Strain identifier
BacDive ID: 133022
Type strain:
Species: Microbacterium sorbitolivorans
Strain Designation: SZDIS-1-1
Strain history: <- M. Cai, Institute Of Microbiology, Chinese Academy of Sciences, Beijing, China; SZDIS-1-1
NCBI tax ID(s): 1867410 (species)
General
@ref: 24810
BacDive-ID: 133022
DSM-Number: 103422
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, Gram-positive, rod-shaped, colony-forming
description: Microbacterium sorbitolivorans SZDIS-1-1 is a facultative anaerobe, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from fermentation bed of a pigpen.
NCBI tax id
- NCBI tax id: 1867410
- Matching level: species
strain history
- @ref: 24810
- history: <- M. Cai, Institute Of Microbiology, Chinese Academy of Sciences, Beijing, China; SZDIS-1-1
doi: 10.13145/bacdive133022.20230509.8.1
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 sorbitolivorans
- full scientific name: Microbacterium sorbitolivorans Meng et al. 2016
@ref: 24810
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Microbacteriaceae
genus: Microbacterium
species: Microbacterium sorbitolivorans
full scientific name: Microbacterium sorbitolivorans Meng et al. 2016
strain designation: SZDIS-1-1
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
25049 | positive | 1.52-1.83 µm | 0.65-1.1 µm | rod-shaped | no | |
69480 | positive | 100 |
colony morphology
- @ref: 25049
- colony color: pale yellow
- colony shape: circular
Culture and growth conditions
culture medium
- @ref: 24810
- name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)
- growth: yes
- link: https://mediadive.dsmz.de/medium/92
- composition: Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
25049 | positive | growth | 10-40 | |
25049 | positive | optimum | 30 | mesophilic |
24810 | positive | growth | 28 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
25049 | positive | growth | 6.0-9.0 | alkaliphile |
25049 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 25049
- oxygen tolerance: facultative anaerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 99 |
69480 | no | 99.997 |
halophily
@ref | salt | tested relation | concentration | growth |
---|---|---|---|---|
25049 | NaCl | optimum | 0 % | |
25049 | NaCl | growth | 0-11.0 %(w/v) | positive |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
25049 | 16808 | 2-dehydro-D-gluconate | - | builds acid from |
25049 | 17426 | 5-dehydro-D-gluconate | - | builds acid from |
25049 | 17924 | D-sorbitol | - | builds acid from |
25049 | 16443 | D-tagatose | - | builds acid from |
25049 | 33984 | fucose | - | builds acid from |
25049 | 16813 | galactitol | - | builds acid from |
25049 | 17268 | myo-inositol | - | builds acid from |
25049 | 18403 | L-arabitol | - | builds acid from |
25049 | 17266 | L-sorbose | - | builds acid from |
25049 | 17632 | nitrate | - | reduction |
25049 | 32032 | potassium gluconate | - | builds acid from |
25049 | 27897 | tryptophan | - | energy source |
25049 | 16199 | urea | - | hydrolysis |
25049 | 16651 | (S)-lactate | + | carbon source |
25049 | 16651 | (S)-lactate | + | nitrogen source |
25049 | 64552 | 2-hydroxybutyrate | + | carbon source |
25049 | 64552 | 2-hydroxybutyrate | + | nitrogen source |
25049 | 30089 | acetate | + | carbon source |
25049 | 30089 | acetate | + | nitrogen source |
25049 | 13705 | acetoacetate | + | carbon source |
25049 | 13705 | acetoacetate | + | nitrogen source |
25049 | 17925 | alpha-D-glucose | + | carbon source |
25049 | 17925 | alpha-D-glucose | + | nitrogen source |
25049 | 27613 | amygdalin | + | builds acid from |
25049 | 18305 | arbutin | + | builds acid from |
25049 | 17057 | cellobiose | + | builds acid from |
25049 | 17057 | cellobiose | + | carbon source |
25049 | 17057 | cellobiose | + | nitrogen source |
25049 | 16947 | citrate | + | carbon source |
25049 | 16947 | citrate | + | nitrogen source |
25049 | 18333 | D-arabitol | + | carbon source |
25049 | 18333 | D-arabitol | + | nitrogen source |
25049 | 15824 | D-fructose | + | builds acid from |
25049 | 15824 | D-fructose | + | carbon source |
25049 | 15824 | D-fructose | + | nitrogen source |
25049 | 78697 | D-fructose 6-phosphate | + | carbon source |
25049 | 78697 | D-fructose 6-phosphate | + | nitrogen source |
25049 | 12936 | D-galactose | + | builds acid from |
25049 | 12936 | D-galactose | + | carbon source |
25049 | 12936 | D-galactose | + | nitrogen source |
25049 | 8391 | D-gluconate | + | carbon source |
25049 | 8391 | D-gluconate | + | nitrogen source |
25049 | 17634 | D-glucose | + | builds acid from |
25049 | 62318 | D-lyxose | + | builds acid from |
25049 | 16899 | D-mannitol | + | builds acid from |
