Strain identifier

BacDive ID: 6376

Type strain: Yes

Species: Lachnoanaerobaculum saburreum

Strain Designation: T2

Strain history: CIP <- 1997, J.P. Carlier, Inst. Pasteur, Paris, France: strain AIP 10202 <- ATCC <- L.V. Holdeman: strain VPI 11763 <- J.M. Hardie: strain T2

NCBI tax ID(s): 887325 (strain), 467210 (species)

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General

@ref: 1556

BacDive-ID: 6376

DSM-Number: 3986

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

description: Lachnoanaerobaculum saburreum T2 is an anaerobe, mesophilic human pathogen that was isolated from human dental plaque.

NCBI tax id

NCBI tax idMatching level
887325strain
467210species

strain history

@refhistory
1556<- ATCC <- L.V. Holdeman, VPI 11763 <- J.M. Hardie, T2
67770CIP 105341 <-- J. P. Carlier AIP 10202 <-- ATCC 33271 <-- L. V. Holdeman VPI 11763 <-- J. M. Hardie T2.
122327CIP <- 1997, J.P. Carlier, Inst. Pasteur, Paris, France: strain AIP 10202 <- ATCC <- L.V. Holdeman: strain VPI 11763 <- J.M. Hardie: strain T2

doi: 10.13145/bacdive6376.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Lachnospiraceae
  • genus: Lachnoanaerobaculum
  • species: Lachnoanaerobaculum saburreum
  • full scientific name: Lachnoanaerobaculum saburreum (Prévot 1966) Hedberg et al. 2012

  • synonyms

    @refsynonym
    20215Catenabacterium saburreum
    20215Eubacterium saburreum

@ref: 1556

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Lachnospiraceae

genus: Lachnoanaerobaculum

species: Lachnoanaerobaculum saburreum

full scientific name: Lachnoanaerobaculum saburreum (Prévot 1966) Hedberg et al. 2012

strain designation: T2

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no91.854
69480100positive

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1556CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)yeshttps://mediadive.dsmz.de/medium/110Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water
39269MEDIUM 187 - for anaerobic bacteriayesDistilled water make up to (1000.000 ml);Glucose (5.000 g);Yeast extract(20.000 g);Tryptone (30.000 g);Cysteine hydrochloride (0.500 g);Hemin solution - M00149(25.000 ml)
122327CIP Medium 187yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=187

culture temp

@refgrowthtypetemperaturerange
1556positivegrowth37mesophilic
39269positivegrowth37mesophilic
49092positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
1556anaerobe
49092anaerobe
69480anaerobe99.999

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.991

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122327-------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample type
1556human dental plaque
49092Human dental plaque
67770Human oral cavity
122327Human, Dental plaque

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body-Site#Oral cavity and airways#Plaque
#Host Body Product#Oral cavity and Airways#Dental plaque

taxonmaps

  • @ref: 69479
  • File name: preview.99_5603.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_353;96_1513;97_1805;98_4180;99_5603&stattab=map
  • Last taxonomy: Lachnoanaerobaculum saburreum
  • 16S sequence: AB525414
  • Sequence Identity:
  • Total samples: 594
  • soil counts: 4
  • aquatic counts: 10
  • animal counts: 578
  • plant counts: 2

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
1556yes, in single cases1Risk group (German classification)
1223271Risk group (French classification)

Sequence information

16S sequences

  • @ref: 1556
  • description: Eubacterium saburreum gene for 16S ribosomal RNA, paertial sequence, strain: JCM 11021
  • accession: AB525414
  • length: 1493
  • database: ena
  • NCBI tax ID: 887325

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lachnoanaerobaculum saburreum DSM 3986887325.3wgspatric887325
66792Lachnoanaerobaculum saburreum DSM 3986649989950draftimg887325
67770Lachnoanaerobaculum saburreum DSM 3986 DSM 3986GCA_000185385scaffoldncbi887325

GC content

  • @ref: 1556
  • GC-content: 37
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes84no
motileno89.799no
flagellatedno94.53no
gram-positiveyes88.052no
anaerobicyes99.404yes
halophileno87.408no
spore-formingno57.076no
thermophileno95.87yes
glucose-utilyes87.372no
aerobicno98.684yes
glucose-fermentyes77.714no

External links

@ref: 1556

culture collection no.: DSM 3986, ATCC 33271, CCUG 28089, CIP 105341, JCM 11021, VPI 11763, AIP 10202

straininfo link

  • @ref: 75849
  • straininfo: 92250

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22228654Lachnoanaerobaculum gen. nov., a new genus in the Lachnospiraceae: characterization of Lachnoanaerobaculum umeaense gen. nov., sp. nov., isolated from the human small intestine, and Lachnoanaerobaculum orale sp. nov., isolated from saliva, and reclassification of Eubacterium saburreum (Prevot 1966) Holdeman and Moore 1970 as Lachnoanaerobaculum saburreum comb. nov.Hedberg ME, Moore ERB, Svensson-Stadler L, Horstedt P, Baranov V, Hernell O, Wai SN, Hammarstrom S, Hammarstrom MLInt J Syst Evol Microbiol10.1099/ijs.0.033613-02012Adult, Bacterial Typing Techniques, Celiac Disease/microbiology, Child, DNA, Bacterial/genetics, Eubacterium/*classification/genetics/isolation & purification, Fatty Acids/analysis, Female, Humans, Intestine, Small/*microbiology, Male, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Saliva/*microbiology, Sequence Analysis, DNAPathogenicity
Enzymology22405584Antimicrobial activity of Streptococcus salivarius K12 on bacteria involved in oral malodour.Masdea L, Kulik EM, Hauser-Gerspach I, Ramseier AM, Filippi A, Waltimo TArch Oral Biol10.1016/j.archoralbio.2012.02.0112012Actinobacteria/*growth & development/isolation & purification, Administration, Oral, Bacterial Proteins/pharmacology, Bacteriocins/pharmacology, Eubacterium/growth & development/isolation & purification, Gram-Positive Bacteria/growth & development/isolation & purification, Halitosis/*microbiology/*prevention & control, Humans, In Vitro Techniques, Linear Models, Microbial Sensitivity Tests, Probiotics/*pharmacology, Streptococcus/*physiologyPhylogeny
Phylogeny31350572Lachnoanaerobaculum gingivalis sp. nov., Isolated from Human Subgingival Dental Plaque of a Gingivitis Lesion.Lim YK, Park SN, Jo E, Shin JH, Chang YH, Shin Y, Paek J, Kim H, Kook JKCurr Microbiol10.1007/s00284-019-01747-z2019Base Composition, Clostridiales/chemistry/*classification/*physiology, DNA, Bacterial/chemistry/genetics, Dental Plaque/*microbiology, Fatty Acids/chemistry, Genome, Bacterial/genetics, Gingivitis/*microbiology, Humans, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityGenetics

Reference

@idauthorscataloguedoi/urltitle
1556Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3986)https://www.dsmz.de/collection/catalogue/details/culture/DSM-3986
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
39269Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17350
49092Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 28089)https://www.ccug.se/strain?id=28089
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/
68371Automatically annotated from API 50CH acid
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
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)
75849Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92250.1StrainInfo: A central database for resolving microbial strain identifiers
122327Curators of the CIPCollection of Institut Pasteur (CIP 105341)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105341