Strain identifier
BacDive ID: 141104
Type strain: 
Species: Nonomuraea glycinis
Strain Designation: NEAU-BB2C19
Strain history: <- J. Zhao, School of Life Science, Northeast Agricultural Univ. (NEAU), Harbin, China; NEAU-BB2C19 <- Z. Li, NEAU, China
NCBI tax ID(s): 2047744 (species)
version 8.1 (current version)
General
@ref: 64981
BacDive-ID: 141104
DSM-Number: 104838
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, Gram-positive
description: Nonomuraea glycinis NEAU-BB2C19 is an aerobe, spore-forming, Gram-positive bacterium that builds an extensively branched substrate mycelium and aerial hyphae and was isolated from root of black soya bean [Glycine max Merr] collected from Harbin.
NCBI tax id
- NCBI tax id: 2047744
- Matching level: species
strain history
- @ref: 64981
- history: <- J. Zhao, School of Life Science, Northeast Agricultural Univ. (NEAU), Harbin, China; NEAU-BB2C19 <- Z. Li, NEAU, China
doi: 10.13145/bacdive141104.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Streptosporangiales
- family: Streptosporangiaceae
- genus: Nonomuraea
- species: Nonomuraea glycinis
- full scientific name: Nonomuraea glycinis Li et al. 2017
@ref: 64981
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Streptosporangiaceae
genus: Nonomuraea
species: Nonomuraea glycinis
full scientific name: Nonomuraea glycinis Li et al. 2017
strain designation: NEAU-BB2C19
type strain: yes
Morphology
cell morphology
| @ref | gram stain | motility | confidence |
|---|---|---|---|
| 44012 | positive | ||
| 69480 | no | 90.316 | |
| 69480 | positive | 100 |
multicellular morphology
- @ref: 44012
- forms multicellular complex: yes
- complex name: extensively branched substrate mycelium and aerial hyphae
- complex color: white and vivid yellow
- medium name: International Streptomyces Project medium
multimedia
- @ref: 64981
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_104838.jpg
- caption: Medium 65 28°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 64981 | GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) | yes | https://mediadive.dsmz.de/medium/65 | Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water |
| 64981 | ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) | yes | https://mediadive.dsmz.de/medium/84 | Name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) Composition: Agar 20.0 g/l Rolled oats 20.0 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 44012 | positive | growth | 10-37 | |
| 44012 | positive | optimum | 28 | mesophilic |
| 64981 | positive | growth | 28 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 44012 | positive | growth | 7.0-9.0 | alkaliphile |
| 44012 | positive | optimum | 7.0-8.0 |
Physiology and metabolism
oxygen tolerance
- @ref: 44012
- oxygen tolerance: aerobe
spore formation
| @ref | spore description | type of spore | spore formation | confidence |
|---|---|---|---|---|
| 44012 | spiral spore chains are composed of 14–16 non-motile spores (0.82 x1.00 µm) with a wrinkled surface that are borne directly on aerial mycelia | spore | yes | |
| 69481 | yes | 100 | ||
| 69480 | yes | 100 |
halophily
- @ref: 44012
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-4 %
observation
- @ref: 44012
- observation: the predominant menaquinones are MK-9(H2) and MK-9(H0)
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 44012 | 5291 | gelatin | - | assimilation |
| 44012 | milk | - | assimilation | |
| 44012 | 15824 | D-fructose | - | carbon source |
| 44012 | 16988 | D-ribose | - | carbon source |
| 44012 | 30849 | L-arabinose | - | carbon source |
| 44012 | 53424 | tween 20 | - | hydrolysis |
| 44012 | 53423 | tween 40 | - | hydrolysis |
| 44012 | 53426 | tween 80 | - | hydrolysis |
| 44012 | 15428 | glycine | - | nitrogen source |
| 44012 | 17115 | L-serine | - | nitrogen source |
| 44012 | 16857 | L-threonine | - | nitrogen source |
| 44012 | 17895 | L-tyrosine | - | nitrogen source |
| 44012 | 17632 | nitrate | - | reduction |
| 44012 | 62968 | cellulose | + | assimilation |
| 44012 | 12936 | D-galactose | + | carbon source |
| 44012 | 17634 | D-glucose | + | carbon source |
| 44012 | 16899 | D-mannitol | + | carbon source |
| 44012 | 16024 | D-mannose | + | carbon source |
| 44012 | 65327 | D-xylose | + | carbon source |
| 44012 | 17268 | myo-inositol | + | carbon source |
| 44012 | 62345 | L-rhamnose | + | carbon source |
| 44012 | 17716 | lactose | + | carbon source |
| 44012 | 17306 | maltose | + | carbon source |
| 44012 | 17992 | sucrose | + | carbon source |
| 44012 | 4853 | esculin | + | hydrolysis |
| 44012 | 16199 | urea | + | hydrolysis |
| 44012 | 16919 | creatine | + | nitrogen source |
| 44012 | 16467 | L-arginine | + | nitrogen source |
| 44012 | 17196 | L-asparagine | + | nitrogen source |
| 44012 | 29991 | L-aspartate | + | nitrogen source |
| 44012 | 29985 | L-glutamate | + | nitrogen source |
