Strain identifier
BacDive ID: 132342
Type strain:
Species: Microlunatus endophyticus
Strain Designation: S3Af-1
Strain history: CGMCC 4.7306 <-- L. Tuo; Inst. of Med. Biotechnol., Chin. Acad. Med. Sci. & Peking Union Med. Coll., China; S3Af-1.
NCBI tax ID(s): 1716077 (species)
General
@ref: 24131
BacDive-ID: 132342
DSM-Number: 100019
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, coccus-shaped, colony-forming
description: Microlunatus endophyticus S3Af-1 is an aerobe, Gram-negative, coccus-shaped bacterium that forms circular colonies and was isolated from surface-sterilized bark of Bruguiera sexangula.
NCBI tax id
- NCBI tax id: 1716077
- Matching level: species
strain history
@ref | history |
---|---|
24131 | <- L. Tuo, Chinese Acad. Med. Sciences & Peking Union Medical College, Beijing, China; S3Af-1 |
67770 | CGMCC 4.7306 <-- L. Tuo; Inst. of Med. Biotechnol., Chin. Acad. Med. Sci. & Peking Union Med. Coll., China; S3Af-1. |
doi: 10.13145/bacdive132342.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Propionibacteriales
- family: Propionibacteriaceae
- genus: Microlunatus
- species: Microlunatus endophyticus
- full scientific name: Microlunatus endophyticus Tuo et al. 2016
@ref: 24131
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Propionibacteriaceae
genus: Microlunatus
species: Microlunatus endophyticus
full scientific name: Microlunatus endophyticus Tuo et al. 2016
strain designation: S3Af-1
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
44060 | negative | 0.5-0.7 µm | 0.5-0.7 µm | coccus-shaped | no | |
69480 | no | 91.699 | ||||
69480 | positive | 100 |
colony morphology
- @ref: 44060
- colony color: yellowish white
- colony shape: circular
- incubation period: 5 days
- medium used: ISP 2 agar
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
44060 | ISP 2 agar | yes | ||
44060 | ISP 3 agar | yes | ||
44060 | ISP 4 agar | no | ||
44060 | ISP 5 agar | no | ||
44060 | ISP 7 agar | no | ||
44060 | LB (Luria-Bertani) MEDIUM | no | ||
44060 | Nutrient agar (NA) | yes | ||
44060 | Reasoner's 2A agar (R2A) | yes | ||
44060 | Trypticase Soy Agar (TSA) | yes | ||
24131 | 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 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
44060 | positive | growth | 20-42 | |
44060 | positive | optimum | 28-30 | mesophilic |
44060 | no | growth | 15 | psychrophilic |
44060 | no | growth | 50 | thermophilic |
24131 | positive | growth | 28 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
44060 | positive | growth | 5.0-9.0 | alkaliphile |
44060 | positive | optimum | 7 | |
44060 | no | growth | 4 | |
44060 | no | growth | 10 |
Physiology and metabolism
oxygen tolerance
- @ref: 44060
- oxygen tolerance: aerobe
spore formation
@ref | type of spore | spore formation | confidence |
---|---|---|---|
44060 | spore | no | |
69480 | no | 99.814 |
halophily
@ref | salt | growth | tested relation | concentration | halophily level |
---|---|---|---|---|---|
44060 | NaCl | positive | growth | 0-2 %(w/v) | |
44060 | NaCl | positive | optimum | 0 %(w/v) | non-halophilic |
44060 | NaCl | no | growth | 3 %(w/v) |
observation
@ref | observation |
---|---|
44060 | substrate mycelium |
44060 | primary mycelium |
67770 | quinones: MK-9(H6), MK-9(H4) |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
44060 | 16808 | 2-dehydro-D-gluconate | - | builds acid from |
44060 | 58143 | 5-dehydro-D-gluconate | - | builds acid from |
44060 | 15963 | ribitol | - | builds acid from |
