087glycogen-builds acid from
6838127941pullulan-builds acid from
6838117306maltose+builds acid from
683816731melezitose-builds acid from
68381320055methyl beta-D-glucopyranoside-builds acid from
6838116443D-tagatose-builds acid from
6838116199urea-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6837015688acetoinno
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
6838115688acetoinno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6838115688acetoin-
6837015688acetoin-
6836815688acetoin-
6836835581indole-
12340515688acetoin-

enzymes

@refvalueactivityec
31461acid phosphatase+3.1.3.2
31461alpha-galactosidase+3.2.1.22
31461urease+3.5.1.5
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
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382lipase (C 14)-
68382esterase (C 4)+
68381urease-3.5.1.5
68381beta-mannosidase-3.2.1.25
68381glycyl tryptophan arylamidase-
68381pyrrolidonyl arylamidase+3.4.19.3
68381Alanyl-Phenylalanyl-Proline arylamidase-
68381alkaline phosphatase-3.1.3.1
68381alpha-galactosidase-3.2.1.22
68381beta-glucuronidase-3.2.1.31
68381arginine dihydrolase-3.5.3.6
68379catalase-1.11.1.6
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase-3.5.1.B15
68370arginine dihydrolase+3.5.3.6
68370leucine arylamidase+3.4.11.1
68370alkaline phosphatase+3.1.3.1
68370beta-galactosidase+3.2.1.23
68370beta-glucuronidase-3.2.1.31
68370alpha-galactosidase+3.2.1.22
68370pyrrolidonyl arylamidase+3.4.19.3
68370beta-glucosidase+3.2.1.21
68368cytochrome oxidase-1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23
123405oxidase-
123405beta-galactosidase+3.2.1.23
123405alcohol dehydrogenase-1.1.1.1
123405catalase-1.11.1.6
123405gamma-glutamyltransferase-2.3.2.2
123405lysine decarboxylase-4.1.1.18
123405ornithine decarboxylase-4.1.1.17

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELControlGLURIBXYLMANMALLACSACGLYGCAT
58055--+--++++---+---+++--

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
58055-++--++---+----+----
123405--++-------+---+----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
58055---------------------

API 20STR

@refVPHIPESCPYRAalpha GALbeta GURbeta GALPALLAPADHRIBARAMANSORLACTREINURAFAMDGLYGbeta HEM
58055-++++-++++----++-++--

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
58055----------++++--------++-+++++++---+---+----------
123405---------++++-----------+/-+-++-++----------------+/-

API rID32STR

@refADH Argbeta GLUbeta GARbeta GURalpha GALPALRIBMANSORLACTRERAFSACLARADARLCDEXVPAPPAbeta GALPyrAbeta NAGGTAHIPGLYGPULMALMELMLZMbeta DGTAGbeta MANURE
7051------+--+--+------+-----++-----
58055-++---+--++-+-----+++-+--+------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling date
7051moist snuff, industrySwedenSWEEurope
58055Moist snuff,industrySwedenSWEEurope2003-10-01
123405Environment, Moist snuff, industrySwedenSWEEurope

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Industrial

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
70511Risk group (German classification)
1234051Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7051
  • description: Atopcoccus sp. CCUG 48253 16S rRNA gene, type strain CCUG 48253T
  • accession: AJ634917
  • length: 1550
  • database: ena
  • NCBI tax ID: 269774

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Atopococcus tabaci DSM 17538GCA_000429585scaffoldncbi1121024
66792Atopococcus tabaci DSM 175381121024.3wgspatric1121024
66792Atopococcus tabaci DSM 175382524023159draftimg1121024

GC content

  • @ref: 7051
  • GC-content: 46

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno87no
motileno65.141yes
flagellatedno87.41yes
gram-positiveyes91.886yes
anaerobicno95.457no
aerobicno70.295yes
halophileyes92.718yes
spore-formingno89.61yes
thermophileno96.809no
glucose-utilyes89.818yes
glucose-fermentyes77.866no

External links

@ref: 7051

culture collection no.: DSM 17538, CCUG 48253, CIP 108502

straininfo link

  • @ref: 71809
  • straininfo: 265383

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16014503Atopococcus tabaci gen. nov., sp. nov., a novel Gram-positive, catalase-negative, coccus-shaped bacterium isolated from tobacco.Collins MD, Wiernik A, Falsen E, Lawson PAInt J Syst Evol Microbiol10.1099/ijs.0.63618-02005Bacterial Typing Techniques, Catalase/*metabolism, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Gram-Positive Cocci/chemistry/*classification/genetics/isolation & purification, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tobacco/*microbiologyGenetics
Phylogeny19329605Lacticigenium naphtae gen. nov., sp. nov., a halotolerant and motile lactic acid bacterium isolated from crude oil.Iino T, Suzuki K, Harayama SInt J Syst Evol Microbiol10.1099/ijs.0.003293-02009Anaerobiosis, Bacterial Typing Techniques, Base Composition, Carbohydrate Metabolism, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, *Environmental Microbiology, Fatty Acids/analysis, Gram-Positive Bacteria/*classification/genetics/*isolation & purification/physiology, Hydrogen-Ion Concentration, Japan, Lactic Acid/metabolism, Locomotion, Molecular Sequence Data, Peptidoglycan/analysis, *Petroleum, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, TemperatureMetabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7051Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17538)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17538
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
31461Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2776228776041
40008Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6132
58055Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 48253)https://www.ccug.se/strain?id=48253
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 life28604660 35: 676-683 2017
68368Automatically annotated from API 20E
68370Automatically annotated from API 20STR
68371Automatically annotated from API 50CH acid
68379Automatically annotated from API Coryne
68381Automatically annotated from API rID32STR
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)
71809Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID265383.1StrainInfo: A central database for resolving microbial strain identifiers
123405Curators of the CIPCollection of Institut Pasteur (CIP 108502)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108502