Strain identifier

BacDive ID: 2131

Type strain: Yes

Species: Campylobacter lari

Strain history: CIP <- 1986, NCTC <- ATCC <- 1980, N.B. Skirrow: strain WRI 3034/77, Larus argintatus

NCBI tax ID(s): 201 (species)

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General

@ref: 4316

BacDive-ID: 2131

DSM-Number: 11375

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, motile

description: Campylobacter lari DSM 11375 is a microaerophile, mesophilic, motile bacterium that was isolated from cloacal swab of herring gulls.

NCBI tax id

  • NCBI tax id: 201
  • Matching level: species

strain history

@refhistory
4316<- NCTC <- M. B. Skirrow
67770CIP 102722 <-- NCTC 11352 <-- ATCC 35221 <-- N. B. Skirrow WRI 3034/77.
120560CIP <- 1986, NCTC <- ATCC <- 1980, N.B. Skirrow: strain WRI 3034/77, Larus argintatus

doi: 10.13145/bacdive2131.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Epsilonproteobacteria
  • order: Campylobacterales
  • family: Campylobacteraceae
  • genus: Campylobacter
  • species: Campylobacter lari
  • full scientific name: Campylobacter lari corrig. Benjamin et al. 1984

  • synonyms

    • @ref: 20215
    • synonym: Campylobacter laridis

@ref: 4316

domain: Bacteria

phylum: Proteobacteria

class: Epsilonproteobacteria

order: Campylobacterales

family: Campylobacteraceae

genus: Campylobacter

species: Campylobacter lari subsp. lari

full scientific name: Campylobacter lari subsp. lari (Benjamin et al. 1984) Debruyne et al. 2009

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes93.891
6948099.983negative
120560yesnegativerod-shaped

colony morphology

  • @ref: 4316
  • type of hemolysis: gamma
  • incubation period: 1-2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4316COLUMBIA 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
41802MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
120560CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
4316positivegrowth37mesophilic
41802positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
4316microaerophile
120560microaerophile

spore formation

@refspore formationconfidence
69481no100
69480no99.998

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12056017632nitrate+reduction
12056016301nitrite-reduction
6837316199urea-hydrolysis
6837317632nitrate+reduction
68373606565hippurate-hydrolysis
6837330089acetate-assimilation
6837317272propionate-assimilation
6837325115malate-assimilation
6837316947citrate-assimilation
6837717634D-glucose-builds acid from
6837715824D-fructose-builds acid from
6837717306maltose-builds acid from
6837716199urea-hydrolysis
6837727897tryptophan-energy source
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate+reduction
6838027897tryptophan-energy source

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.
6837348923erythromycinyesyes14 µg
68373100147nalidixic acidyesyes84 µg

metabolite production

@refChebi-IDmetaboliteproduction
6837735581indoleno
6837316136hydrogen sulfideno
12056035581indoleno
6838035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
6838035581indole-
6837735581indole-

enzymes

@refvalueactivityec
4316catalase+1.11.1.6
4316cytochrome-c oxidase+1.9.3.1
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
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 (C 4)-
68380serine arylamidase-
68380glutamyl-glutamate 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 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
68377tryptophan deaminase-4.1.99.1
68377beta-galactosidase-3.2.1.23
68377alkaline phosphatase-3.1.3.1
68377lipase-
68377urease-3.5.1.5
68377beta-lactamase-3.5.2.6
68373catalase+1.11.1.6
68373L-aspartate arylamidase-3.4.11.21
68373pyrrolidonyl arylamidase-3.4.19.3
68373urease-3.5.1.5
120560oxidase+
120560catalase+1.11.1.6
120560urease-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
65632-+---+----+---------
120560---+-+----+----+----

API CAM

@refURENITESTHIPGGTTTCPYRAArgAAspAPALH2SGLUSUTNALCFZACEPROPMLTCITEROCAT
4316-+--+/-+/--+------------+
4316-+--++---+/--++-+/------+
4316-+--++-+-+----------+
4316-+------------------+
4316-+--++-+------------
4316-+--++-+-+
4316-++/--++/--+/--+/-
4316-+---+--------------+
4316-+--++/--+/--+/-----------
4316-+--++--------------
4316-+--+/-----++
65632-++--+-+-+----------+

