Strain identifier

BacDive ID: 131334

Type strain: Yes

Species: Hymenobacter latericoloratus

Strain history: W.-J. Li; Yunnan Inst. of Microbiol., Yunnan Univ., China; YIM 77920.

NCBI tax ID(s): 1411121 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 22561

BacDive-ID: 131334

DSM-Number: 26701

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative

description: Hymenobacter latericoloratus DSM 26701 is a mesophilic, Gram-negative bacterium that was isolated from freshwater sediment.

NCBI tax id

  • NCBI tax id: 1411121
  • Matching level: species

strain history

@refhistory
22561<- S.-K. Tang, YIM; YIM 77920 <- E.-M. Zhou
67770W.-J. Li; Yunnan Inst. of Microbiol., Yunnan Univ., China; YIM 77920.

doi: 10.13145/bacdive131334.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Hymenobacteraceae
  • genus: Hymenobacter
  • species: Hymenobacter latericoloratus
  • full scientific name: Hymenobacter latericoloratus Liu et al. 2015

@ref: 22561

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Hymenobacteraceae

genus: Hymenobacter

species: Hymenobacter latericoloratus

full scientific name: Hymenobacter latericoloratus Liu et al. 2015

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.993

Culture and growth conditions

culture medium

  • @ref: 22561
  • name: ISP2 MEDIUM (DSMZ Medium 987)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/987
  • composition: Name: ISP 2 MEDIUM (DSMZ Medium 987) Composition: Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
22561positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.999

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
22561freshwater sedimentYunnan province, Yiliang county, Jiuxiang tourist cave (E 103° 22.791', N 25° 04.270')ChinaCHNAsia25.0712103.38
67770Freshwater sediment of Jiuxiang tourist cave in Yiliang countryYunnan ProvinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Sediment
#Environmental#Aquatic#Freshwater

taxonmaps

  • @ref: 69479
  • File name: preview.99_84110.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_263;96_21517;97_26865;98_34197;99_84110&stattab=map
  • Last taxonomy: Hymenobacter
  • 16S sequence: AB859260
  • Sequence Identity:
  • Total samples: 1217
  • soil counts: 123
  • aquatic counts: 150
  • animal counts: 891
  • plant counts: 53

Safety information

risk assessment

  • @ref: 22561
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 22561
  • description: Hymenobacter latericoloratus gene for 16S ribosomal RNA, partial sequence
  • accession: AB859260
  • length: 1540
  • database: ena
  • NCBI tax ID: 1411121

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Hymenobacter latericoloratus DSM 26701GCA_014199535scaffoldncbi1411121
66792Hymenobacter latericoloratus strain DSM 267011411121.3wgspatric1411121
66792Hymenobacter latericoloratus DSM 267012828589702draftimg1411121

GC content

  • @ref: 22561
  • GC-content: 57.5
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno96.956no
gram-positiveno97.208no
anaerobicno99.402no
aerobicyes90.641no
halophileno93.635no
spore-formingno93.893no
glucose-utilyes80.003no
thermophileno95.886yes
glucose-fermentno91.003no
motileno90.812no

External links

@ref: 22561

culture collection no.: DSM 26701, CCTCC AB 2012949, JCM 30327, YIM 77920

straininfo link

  • @ref: 89775
  • straininfo: 400413

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny25348876Hymenobacter latericoloratus sp. nov. and Hymenobacter luteus sp. nov., isolated from freshwater sediment.Liu L, Zhou EM, Jiao JY, Manikprabhu D, Ming H, Liu WH, Hozzein WN, Shu WS, Li WJAntonie Van Leeuwenhoek10.1007/s10482-014-0314-12014Aerobiosis, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, Cytophagaceae/*classification/genetics/*isolation & purification, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Fresh Water/*microbiology, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny31961285Hymenobacter sediminis sp. nov., isolated from lake sediment.Wang C, Liu BT, Zhang R, Liu CL, Du ZJInt J Syst Evol Microbiol10.1099/ijsem.0.0039902020Bacterial Typing Techniques, Base Composition, China, Cytophagaceae/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Lakes/*microbiology, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcatalogue
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
22561Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-26701Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26701)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
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
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
89775Reimer, 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-ID400413.1