Strain identifier

BacDive ID: 6705

Type strain: Yes

Species: Lactobacillus hominis

Strain Designation: 61D, 361 D

Strain history: CIP <- 2009, F. Gasser, Institut Pasteur, Paris, France: strain 361 D

NCBI tax ID(s): 1423758 (strain), 1203033 (species)

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General

@ref: 17362

BacDive-ID: 6705

DSM-Number: 23910

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-positive, rod-shaped, colony-forming

description: Lactobacillus hominis 61D is a microaerophile, mesophilic, Gram-positive bacterium that forms round colonies and was isolated from human intestine.

NCBI tax id

NCBI tax idMatching level
1203033species
1423758strain

strain history

@refhistory
17362<- S. Cousin, CIP, Genopole; CRBIP 24.179
67770CRBIP 24.179 <-- F. Gasser 61D.
67771<- DSM <- S Cousin, CIP, Genopole, CRBIP 24.179
119948CIP <- 2009, F. Gasser, Institut Pasteur, Paris, France: strain 361 D

doi: 10.13145/bacdive6705.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Lactobacillus
  • species: Lactobacillus hominis
  • full scientific name: Lactobacillus hominis Cousin et al. 2013

@ref: 17362

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Lactobacillus

species: Lactobacillus hominis

full scientific name: Lactobacillus hominis Cousin et al. 2013

strain designation: 61D, 361 D

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30463positive2.65 µm0.55 µmrod-shapedno
67771rod-shapedno
67771positive
69480no95.536
69480positive100
119948positiverod-shaped

colony morphology

@refcolony colorcolony shapemedium used
119948whiteroundDe Man, Rogosa and Sharpe Agar
119948translucentroundTrypticase Soy Agar

pigmentation

  • @ref: 30463
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17362MRS MEDIUM (DSMZ Medium 11)yeshttps://mediadive.dsmz.de/medium/11Name: MRS MEDIUM (DSMZ Medium 11) Composition: Glucose 20.0 g/l Casein peptone 10.0 g/l Meat extract 10.0 g/l Na-acetate 5.0 g/l Yeast extract 5.0 g/l (NH4)3 citrate 2.0 g/l K2HPO4 2.0 g/l Tween 80 1.0 g/l MgSO4 x 7 H2O 0.2 g/l MnSO4 x H2O 0.05 g/l Distilled water
119948De Man, Rogosa and Sharpe Agaryes
119948Trypticase Soy Agaryes

culture temp

@refgrowthtypetemperaturerange
17362positivegrowth37mesophilic
30463positivegrowth25-45
30463positiveoptimum37mesophilic
67770positivegrowth37mesophilic
67771positivegrowth37mesophilic
119948positivegrowth22-45
119948nogrowth15psychrophilic

culture pH

@refabilitytypepH
30463positivegrowth05-08
30463positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
17362microaerophile
30463facultative anaerobe
67771microaerophile
119948facultative anaerobe

spore formation

@refspore formationconfidence
30463no
67771no
69481no100
69480no99.983

halophily

@refsaltgrowthtested relationconcentration
30463NaClpositivegrowth0-5 %
30463NaClpositiveoptimum2.5 %

murein

  • @ref: 17362
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

observation

  • @ref: 30463
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3046317057cellobiose+carbon source
3046328757fructose+carbon source
3046328260galactose+carbon source
3046317234glucose+carbon source
3046317716lactose+carbon source
3046317306maltose+carbon source
3046337684mannose+carbon source
30463506227N-acetylglucosamine+carbon source
3046316634raffinose+carbon source
3046317814salicin+carbon source
3046317992sucrose+carbon source
3046327082trehalose+carbon source
304634853esculin+hydrolysis
68371Potassium 5-ketogluconate-builds acid from
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
683716731melezitose-builds acid from
6837115443inulin-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
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
11994817632nitrate-reduction
11994816301nitrite-reduction
11994817632nitrate+respiration

metabolite tests

  • @ref: 119948
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
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
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 lipase (C 8)-
68382esterase (C 4)-
68382alkaline phosphatase-3.1.3.1
119948oxidase-
119948alcohol dehydrogenase-1.1.1.1
119948catalase-1.11.1.6
119948lysine decarboxylase-4.1.1.18
119948ornithine decarboxylase-4.1.1.17