44060 | 18333 | D-arabitol | - | builds acid from |
44060 | 15824 | D-fructose | - | builds acid from |
44060 | 28847 | D-fucose | - | builds acid from |
44060 | 16443 | D-tagatose | - | builds acid from |
44060 | 65327 | D-xylose | - | builds acid from |
44060 | 16813 | galactitol | - | builds acid from |
44060 | 17113 | erythritol | - | builds acid from |
44060 | 24265 | gluconate | - | builds acid from |
44060 | 28087 | glycogen | - | builds acid from |
44060 | 13643 | glycol | - | builds acid from |
44060 | 17268 | myo-inositol | - | builds acid from |
44060 | 15443 | inulin | - | builds acid from |
44060 | 18403 | L-arabitol | - | builds acid from |
44060 | 18287 | L-fucose | - | builds acid from |
44060 | 62345 | L-rhamnose | - | builds acid from |
44060 | 17266 | L-sorbose | - | builds acid from |
44060 | 65328 | L-xylose | - | builds acid from |
44060 | 29864 | mannitol | - | builds acid from |
44060 | 30911 | sorbitol | - | builds acid from |
44060 | 17151 | xylitol | - | builds acid from |
44060 | 1 % sodium lactate | - | growth | |
44060 | 161680 | aztreonam | - | growth |
44060 | 71321 | fusidate | - | growth |
44060 | 32735 | guanidinium chloride | - | growth |
44060 | 6472 | lincomycin | - | growth |
44060 | 48607 | lithium chloride | - | growth |
44060 | 50694 | minocycline | - | growth |
44060 | 75273 | niaproof | - | growth |
44060 | 75229 | sodium bromate | - | growth |
44060 | 64103 | sodium butyrate | - | growth |
44060 | 75198 | tetrazolium blue | - | growth |
44060 | 75193 | tetrazolium violet | - | growth |
44060 | 45735 | troleandomycin | - | growth |
44060 | 28001 | vancomycin | - | growth |
44060 | 5291 | gelatin | - | hydrolysis |
44060 | 53426 | tween 80 | - | hydrolysis |
44060 | 13705 | acetoacetate | - | oxidation |
44060 | 16523 | D-serine | - | oxidation |
44060 | 17272 | propionate | - | oxidation |
44060 | 17632 | nitrate | - | reduction |
44060 | 27613 | amygdalin | + | builds acid from |
44060 | 18305 | arbutin | + | builds acid from |
44060 | 17057 | cellobiose | + | builds acid from |
44060 | 17108 | D-arabinose | + | builds acid from |
44060 | 12936 | D-galactose | + | builds acid from |
44060 | 16988 | D-ribose | + | builds acid from |
44060 | 65327 | D-xylose | + | builds acid from |
44060 | 4853 | esculin | + | builds acid from |
44060 | 28066 | gentiobiose | + | builds acid from |
44060 | 30849 | L-arabinose | + | builds acid from |
44060 | 17306 | maltose | + | builds acid from |
44060 | 6731 | melezitose | + | builds acid from |
44060 | 28053 | melibiose | + | builds acid from |
44060 | 320061 | methyl alpha-D-glucopyranoside | + | builds acid from |
44060 | 43943 | methyl alpha-D-mannoside | + | builds acid from |
44060 | 74863 | methyl beta-D-xylopyranoside | + | builds acid from |
44060 | 506227 | N-acetylglucosamine | + | builds acid from |
44060 | 16634 | raffinose | + | builds acid from |
44060 | 17814 | salicin | + | builds acid from |
44060 | 17992 | sucrose | + | builds acid from |
44060 | 27082 | trehalose | + | builds acid from |
44060 | 32528 | turanose | + | builds acid from |
44060 | 100147 | nalidixic acid | + | growth |
44060 | 75248 | potassium tellurite | + | growth |
44060 | 29673 | rifamycin sv | + | growth |
44060 | 28017 | starch | + | hydrolysis |
44060 | 53424 | tween 20 | + | hydrolysis |
44060 | 53423 | tween 40 | + | hydrolysis |
44060 | 16651 | (S)-lactate | + | oxidation |
44060 | 30916 | 2-oxoglutarate | + | oxidation |
