Strain identifier

BacDive ID: 158442

Type strain: Yes

Species: Microbacterium halophytorum

Strain history: <- Dengdi An, Xinjiang Normal Univ.

NCBI tax ID(s): 2067568 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 8.1 (current version)

General

@ref: 65118

BacDive-ID: 158442

DSM-Number: 106431

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

description: Microbacterium halophytorum DSM 106431 is an aerobe, mesophilic, Gram-positive bacterium that forms circular colonies and was isolated from Kalidium foliatum, leaf.

NCBI tax id

  • NCBI tax id: 2067568
  • Matching level: species

strain history

@refhistory
65118<- D. An, Xuzhou Normal Univ., School of Life Science, Urumqi, P.R. China; YJYP 303
67771<- Dengdi An, Xinjiang Normal Univ.

doi: 10.13145/bacdive158442.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Microbacterium
  • species: Microbacterium halophytorum
  • full scientific name: Microbacterium halophytorum Li et al. 2018

@ref: 65118

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium halophytorum

full scientific name: Microbacterium halophytorum Li et al. 2018

type strain: yes

Morphology

cell morphology

  • @ref: 66788
  • gram stain: positive
  • cell length: 0.8-1.0 µm
  • cell width: 0.4-0.5 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 66788
  • colony color: pale yellow
  • colony shape: circular
  • medium used: ISP 3

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
65118TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)yeshttps://mediadive.dsmz.de/medium/545Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water
66788ISP 3yes
66788Reasoner's 2A agar (R2A)yes
66788tryptic soy broth (Difco)yes

culture temp

@refgrowthtypetemperaturerange
65118positivegrowth28mesophilic
66788positiveoptimum28mesophilic
66788positivegrowth4-44
67771positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
66788positiveoptimum7
66788positivegrowth6-12alkaliphile

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
66788aerobe
67771aerobe

halophily

@refsaltgrowthtested relationconcentration
66788NaClpositivegrowth0-15 %(w/v)
66788NaClpositiveoptimum2-4 %(w/v)

observation

  • @ref: 66788
  • observation: The whole-cell sugars are mannose, ribose, rhamnose, glucose, galactose and two unidentified sugars. The cell-wall characteristic amino acids are glutamic acid, ornithine, glycine and alanine. The predominant respiratory quinone is MK-11, followed by MK-10 and MK-12. The polar lipids are diphosphatidylglycerol, phosphatidylglycerol, an unidentified phospholipid and an unidentified

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
667888295beta-hydroxybutyrate-assimilation
6678817968butyrate-assimilation
6678828800N-acetylgalactosamine-assimilation
6678851850methyl pyruvate-assimilation
667885291gelatin+assimilation
6678815748D-glucuronate+assimilation
6678815895D-galactonic acid lactone+assimilation
6678816467L-arginine+assimilation
6678817306maltose+assimilation
6678818024D-galacturonic acid+assimilation
66788181014-hydroxyphenylacetic acid+assimilation
6678818183L-pyroglutamic acid+assimilation
6678824996lactate+assimilation
6678825115malate+assimilation
6678828053melibiose+assimilation
6678829990D-aspartate+assimilation
66788739183-O-methyl-D-glucose+assimilation
66788alpha-hydroxybutyrate+assimilation
6678816443D-tagatose-builds acid from
6678817113erythritol-builds acid from
6678817266L-sorbose-builds acid from
6678817716lactose-builds acid from
6678818333D-arabitol-builds acid from
6678865328L-xylose-builds acid from
6678817268myo-inositol+builds acid from
6678818287L-fucose+builds acid from
6678818305arbutin+builds acid from
6678822599arabinose+builds acid from
6678825097lyxose+builds acid from
6678826490quinate+builds acid from
6678827613amygdalin+builds acid from
6678828260galactose+builds acid from
6678832528turanose+builds acid from
6678859640N-acetylglucosamine+builds acid from
6678874863methyl beta-D-xylopyranoside+builds acid from
66788320061methyl alpha-D-glucopyranoside+builds acid from
6678828017starch-hydrolysis
6678853424tween 20-hydrolysis
6678853425tween 60-hydrolysis
6678862968cellulose-hydrolysis
667885291gelatin+hydrolysis
6678853423tween 40+hydrolysis
6678853425tween 60+hydrolysis

metabolite production

  • @ref: 66788
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: no

enzymes

@refvalueactivityec
66788alpha-glucosidase+3.2.1.20
66788beta-galactosidase+3.2.1.23
66788catalase+1.11.1.6
66788cytochrome oxidase+1.9.3.1
66788esterase (C 4)+
66788leucine arylamidase+3.4.11.1
66788urease+3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    66788C17:0 anteiso15.7
    66788C15:0 anteiso32.8
    66788C16:0 iso39.7
  • type of FA analysis: whole cell analysis
  • incubation medium: tryptic soy broth (Difco)
  • incubation temperature: 28
  • incubation time: 5
  • software version: Sherlock 6.1
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • method/protocol: Sasser, 1990

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperatureisolation procedure
65118Kalidium foliatum, leafGurbantunggut desert, XinjiangChinaCHNAsia
66788leaf of Kalidium foliatum, a halophytesouthern edge of the Gurbantunggut Desert, Xinjiang,ChinaCHNAsia44.233387.7ISP 32 weeks28The fresh leaves (1 gram each) were washed and surface-sterilized, ground to slurry by sterilized with 9 ml sterilized water, and the homogenate (200 µl) spread on ISP 3 agar media.
67771From Kalidium foliatum (Poll.) Moq.XinjiangChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Leaf (Phyllosphere)

Sequence information

16S sequences

  • @ref: 65118
  • description: Microbacterium sp. strain YJYP303 16S ribosomal RNA gene, partial sequence
  • accession: MF084211
  • length: 1532
  • database: ena
  • NCBI tax ID: 51671

GC content

@refGC-contentmethod
6511869.72
6678869.72genome sequence analysis

External links

@ref: 65118

culture collection no.: DSM 106431, CGMCC 1.16264, YJYP 303, KCTC 49100

straininfo link

  • @ref: 111243
  • straininfo: 405757

literature

  • topic: Phylogeny
  • Pubmed-ID: 30362936
  • title: Microbacterium halophytorum sp. nov., a novel endophytic actinobacterium isolated from halophytes.
  • authors: Li YR, Zhu ZN, Li YQ, Xiao M, Han MX, Wadaan MAM, Hozzein WN, An DD, Li WJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003092
  • year: 2018
  • mesh: Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Endophytes/classification/genetics/isolation & purification, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Salt-Tolerant Plants/*microbiology, Sequence Analysis, DNA, Vitamin K 2/chemistry
  • topic2: Enzymology

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
65118Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-106431Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 106431)
66788Yan-Ru Li, Zhi-Nan Zhu, Yu-Qian Li, Min Xiao, Ming-Xian Han, Mohammed A. M. Wadaan, Wael N. Hozzein, Deng-Di An and Wen-Jun LiMicrobacterium halophytorum sp. nov., a novel endophytic actinobacterium isolated from halophytes10.1099/ijsem.0.003092IJSEM 68: 3928-3934 201830362936
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
111243Reimer, 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-ID405757.1