Strain identifier

BacDive ID: 11368

Type strain: Yes

Species: Herbaspirillum huttiense subsp. putei

Strain Designation: 7-2

Strain history: IAM 15032 <-- A. Yokota 7-2.

NCBI tax ID(s): 230311 (subspecies)

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General

@ref: 16017

BacDive-ID: 11368

DSM-Number: 21883

keywords: genome sequence, 16S sequence, Bacteria, aerobe, motile

description: Herbaspirillum huttiense subsp. putei 7-2 is an aerobe, motile bacterium that was isolated from well water.

NCBI tax id

  • NCBI tax id: 230311
  • Matching level: subspecies

strain history

@refhistory
16017<- CCUG <- A. Yokota, IAM; strain 7-2
67770IAM 15032 <-- A. Yokota 7-2.

doi: 10.13145/bacdive11368.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Oxalobacteraceae
  • genus: Herbaspirillum
  • species: Herbaspirillum huttiense subsp. putei
  • full scientific name: Herbaspirillum huttiense subsp. putei (Ding and Yokota 2004) Dobritsa et al. 2010

  • synonyms

    • @ref: 20215
    • synonym: Herbaspirillum putei

@ref: 16017

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Oxalobacteraceae

genus: Herbaspirillum

species: Herbaspirillum huttiense

full scientific name: Herbaspirillum huttiense (Leifson 1962) Ding and Yokota 2004 emend. Dobritsa et al. 2010

strain designation: 7-2

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes92.823
6948099.999negative

Culture and growth conditions

culture medium

  • @ref: 16017
  • name: NUTRIENT AGAR (DSMZ Medium 1)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1
  • composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
16017positivegrowth22-37
58564positivegrowth22-37
67770positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 58564
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no100

observation

  • @ref: 67770
  • observation: quinones: Q-8

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16017well waterOsakaJapanJPNAsia
67770Well waterOsakaJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic
#Engineered#Built environment#Water reservoir (Aquarium/pool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_3619.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_128;97_137;98_154;99_3619&stattab=map
  • Last taxonomy: Herbaspirillum
  • 16S sequence: AB681762
  • Sequence Identity:
  • Total samples: 1693
  • soil counts: 197
  • aquatic counts: 342
  • animal counts: 743
  • plant counts: 411

Safety information

risk assessment

  • @ref: 16017
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Herbaspirillum huttiense subsp. putei gene for 16S rRNA, partial sequence, strain: NBRC 102406AB6817621458ena1235558
16017Herbaspirillum putei gene for 16S rRNA, partial sequenceAB1098901496ena1235558
16017Herbaspirillum huttiense subsp. putei strain ATCC BAA-806 16S ribosomal RNA gene, partial sequenceEU0465561455ena1235558

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Herbaspirillum huttiense subsp. putei IAM 150321235558.4wgspatric1235558
66792Herbaspirillum huttiense putei IAM 150322551306420draftimg1235558
67770Herbaspirillum huttiense subsp. putei IAM 15032GCA_000478365contigncbi1235558

GC content

@refGC-contentmethod
1601766.2high performance liquid chromatography (HPLC)
6777062.1high performance liquid chromatography (HPLC)
6777062.9high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes90.53no
gram-positiveno99.002no
anaerobicno98.913yes
aerobicyes87.344yes
halophileno95.999no
spore-formingno93.895no
thermophileno99.137yes
glucose-utilyes89.756no
flagellatedyes53.705no
glucose-fermentno90.225no

External links

@ref: 16017

culture collection no.: DSM 21883, ATCC BAA 806, CCUG 49453, IAM 15032, JCM 21495, NBRC 102406, CIP 108607

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15545462Proposals of Curvibacter gracilis gen. nov., sp. nov. and Herbaspirillum putei sp. nov. for bacterial strains isolated from well water and reclassification of [Pseudomonas] huttiensis, [Pseudomonas] lanceolata, [Aquaspirillum] delicatum and [Aquaspirillum] autotrophicum as Herbaspirillum huttiense comb. nov., Curvibacter lanceolatus comb. nov., Curvibacter delicatus comb. nov. and Herbaspirillum autotrophicum comb. nov.Ding L, Yokota AInt J Syst Evol Microbiol10.1099/ijs.0.02975-02004Bacterial Typing Techniques, Base Composition, Comamonadaceae/chemistry/*classification/*isolation & purification/physiology, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Flagella/ultrastructure, Fresh Water/*microbiology, Genes, rRNA, Gentian Violet, Herbaspirillum/*classification/cytology/*isolation & purification/physiology, Microscopy, Electron, Molecular Sequence Data, Neisseriaceae, Nitrogen Fixation, Nucleic Acid Hybridization, Phenazines, Phylogeny, Pseudomonas, Quinones/analysis/isolation & purification, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Water MicrobiologyEnzymology
Phylogeny19671717Reclassification of Herbaspirillum putei as a later heterotypic synonym of Herbaspirillum huttiense, with the description of H. huttiense subsp. huttiense subsp. nov. and H. huttiense subsp. putei subsp. nov., comb. nov., and description of Herbaspirillum aquaticum sp. nov.Dobritsa AP, Reddy MCS, Samadpour MInt J Syst Evol Microbiol10.1099/ijs.0.009381-02009Base Composition, Base Sequence, DNA Primers, DNA, Bacterial/genetics, Fatty Acids/analysis, Genome, Herbaspirillum/*classification/*genetics/metabolism, Molecular Sequence Data, Peptide Fragments/chemistry, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/geneticsGenetics
Genetics23469362Draft Genome Sequence of Herbaspirillum huttiense subsp. putei IAM 15032, a Strain Isolated from Well Water.de Souza V, Piro VC, Faoro H, Tadra-Sfeir MZ, Chicora VK, Guizelini D, Weiss V, Vialle RA, Monteiro RA, Steffens MB, Marchaukoski JN, Pedrosa FO, Cruz LM, Chubatsu LS, Raittz RTGenome Announc10.1128/genomeA.00252-122013Phylogeny
Metabolism30655589Novel non-phosphorylative pathway of pentose metabolism from bacteria.Watanabe S, Fukumori F, Nishiwaki H, Sakurai Y, Tajima K, Watanabe YSci Rep10.1038/s41598-018-36774-62019Bacterial Proteins/*metabolism, Computational Biology/methods, Herbaspirillum/*genetics/*metabolism, Metabolic Networks and Pathways, Multigene Family, Pentoses/*metabolism, Phosphorylation
Metabolism30985034Substrate and metabolic promiscuities of d-altronate dehydratase family proteins involved in non-phosphorylative d-arabinose, sugar acid, l-galactose and l-fucose pathways from bacteria.Watanabe S, Fukumori F, Watanabe YMol Microbiol10.1111/mmi.142592019Amino Acid Sequence/genetics, Arabinose/metabolism, Cloning, Molecular/methods, Fucose/metabolism, Galactose/metabolism, Genome, Bacterial/genetics, Gluconates/metabolism, Herbaspirillum/genetics/metabolism, Hydro-Lyases/*genetics/*metabolism/physiology, Multigene Family/genetics, Sugar Acids/metabolismEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16017Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21883)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21883
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
58564Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 49453)https://www.ccug.se/strain?id=49453
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/
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