Strain identifier
BacDive ID: 158442
Type strain:
Species: Microbacterium halophytorum
Strain history: <- Dengdi An, Xinjiang Normal Univ.
NCBI tax ID(s): 2067568 (species)
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
@ref | history |
---|---|
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
@ref | name | growth | link | composition |
---|---|---|---|---|
65118 | TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) | yes | https://mediadive.dsmz.de/medium/545 | Name: 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 |
66788 | ISP 3 | yes | ||
66788 | Reasoner's 2A agar (R2A) | yes | ||
66788 | tryptic soy broth (Difco) | yes |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
65118 | positive | growth | 28 | mesophilic |
66788 | positive | optimum | 28 | mesophilic |
66788 | positive | growth | 4-44 | |
67771 | positive | growth | 28 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
66788 | positive | optimum | 7 | |
66788 | positive | growth | 6-12 | alkaliphile |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
66788 | aerobe |
67771 | aerobe |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
66788 | NaCl | positive | growth | 0-15 %(w/v) |
66788 | NaCl | positive | optimum | 2-4 %(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
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
66788 | 8295 | beta-hydroxybutyrate | - | assimilation |
66788 | 17968 | butyrate | - | assimilation |
66788 | 28800 | N-acetylgalactosamine | - | assimilation |
66788 | 51850 | methyl pyruvate | - | assimilation |
66788 | 5291 | gelatin | + | assimilation |
66788 | 15748 | D-glucuronate | + | assimilation |
66788 | 15895 | D-galactonic acid lactone | + | assimilation |
66788 | 16467 | L-arginine | + | assimilation |
66788 | 17306 | maltose | + | assimilation |
66788 | 18024 | D-galacturonic acid | + | assimilation |
66788 | 18101 | 4-hydroxyphenylacetic acid | + | assimilation |
66788 | 18183 | L-pyroglutamic acid | + | assimilation |
66788 | 24996 | lactate | + | assimilation |
66788 | 25115 | malate | + | assimilation |
66788 | 28053 | melibiose | + | assimilation |
66788 | 29990 | D-aspartate | + | assimilation |
66788 | 73918 | 3-O-methyl-D-glucose | + | assimilation |
66788 | alpha-hydroxybutyrate | + | assimilation | |
66788 | 16443 | D-tagatose | - | builds acid from |
66788 | 17113 | erythritol | - | builds acid from |
66788 | 17266 | L-sorbose | - | builds acid from |
66788 | 17716 | lactose | - | builds acid from |
66788 | 18333 | D-arabitol | - | builds acid from |
66788 | 65328 | L-xylose | - | builds acid from |
66788 | 17268 | myo-inositol | + | builds acid from |
66788 | 18287 | L-fucose | + | builds acid from |
66788 | 18305 | arbutin | + | builds acid from |
66788 | 22599 | arabinose | + | builds acid from |
66788 | 25097 | lyxose | + | builds acid from |
66788 | 26490 | quinate | + | builds acid from |
66788 | 27613 | amygdalin | + | builds acid from |
66788 | 28260 | galactose | + | builds acid from |
66788 | 32528 | turanose | + | builds acid from |
66788 | 59640 | N-acetylglucosamine | + | builds acid from |
66788 | 74863 | methyl beta-D-xylopyranoside | + | builds acid from |
66788 | 320061 | methyl alpha-D-glucopyranoside | + | builds acid from |
66788 | 28017 | starch | - | hydrolysis |
66788 | 53424 | tween 20 | - | hydrolysis |
66788 | 53425 | tween 60 | - | hydrolysis |
66788 | 62968 | cellulose | - | hydrolysis |
66788 | 5291 | gelatin | + | hydrolysis |
66788 | 53423 | tween 40 | + | hydrolysis |
66788 | 53425 | tween 60 | + | hydrolysis |
metabolite production
- @ref: 66788
- Chebi-ID: 16136
- metabolite: hydrogen sulfide
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
66788 | alpha-glucosidase | + | 3.2.1.20 |
66788 | beta-galactosidase | + | 3.2.1.23 |
66788 | catalase | + | 1.11.1.6 |
66788 | cytochrome oxidase | + | 1.9.3.1 |
66788 | esterase (C 4) | + | |
66788 | leucine arylamidase | + | 3.4.11.1 |
66788 | urease | + | 3.5.1.5 |
fatty acid profile
fatty acids
@ref fatty acid percentage 66788 C17:0 anteiso 15.7 66788 C15:0 anteiso 32.8 66788 C16:0 iso 39.7 - 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
@ref | sample type | geographic location | country | origin.country | continent | latitude | longitude | enrichment culture | enrichment culture duration | enrichment culture temperature | isolation procedure |
---|---|---|---|---|---|---|---|---|---|---|---|
65118 | Kalidium foliatum, leaf | Gurbantunggut desert, Xinjiang | China | CHN | Asia | ||||||
66788 | leaf of Kalidium foliatum, a halophyte | southern edge of the Gurbantunggut Desert, Xinjiang, | China | CHN | Asia | 44.2333 | 87.7 | ISP 3 | 2 weeks | 28 | The 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. |
67771 | From Kalidium foliatum (Poll.) Moq. | Xinjiang | China | CHN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | GC-content | method |
---|---|---|
65118 | 69.72 | |
66788 | 69.72 | genome 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
@id | authors | title | doi/url | catalogue | journal | pubmed |
---|---|---|---|---|---|---|
20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | |||
65118 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-106431 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 106431) | |||
66788 | Yan-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 Li | Microbacterium halophytorum sp. nov., a novel endophytic actinobacterium isolated from halophytes | 10.1099/ijsem.0.003092 | IJSEM 68: 3928-3934 2018 | 30362936 | |
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
111243 | Reimer, 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 identifiers | 10.60712/SI-ID405757.1 |