| 44012 | 18050 | L-glutamine | + | nitrogen source |
metabolite production
- @ref: 44012
- Chebi-ID: 15138
- metabolite: sulfide
- production: no
enzymes
- @ref: 44012
- value: catalase
- activity: -
- ec: 1.11.1.6
fatty acid profile
fatty acids
@ref fatty acid percentage 44012 10-methyl C17:0 17.6 44012 10-methyl C18:0 10.7 44012 10-methyl C16:0 3.8 44012 C17:0 anteiso 2.9 44012 C15:0 3.5 44012 C16:0 8.3 44012 C16:1ω7c 1.9 44012 C17:0 5 44012 C17:1ω7c 6.4 44012 C18:0 4.2 44012 C18:1ω7c 4.1 44012 C15:0 iso 2 44012 C16:0 iso 27.3 - type of FA analysis: whole cell analysis
- incubation medium: ISP 2 broth
- agar/liquid: liquid
- incubation temperature: 28
- incubation time: 5
- treatment: cultivation in ISP 2 broth for 5 days in shake flasks
- system: MIS MIDI
- method/protocol: Xiang et al. 2011
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
|---|---|---|---|---|---|---|---|
| 44012 | root of black soya bean [Glycine max (L.) Merr] collected from Harbin | Heilongjiang Province | China | CHN | Asia | ||
| 64981 | surface-sterilized root of black soya bean (Glycine max) (L.) Merr | Heilongjiang Province, Harbin, Northeast Agriculture University (44° 04' N, 125° 42' E) | China | CHN | Asia | 44.0667 | 125.7 |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
| #Host Body-Site | #Plant | #Root (Rhizome) |
Safety information
risk assessment
- @ref: 64981
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 64981
- description: Nonomuraea glycinis strain NEAU-BB2C19 16S ribosomal RNA gene, partial sequence
- accession: KY328642
- length: 1514
- database: ena
- NCBI tax ID: 2047744
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Nonomuraea glycinis CGMCC 4.7430 | GCA_014646515 | scaffold | ncbi | 2047744 |
| 66792 | Nonomuraea glycinis NEAU-BB2C19 | GCA_020215885 | scaffold | ncbi | 2047744 |
| 66792 | Nonomuraea glycinis strain CGMCC 4.7430 | 2047744.3 | wgs | patric | 2047744 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 44012 | 67.08-68.6 | thermal denaturation, midpoint method (Tm) |
| 64981 | 68.2 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| flagellated | no | 97.877 | no |
| gram-positive | yes | 91.106 | yes |
| anaerobic | no | 98.775 | yes |
| aerobic | yes | 90.468 | no |
| halophile | no | 92.252 | no |
| spore-forming | yes | 96.589 | no |
| thermophile | no | 97.648 | no |
| glucose-util | yes | 88.073 | no |
| motile | no | 91.993 | no |
| glucose-ferment | no | 91.641 | no |
External links
@ref: 64981
culture collection no.: CGMCC 4.7430, DSM 104838
straininfo link
- @ref: 96856
- straininfo: 407016
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 29043953 | Nonomuraea glycinis sp. nov., a novel actinomycete isolated from the root of black soya bean [Glycine max (L.) Merr]. | Li Z, Song W, Zhao J, Zhuang X, Zhao Y, Wang X, Xiang W | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002406 | 2017 | Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soybeans/*microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
| Phylogeny | 29744692 | Nonomuraea rhizosphaerae sp. nov., an actinomycete isolated from the rhizosphere soil of a rubber tree (Hevea brasiliensis Muell. Arg). | Zhao J, Mu S, Zhao Q, Jiang S, Cao P, Guo X, Wang X, Xiang W | Antonie Van Leeuwenhoek | 10.1007/s10482-018-1094-9 | 2018 | Actinomycetales/classification/genetics/*isolation & purification/metabolism, Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Fatty Acids/chemistry/metabolism, Hevea/growth & development, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizosphere, *Soil Microbiology | Metabolism |
| Phylogeny | 35666673 | Nonomuraea aurantiaca sp. nov., a novel cellulase-producing actinobacterium isolated from soil. | Lin J, Zhang L, Qian L, Yang Y, Xiang W, Zhao J, Wang X | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005411 | 2022 | *Actinomycetales, Bacterial Typing Techniques, Base Composition, *Cellulase/genetics, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phosphatidylethanolamines, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, Soil Microbiology | Transcriptome |
Reference
| @id | authors | title | doi/url | journal | pubmed | catalogue |
|---|---|---|---|---|---|---|
| 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 | |||
| 44012 | Zhilei Li, Wei Song, Junwei Zhao, Xiaoxin Zhuang, Yue Zhao, Xiangjing Wang, Wensheng Xiang | Nonomuraea glycinis sp. nov., a novel actinomycete isolated from the root of black soya bean [Glycine max (L.) Merr] | 10.1099/ijsem.0.002406 | IJSEM 67: 5026-5031 2017 | 29043953 | |
| 64981 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-104838 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104838) | |||
| 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 | |||
| 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 | |||
| 96856 | 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-ID407016.1 |