25049 | 16899 | D-mannitol | + | carbon source |
25049 | 16899 | D-mannitol | + | nitrogen source |
25049 | 16024 | D-mannose | + | builds acid from |
25049 | 16024 | D-mannose | + | carbon source |
25049 | 16024 | D-mannose | + | nitrogen source |
25049 | 16988 | D-ribose | + | builds acid from |
25049 | 17924 | D-sorbitol | + | carbon source |
25049 | 17924 | D-sorbitol | + | nitrogen source |
25049 | 65327 | D-xylose | + | builds acid from |
25049 | 23652 | dextrin | + | carbon source |
25049 | 23652 | dextrin | + | nitrogen source |
25049 | 17113 | erythritol | + | builds acid from |
25049 | 4853 | esculin | + | degradation |
25049 | 4853 | esculin | + | builds acid from |
25049 | esculin ferric citrate | + | builds acid from | |
25049 | 28066 | gentiobiose | + | builds acid from |
25049 | 28066 | gentiobiose | + | carbon source |
25049 | 28066 | gentiobiose | + | nitrogen source |
25049 | 17754 | glycerol | + | builds acid from |
25049 | 17754 | glycerol | + | carbon source |
25049 | 17754 | glycerol | + | nitrogen source |
25049 | 28087 | glycogen | + | builds acid from |
25049 | 17596 | inosine | + | carbon source |
25049 | 17596 | inosine | + | nitrogen source |
25049 | 30849 | L-arabinose | + | builds acid from |
25049 | 29991 | L-aspartate | + | carbon source |
25049 | 29991 | L-aspartate | + | nitrogen source |
25049 | 18287 | L-fucose | + | carbon source |
25049 | 18287 | L-fucose | + | nitrogen source |
25049 | 29985 | L-glutamate | + | carbon source |
25049 | 29985 | L-glutamate | + | nitrogen source |
25049 | 62345 | L-rhamnose | + | builds acid from |
25049 | 62345 | L-rhamnose | + | carbon source |
25049 | 62345 | L-rhamnose | + | nitrogen source |
25049 | 17716 | lactose | + | builds acid from |
25049 | 17716 | lactose | + | carbon source |
25049 | 17716 | lactose | + | nitrogen source |
25049 | 17306 | maltose | + | builds acid from |
25049 | 17306 | maltose | + | carbon source |
25049 | 17306 | maltose | + | nitrogen source |
25049 | 6731 | melezitose | + | builds acid from |
25049 | 28053 | melibiose | + | builds acid from |
25049 | 28053 | melibiose | + | carbon source |
25049 | 28053 | melibiose | + | nitrogen source |
25049 | 320055 | methyl beta-D-glucopyranoside | + | carbon source |
25049 | 320055 | methyl beta-D-glucopyranoside | + | nitrogen source |
25049 | 506227 | N-acetylglucosamine | + | builds acid from |
25049 | 506227 | N-acetylglucosamine | + | carbon source |
25049 | 506227 | N-acetylglucosamine | + | nitrogen source |
25049 | 17309 | pectin | + | carbon source |
25049 | 17309 | pectin | + | nitrogen source |
25049 | 16634 | raffinose | + | builds acid from |
25049 | 16634 | raffinose | + | carbon source |
25049 | 16634 | raffinose | + | nitrogen source |
25049 | 17814 | salicin | + | builds acid from |
25049 | 17814 | salicin | + | carbon source |
25049 | 17814 | salicin | + | nitrogen source |
25049 | 17164 | stachyose | + | carbon source |
25049 | 17164 | stachyose | + | nitrogen source |
25049 | 28017 | starch | + | builds acid from |
25049 | 17992 | sucrose | + | builds acid from |
25049 | 17992 | sucrose | + | carbon source |
25049 | 17992 | sucrose | + | nitrogen source |
25049 | 27082 | trehalose | + | builds acid from |
25049 | 27082 | trehalose | + | carbon source |
25049 | 27082 | trehalose | + | nitrogen source |
25049 | 32528 | turanose | + | builds acid from |
25049 | 32528 | turanose | + | carbon source |
25049 | 32528 | turanose | + | nitrogen source |
25049 | 53423 | tween 40 | + | carbon source |
25049 | 53423 | tween 40 | + | nitrogen source |
25049 | 17151 | xylitol | + | builds acid from |
antibiotic resistance
@ref | ChEBI | metabolite | is antibiotic | is resistant |
---|---|---|---|---|
25049 | 31810 | fleroxacin | yes | yes |
25049 | 116278 | lomefloxacin | yes | yes |
25049 | 17698 | chloramphenicol | yes | yes |
25049 | 2955 | azithromycin | yes | yes |
25049 | 3745 | clindamycin | yes | yes |
25049 | 27902 | tetracycline | yes | yes |
25049 | 9332 | sulfamethoxazole | yes | yes |
25049 | 3508 | ceftazidime | yes | yes |
25049 | 7809 | oxacillin | yes | yes |
25049 | 71415 | nitrofurantoin | yes | yes |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
25049 | 35581 | indole | no |
25049 | 15688 | acetoin | yes |
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | indole test |
---|---|---|---|---|
25049 | 15688 | acetoin | + | |
25049 | 35581 | indole | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
25049 | acid phosphatase | - | 3.1.3.2 |
25049 | alkaline phosphatase | - | 3.1.3.1 |
25049 | alpha-chymotrypsin | - | 3.4.21.1 |
25049 | alpha-fucosidase | - | 3.2.1.51 |
25049 | alpha-galactosidase | - | 3.2.1.22 |