API NH

@refPENGLUFRUMALSACODCURELIPPALbeta GALProAGGTIND
4316----+-----+--
4316-----+-----+-

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
65632--------------+-++---+--+----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinenthost speciesisolation date
4316cloacal swab of herring gullsUnited KingdomGBREurope
67770Cloacal swab of herring gull (Larus argentatus)Larus argentatus
120560Animal, Herring, gull cloacal swab1977

isolation source categories

Cat1Cat2Cat3
#Infection#Patient#Swab
#Host#Birds
#Host Body-Site#Gastrointestinal tract
#Host Body-Site#Urogenital tract

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
43162Risk group (German classification)
1205602Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Campylobacter lari gene for 16S ribosomal RNA, strain:JCM2530AB1813681435ena201
20218Campylobacter lari genes for 16S rRNA, tRNA-Ala, tRNA-Ile, 23S rRNA, partial and complete sequence, strain: JCM 2530AB573229946ena201
20218Campylobacter lari DNA, 16S rRNA, 16S-23S ribosomal RNA intergenic spacer, 23S rRNA, complete and partial sequence, strain: JCM 2530AB644222730ena201
20218Campylobacter lari subsp. lari strain NCTC 11352 16S ribosomal RNA (rrs) gene, partial sequenceDQ1741451341ena650054
20218Campylobacter lari strain DSM 11375 16S ribosomal RNA gene, partial sequenceHM0075711338ena201
20218Campylobacter lari subsp. lari strain ATCC 35221 16S ribosomal RNA gene, partial sequenceJX9125221435ena650054
20218Campylobacter lari subsp. lari strain CCUG 23947 16S ribosomal RNA, complete sequenceL043161459ena650054
20218Campylobacter laridis (VC187) 16S ribosomal RNA, 3' segmentM92310359ena201
4316Campylobacter lari subsp. lari strain ATCC 35221 16S ribosomal RNA gene, partial sequenceAY6211141441ena650054

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Campylobacter lari subsp. lari LMG 8846GCA_013372185completencbi650054
66792Campylobacter lari strain FDAARGOS_1101201.72completepatric201
66792Campylobacter lari strain NCTC11352201.33wgspatric201
66792Campylobacter lari subsp. lari650054.3wgspatric650054
66792Campylobacter lari subsp. lari strain LMG 8846650054.4completepatric650054
66792Campylobacter lari ATCC 352212675903699draftimg650054
67770Campylobacter lari subsp. lari ATCC 35221GCA_900111465contigncbi650054
67770Campylobacter lari NCTC11352GCA_900446615contigncbi201

GC content

  • @ref: 4316
  • GC-content: 32.5
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes60.154no
gram-positiveno99.109no
anaerobicno86.019yes
aerobicno98.157yes
halophileno81.681no
spore-formingno97.079no
thermophileno78.298no
glucose-utilno84.578no
motileyes86.646no
glucose-fermentno86.2no

External links

@ref: 4316

culture collection no.: DSM 11375, ATCC 35221, CCUG 10773, CCUG 23947, CIP 102722, JCM 2530, LMG 8846, NCTC 11352, WRI 3034/77, JCM 14870, CCM 4897, LMG 7605, WDCM 00204

