Strain identifier

BacDive ID: 133465

Type strain: Yes

Species: Sphingobium indicum

NCBI tax ID(s): 332055 (species)

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General

@ref: 29075

BacDive-ID: 133465

keywords: 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped

description: Sphingobium indicum MTCC 8598 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from HCH dumpsite.

NCBI tax id

  • NCBI tax id: 332055
  • Matching level: species

doi: 10.13145/bacdive133465.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingomonadaceae
  • genus: Sphingobium
  • species: Sphingobium indicum
  • full scientific name: Sphingobium indicum Pal et al. 2005

  • synonyms

    @refsynonym
    20215Sphingobium chinhatense
    20215Sphingobium japonicum
    20215Sphingobium francense
    20215Sphingobium lucknowense

@ref: 29075

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingobium

species: Sphingobium chinhatense

type strain: yes

Morphology

cell morphology

  • @ref: 29075
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

pigmentation

  • @ref: 29075
  • production: yes

Culture and growth conditions

culture temp

  • @ref: 29075
  • growth: positive
  • type: growth
  • temperature: 20-40

culture pH

  • @ref: 29075
  • ability: positive
  • type: growth
  • pH: 06-09
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 29075
  • oxygen tolerance: aerobe

spore formation

  • @ref: 29075
  • spore formation: no

halophily

  • @ref: 29075
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2907522599arabinose+carbon source
2907527689decanoate+carbon source
2907528757fructose+carbon source
2907528260galactose+carbon source
2907517234glucose+carbon source
2907517268myo-inositol+carbon source
2907526271proline+carbon source
2907533942ribose+carbon source
2907517814salicin+carbon source
2907517822serine+carbon source
2907527082trehalose+carbon source
2907518222xylose+carbon source
290754853esculin+hydrolysis

enzymes

@refvalueactivityec
29075catalase+1.11.1.6
29075cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 29075
  • sample type: HCH dumpsite

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Built environment

taxonmaps

  • @ref: 69479
  • File name: preview.99_60.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_32;97_33;98_56;99_60&stattab=map
  • Last taxonomy: Sphingobium
  • 16S sequence: EF190507
  • Sequence Identity:
  • Total samples: 636
  • soil counts: 78
  • aquatic counts: 363
  • animal counts: 118
  • plant counts: 77

Sequence information

16S sequences

  • @ref: 29075
  • description: Sphingobium chinhatense strain IP26 16S ribosomal RNA gene, partial sequence
  • accession: EF190507
  • length: 1441
  • database: nuccore
  • NCBI tax ID: 1346790

External links

@ref: 29075

culture collection no.: MTCC 8598, CCM 7432, IP 26

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19643888Sphingobium chinhatense sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from an HCH dumpsite.Dadhwal M, Jit S, Kumari H, Lal RInt J Syst Evol Microbiol10.1099/ijs.0.005553-02009Biodegradation, Environmental, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Hexachlorocyclohexane/*metabolism, *Industrial Waste, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sphingomonadaceae/*classification/genetics/*isolation & purification/metabolismMetabolism
Genetics23990581Draft Genome Sequence of Sphingobium chinhatense Strain IP26T, Isolated from a Hexachlorocyclohexane Dumpsite.Niharika N, Sangwan N, Ahmad S, Singh P, Khurana JP, Lal RGenome Announc10.1128/genomeA.00680-132013Phylogeny
Metabolism28521164Biotransformation of hexabromocyclododecanes with hexachlorocyclohexane-transforming Sphingobium chinhatense strain IP26.Heeb NV, Grubelnik A, Geueke B, Kohler HE, Lienemann PChemosphere10.1016/j.chemosphere.2017.05.0472017Biodegradation, Environmental, Biotransformation, Environmental Pollutants/analysis/*metabolism, Flame Retardants/analysis/*metabolism, Halogenation, Hexachlorocyclohexane/analysis/*metabolism, Hydrocarbons, Brominated/analysis/*metabolism, Sphingomonadaceae/*metabolism, Stereoisomerism
Phylogeny32048985Sphingobium estronivorans sp. nov. and Sphingobium bisphenolivorans sp. nov., isolated from a wastewater treatment plant.Qin D, Ma C, Lv M, Yu CPInt J Syst Evol Microbiol10.1099/ijsem.0.0039782020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Spermidine/chemistry, Sphingomonadaceae/*classification/isolation & purification, Ubiquinone/analogs & derivatives/chemistry, Waste Water/*microbiologyTranscriptome

Reference

@idauthorstitledoi/urlID_cross_referencepubmed
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
29075Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172550528776041
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/