25049 | alpha-glucosidase | + | 3.2.1.20 |
25049 | alpha-mannosidase | - | 3.2.1.24 |
25049 | arginine dihydrolase | - | 3.5.3.6 |
25049 | beta-glucosidase | + | 3.2.1.21 |
25049 | beta-glucuronidase | - | 3.2.1.31 |
25049 | catalase | + | 1.11.1.6 |
25049 | cystine arylamidase | + | 3.4.11.3 |
25049 | esterase lipase (C 8) | + | |
25049 | leucine arylamidase | + | 3.4.11.1 |
25049 | lipase | - | |
25049 | lysine decarboxylase | - | 4.1.1.18 |
25049 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
25049 | naphthol-AS-BI-phosphohydrolase | - | |
25049 | ornithine decarboxylase | - | 4.1.1.17 |
25049 | tryptophan deaminase | - | 4.1.99.1 |
25049 | valine arylamidase | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | enrichment culture | enrichment culture composition | enrichment culture duration | enrichment culture temperature |
---|---|---|---|---|---|---|---|---|---|
24810 | fermentation bed of a pigpen | Fujian Province, Xiamen | China | CHN | Asia | ||||
25049 | dextran-inorganic salt agar plates | 1/l: 10g dextran, 2g KNO3, 0.05g MgSO4.7H2O, 2g K2HPO4.3H2O, 0.02g CaCO3, 0.01g FeSO4.7H2O, 10g NaCl, 2g KCl, 3g MgSO4.6H2O | 7 days | 30 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Agriculture | #Livestock (Husbandry) |
#Host | #Mammals | #Suidae (Pig,Swine) |
taxonmaps
- @ref: 69479
- File name: preview.99_31908.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_1340;97_1590;98_23679;99_31908&stattab=map
- Last taxonomy: Microbacterium
- 16S sequence: KX250270
- Sequence Identity:
- Total samples: 655
- soil counts: 83
- aquatic counts: 62
- animal counts: 474
- plant counts: 36
Safety information
risk assessment
- @ref: 24810
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 24810
- description: Microbacterium sorbitolivorans strain SZDIS-1-1 16S ribosomal RNA gene, partial sequence
- accession: KX250270
- length: 1445
- database: ena
- NCBI tax ID: 1867410
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Microbacterium sorbitolivorans CGMCC 1.15228 | GCA_003327285 | scaffold | ncbi | 1867410 |
66792 | Microbacterium sorbitolivorans CGMCC 1.15228 | GCA_014641475 | scaffold | ncbi | 1867410 |
66792 | Microbacterium sorbitolivorans strain CGMCC 1.15228 | 1867410.4 | wgs | patric | 1867410 |
GC content
- @ref: 24810
- GC-content: 67.6
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 99 | no |
motile | no | 93.654 | yes |
flagellated | no | 97.307 | yes |
gram-positive | yes | 92.939 | yes |
anaerobic | no | 99.561 | yes |
aerobic | yes | 82.642 | no |
halophile | no | 72.652 | no |
spore-forming | no | 93.604 | no |
glucose-util | yes | 85.723 | yes |
thermophile | no | 99.081 | yes |
glucose-ferment | no | 72.982 | no |
External links
@ref: 24810
culture collection no.: DSM 103422, CGMCC 1.15228
straininfo link
- @ref: 91296
- straininfo: 400044
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 27902249 | Microbacterium sorbitolivorans sp. nov., a novel member of Microbacteriaceae isolated from fermentation bed in pigpen. | Meng YC, Liu HC, Yang LL, Kang YQ, Zhou YG, Cai M | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001556 | 2016 | Actinomycetales/*classification/genetics/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Fermentation, Glycolipids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Swine, Vitamin K 2/chemistry | Transcriptome |
Phylogeny | 30547854 | Microbacterium suaedae sp. nov., isolated from Suaeda aralocaspica. | Zhu ZN, Li YR, Li YQ, Xiao M, Han MX, Wadaan MAM, Hozzein WN, An DD, Li WJ | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003162 | 2018 | Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Chenopodiaceae/*microbiology, China, DNA, Bacterial/genetics, *Desert Climate, 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 | Transcriptome |
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 | |||
24810 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-103422 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103422) | |||
25049 | Y. C. L. Meng, H. C.,Yang, L. L.,Kang, Y. Q.,Zhou, Y. G.,Cai, M. | Microbacterium sorbitolivorans sp. nov., a novel member of Microbacteriaceae isolated from fermentation bed in pigpen | 10.1099/ijsem.0.001556 | IJSEM 66: 5556-5561 2016 | 27902249 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
69479 | João 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 beta | https://microbeatlas.org/ | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions 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 | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
91296 | 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-ID400044.1 |