straininfo link

  • @ref: 71759
  • straininfo: 1533

literature

topicPubmed-IDtitleauthorsjournalyearmeshtopic2DOI
Enzymology1328825Analysis of chromosome-sized DNA from the bacterial genome of thermophilic Campylobacter laridis by pulsed-field gel electrophoresis and physical mapping.Matsumoto K, Matsuda M, Kaneuchi CMicrobios1992Base Sequence, Campylobacter/*genetics, Chromosome Mapping, Chromosomes, Bacterial, DNA Restriction Enzymes, DNA, Bacterial/*genetics, Electrophoresis, Gel, Pulsed-Field, Molecular Sequence DataGenetics
Genetics8593626Lipo-oligosaccharide of the Campylobacter lari type strain ATCC 35221. Structure of the liberated oligosaccharide and an associated extracellular polysaccharide.Aspinall GO, Monteiro MA, Pang HCarbohydr Res1995Acetylgalactosamine, Acetylglucosamine/analysis, Campylobacter/*chemistry, Carbohydrate Conformation, Carbohydrate Sequence, Deoxy Sugars/analysis/chemistry, Galactose/analysis, Glucose/analysis, Heptoses/analysis/chemistry, Lipopolysaccharides/*chemistry/isolation & purification, Magnetic Resonance Spectroscopy, Mass Spectrometry, Molecular Sequence Data, Molecular Structure, Polysaccharides, Bacterial/*chemistry, Sugar PhosphatesEnzymology10.1016/0008-6215(95)00284-7
Phylogeny19406805Novel Campylobacter lari-like bacteria from humans and molluscs: description of Campylobacter peloridis sp. nov., Campylobacter lari subsp. concheus subsp. nov. and Campylobacter lari subsp. lari subsp. nov.Debruyne L, On SL, De Brandt E, Vandamme PInt J Syst Evol Microbiol2009Animals, Bacterial Proteins/chemistry/genetics, Bacterial Typing Techniques, Bivalvia/*microbiology, Campylobacter/*classification/genetics/isolation & purification/physiology, Campylobacter Infections/*microbiology, Campylobacter lari/*classification/genetics/isolation & purification/physiology, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Diarrhea/microbiology, Genes, rRNA, Heat-Shock Proteins/genetics, Humans, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Polymorphism, Restriction Fragment Length, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Shellfish/*microbiology, Species SpecificityEnzymology10.1099/ijs.0.000851-0
Pathogenicity20973408Structural analysis and expression of the full-length cytochrome P450 gene operon in Campylobacter lari.Nakanishi S, Tazumi A, Aihara N, Sekizuka T, Amano K, Moore JE, Millar BC, Matsuda MBr J Biomed Sci2010Amino Acid Sequence, Animals, Base Sequence, Campylobacter lari/*genetics, Cytochrome P-450 Enzyme System/*genetics, Genes, Bacterial, Humans, Molecular Sequence Data, Operon/genetics, Phylogeny, Sequence AlignmentGenetics10.1080/09674845.2010.11730310
Pathogenicity22359318Comparative analysis of Campylobacter lari cytolethal distending toxin (CDT) effect on HeLa cells.Nakajima T, Hirayama J, Tazumi A, Hayashi K, Tasaki E, Asakura M, Yamasaki S, Moore JE, Millar BC, Matsuda MJ Basic Microbiol2012Bacterial Toxins/*metabolism/*toxicity, Blotting, Western, Campylobacter lari/*pathogenicity, Epithelial Cells/*drug effects, HeLa Cells, Humans, MicroscopyMetabolism10.1002/jobm.201100297
Phylogeny22806114Molecular analysis of the 16S-23S rDNA internal spacer region (ISR) and truncated tRNA(Ala) gene segments in Campylobacter lari.Hayashi K, Tazumi A, Nakanishi S, Nakajima T, Matsubara K, Ueno H, Moore JE, Millar BC, Matsuda MWorld J Microbiol Biotechnol2012Campylobacter lari/*genetics, DNA, Ribosomal Spacer/*genetics, Polymerase Chain Reaction, RNA, Ribosomal, 16S/*genetics, RNA, Ribosomal, 23S/*genetics10.1007/s11274-012-1049-7
Pathogenicity24693571Molecular structural analysis of major outer membrane protein (MOMP) gene clusters in Campylobacter lari.Nakajima T, Ara W, Saito K, Moores JE, Millar BC, Matsuda MBr J Biomed Sci2014Animals, Bacterial Proteins/chemistry/*genetics, Blotting, Northern, Blotting, Southern, Campylobacter lari/*genetics, Humans, Molecular Structure, Multigene Family, Sequence Alignment, Sequence Analysis, DNA, Sequence Homology, Nucleic AcidTranscriptome10.1080/09674845.2014.11669958

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4316Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11375)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11375
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
41802Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14440
65632Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 23947)https://www.ccug.se/strain?id=23947
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/
68373Automatically annotated from API CAM
68377Automatically annotated from API NH
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
71759Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1533.1StrainInfo: A central database for resolving microbial strain identifiers
120560Curators of the CIPCollection of Institut Pasteur (CIP 102722)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102722