Strain identifier

BacDive ID: 158412

Type strain: Yes

Species: Apilactobacillus timberlakei

Strain Designation: HV_12

Strain history: DSM 104128 <-- J. A. Rothman, Univ. of California, Riverside, USA; HV_12.

NCBI tax ID(s): 2008380 (species)

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General

@ref: 65088

BacDive-ID: 158412

DSM-Number: 104128

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

description: Apilactobacillus timberlakei HV_12 is an aerobe, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from gut of sweet bee Agapostemon.

NCBI tax id

  • NCBI tax id: 2008380
  • Matching level: species

strain history

@refhistory
65088<- J. Rothman, UC Riverside, Riverside, USA; HV_12
67770DSM 104128 <-- J. A. Rothman, Univ. of California, Riverside, USA; HV_12.

doi: 10.13145/bacdive158412.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Apilactobacillus
  • species: Apilactobacillus timberlakei
  • full scientific name: Apilactobacillus timberlakei (McFrederick et al. 2018) Zheng et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus timberlakei

@ref: 65088

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Apilactobacillus

species: Apilactobacillus timberlakei

full scientific name: Apilactobacillus timberlakei (McFrederick et al. 2018) Zheng et al. 2020

strain designation: HV_12

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
65392positive0.8-1.6 µm0.5-0.7 µmrod-shapedno
69480positive92.979
69480no92

colony morphology

  • @ref: 65392
  • colony color: white
  • colony shape: circular
  • medium used: De Man, Rogosa, Sharpe agar

Culture and growth conditions

culture medium

  • @ref: 65088
  • name: MRS MEDIUM (DSMZ Medium 11)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/11
  • composition: Name: 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

culture temp

@refgrowthtypetemperature
65088positivegrowth30
65392positivegrowth15-35
65392positiveoptimum30-35
67770positivegrowth30

culture pH

@refabilitytypepHPH range
65392positivegrowth2-6acidophile
65392positiveoptimum5
65392nogrowth7
65392nogrowth>7

Physiology and metabolism

oxygen tolerance

  • @ref: 65392
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
65392no
69480no92.881

observation

  • @ref: 65392
  • observation: heterofermentive

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6539215824D-fructose+builds acid from
6539217634D-glucose+builds acid from
6539217234glucose+fermentation

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
6539217076streptomycinyesyes10 µg (disc)
6539228669bacitracinyesyes10 Unit (disc)
6539217334penicillinyesyes10 Unit (disc)
6539248923erythromycinyesyes15 µg (disc)
65392209807cefoxitinyesyes30 µg (disc)
6539227902tetracyclineyesyes30 µg (disc)
653923393carbenicillinyesyes100 µg (disc)
653928309polymyxin byesyes300 Unit (disc)
6539228971ampicillinyesyes10 µg (disc)
6539217698chloramphenicolyesyes30 µg (disc)
6539228001vancomycinyesyes30 µg (disc)
653926104kanamycinyesyes30 µg (disc)

enzymes

@refvalueactivityec
65392alkaline phosphatase+3.1.3.1
65392acid phosphatase+3.1.3.2
65392naphthol-AS-BI-phosphohydrolase+
65392leucine arylamidase+3.4.11.1
65392catalase+1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperatureisolation procedurehost species
65088gut of sweet bee Agapostemon33.9706N, 117.3201WUSAUSANorth America
65392gut of a sweat bee (Agapostemon sp.)campus of UC Riverside, Riverside, CAUSAUSANorth AmericaDe Man, Rogosa, Sharpe agarsupplemented with 20 % D-fructose2-3 days24Bee guts were dissected in sterile water then homogenized in sterile physiologic saline. The gut homogenates were plated on De Man, Rogosa, Sharpe agar plates supplemented with 20 % D-fructose, then incubated in an aerobic environment for 2-3 days at 24°C.
67770Gut of a sweat bee (Halictus ligatus) caught at the Hornsby Bend Center for Environmental ResearchAustin, TXUSAUSANorth AmericaHalictus ligatus

isolation source categories

Cat1Cat2Cat3
#Host#Arthropoda#Insecta
#Host Body-Site#Gastrointestinal tract

taxonmaps

  • @ref: 69479
  • File name: preview.99_13474.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_245;97_8290;98_10183;99_13474&stattab=map
  • Last taxonomy: Apilactobacillus micheneri subclade
  • 16S sequence: KX656650
  • Sequence Identity:
  • Total samples: 1872
  • soil counts: 84
  • aquatic counts: 107
  • animal counts: 1575
  • plant counts: 106

Sequence information

16S sequences

  • @ref: 65088
  • description: Apilactobacillus timberlakei strain HV_12 16S ribosomal RNA gene, partial sequence
  • accession: KX656650
  • length: 1431
  • database: nuccore
  • NCBI tax ID: 2008380

Genome sequences

  • @ref: 67770
  • description: Apilactobacillus timberlakei HV_12
  • accession: GCA_002993965
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 2008380

GC content

@refGC-contentmethod
6508830.5
6539230.5genome sequence analysis

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingyes92.979no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no81.932yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no83.269no
69480spore-formingspore-formingAbility to form endo- or exosporesno92.881no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno94.5yes
69480flagellatedmotile2+Ability to perform flagellated movementno92yes

External links

@ref: 65088

culture collection no.: DSM 104128, NRRL B-65472, JCM 33325

straininfo link

  • @ref: 111215
  • straininfo: 400334

literature

  • topic: Phylogeny
  • Pubmed-ID: 29648528
  • title: Lactobacillus micheneri sp. nov., Lactobacillus timberlakei sp. nov. and Lactobacillus quenuiae sp. nov., lactic acid bacteria isolated from wild bees and flowers.
  • authors: McFrederick QS, Vuong HQ, Rothman JA
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002758
  • year: 2018
  • mesh: Animals, Bacterial Typing Techniques, Base Composition, Bees/*microbiology, California, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flowers/*microbiology, Lactobacillus/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
65088Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-104128Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104128)
65392Quinn S. McFrederick, Hoang Q. Vuong, Jason A. RothmanLactobacillus micheneri sp. nov., Lactobacillus timberlakei sp. nov. and Lactobacillus quenuiae sp. nov., lactic acid bacteria isolated from wild bees and flowers10.1099/ijsem.0.002758IJSEM 68: 1879-1884 201829648528
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
111215Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID400334.1