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119948-----+----+-++++----

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
17362----------++++--------++-++++++++--++--+----------
119948---------+/-+/-+/-+/---------+/---+/-+/-+/-+/-+/--+/-+/---+/-+/---+/-----------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
17362human intestineFranceFRAEurope
67770Human intestine
67771From human intestineFranceFRAEurope
119948Human, Intestine

isolation source categories

Cat1Cat2
#Host#Human
#Host Body Product#Gastrointestinal tract

taxonmaps

  • @ref: 69479
  • File name: preview.99_3899.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_46;96_506;97_581;98_668;99_3899&stattab=map
  • Last taxonomy: Lactobacillus hominis
  • 16S sequence: LC589211
  • Sequence Identity:
  • Total samples: 156859
  • soil counts: 4045
  • aquatic counts: 3638
  • animal counts: 147781
  • plant counts: 1395

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
173621Risk group (German classification)
1199481Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
17362Lactobacillus hominis partial 16S rRNA gene, strain CRBIP 24.179FR6819021718ena1423758
67770Lactobacillus hominis JCM 18988 gene for 16S rRNA, partial sequenceLC5892111508ena1203033

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactobacillus hominis CRBIP 24.179872328.3wgspatric1423758
66792Lactobacillus hominis DSM 23910 = CRBIP 24.1791423758.3wgspatric1423758
66792Lactobacillus hominis CRBIP 24.1792537561925draftimg1423758
66792Lactobacillus hominis DSM 239102663763150draftimg1423758
67770Lactobacillus hominis DSM 23910 = CRBIP 24.179GCA_001436125scaffoldncbi1423758
67771Lactobacillus hominis DSM 23910 = CRBIP 24.179 type strain:CRBIP 24.179GCA_000296835contigncbi1423758

GC content

@refGC-contentmethod
1736242.8high performance liquid chromatography (HPLC)
3046342.8
6777035.2genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno95.053yes
flagellatedno97.955yes
gram-positiveyes95.666yes
anaerobicyes53.55yes
halophileyes84.77no
spore-formingno94.062no
thermophileno99.128yes
glucose-utilyes94.106no
aerobicno97.968no
glucose-fermentyes89.32no

External links

@ref: 17362

culture collection no.: DSM 23910, KCTC 21045, JCM 18988, CRBIP24.179

straininfo link

  • @ref: 76179
  • straininfo: 386783

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22328611Lactobacillus pasteurii sp. nov. and Lactobacillus hominis sp. nov.Cousin S, Motreff L, Gulat-Okalla ML, Gouyette C, Sproer C, Schumann P, Begaud E, Bouchier C, Clermont D, Bizet CInt J Syst Evol Microbiol10.1099/ijs.0.036665-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Lactobacillus/*classification/genetics/metabolism, Molecular Sequence Data, Multilocus Sequence Typing, Nucleic Acid Hybridization, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Genetics23969062Draft Genome Sequence of Lactobacillus hominis Strain CRBIP 24.179T, Isolated from Human Intestine.Cousin S, Creno S, Ma L, Clermont D, Loux V, Bizet C, Bouchier CGenome Announc10.1128/genomeA.00662-132013Phylogeny

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
17362Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23910)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23910
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
30463Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2679828776041
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)
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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)
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
76179Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID386783.1StrainInfo: A central database for resolving microbial strain identifiers
119948Curators of the CIPCollection of Institut Pasteur (CRBIP24.179 )https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CRBIP24.179%20