44060 | 37054 | 3-hydroxybutyrate | + | oxidation |
44060 | 73918 | 3-O-methyl-D-glucose | + | oxidation |
44060 | 18101 | 4-hydroxyphenylacetic acid | + | oxidation |
44060 | 30089 | acetate | + | oxidation |
44060 | 17925 | alpha-D-glucose | + | oxidation |
44060 | 64552 | 2-hydroxybutyrate | + | oxidation |
44060 | 36219 | alpha-lactose | + | oxidation |
44060 | 73706 | bromosuccinate | + | oxidation |
44060 | 17057 | cellobiose | + | oxidation |
44060 | 16947 | citrate | + | oxidation |
44060 | 15570 | D-alanine | + | oxidation |
44060 | 18333 | D-arabitol | + | oxidation |
44060 | 29990 | D-aspartate | + | oxidation |
44060 | 15824 | D-fructose | + | oxidation |
44060 | 78697 | D-fructose 6-phosphate | + | oxidation |
44060 | 28847 | D-fucose | + | oxidation |
44060 | 12936 | D-galactose | + | oxidation |
44060 | 18024 | D-galacturonic acid | + | oxidation |
44060 | 8391 | D-gluconate | + | oxidation |
44060 | 14314 | D-glucose 6-phosphate | + | oxidation |
44060 | 15748 | D-glucuronate | + | oxidation |
44060 | 15588 | D-malate | + | oxidation |
44060 | 16899 | D-mannitol | + | oxidation |
44060 | 16024 | D-mannose | + | oxidation |
44060 | 33801 | D-saccharate | + | oxidation |
44060 | 17924 | D-sorbitol | + | oxidation |
44060 | 23652 | dextrin | + | oxidation |
44060 | 15740 | formate | + | oxidation |
44060 | 16537 | galactarate | + | oxidation |
44060 | 16865 | gamma-aminobutyric acid | + | oxidation |
44060 | 5291 | gelatin | + | oxidation |
44060 | 28066 | gentiobiose | + | oxidation |
44060 | 32323 | glucuronamide | + | oxidation |
44060 | 17754 | glycerol | + | oxidation |
44060 | 70744 | glycine-proline | + | oxidation |
44060 | 17596 | inosine | + | oxidation |
44060 | 16467 | L-arginine | + | oxidation |
44060 | 29991 | L-aspartate | + | oxidation |
44060 | 18287 | L-fucose | + | oxidation |
44060 | 29985 | L-glutamate | + | oxidation |
44060 | 15971 | L-histidine | + | oxidation |
44060 | 15589 | L-malate | + | oxidation |
44060 | 18183 | L-pyroglutamic acid | + | oxidation |
44060 | 62345 | L-rhamnose | + | oxidation |
44060 | 17115 | L-serine | + | oxidation |
44060 | 17306 | maltose | + | oxidation |
44060 | 28053 | melibiose | + | oxidation |
44060 | 74611 | methyl (R)-lactate | + | oxidation |
44060 | 320055 | methyl beta-D-glucopyranoside | + | oxidation |
44060 | 51850 | methyl pyruvate | + | oxidation |
44060 | 17268 | myo-inositol | + | oxidation |
44060 | 63153 | N-acetyl-D-mannosamine | + | oxidation |
44060 | 28037 | N-acetylgalactosamine | + | oxidation |
44060 | 506227 | N-acetylglucosamine | + | oxidation |
44060 | 35418 | n-acetylneuraminate | + | oxidation |
44060 | 17309 | pectin | + | oxidation |
44060 | 26490 | quinate | + | oxidation |
44060 | 16634 | raffinose | + | oxidation |
44060 | 17814 | salicin | + | oxidation |
44060 | 17164 | stachyose | + | oxidation |
44060 | 17992 | sucrose | + | oxidation |
44060 | 27082 | trehalose | + | oxidation |
44060 | 32528 | turanose | + | oxidation |
44060 | 53423 | tween 40 | + | oxidation |
44060 | 17634 | D-glucose | +/- | builds acid from |
44060 | 16024 | D-mannose | +/- | builds acid from |
44060 | 17716 | lactose | +/- | builds acid from |
44060 | 28017 | starch | +/- | builds acid from |
44060 | casein | +/- | hydrolysis |
metabolite production
- @ref: 44060
- Chebi-ID: 16136
- metabolite: hydrogen sulfide
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
44060 | catalase | + | 1.11.1.6 |
44060 | cytochrome oxidase | + | 1.9.3.1 |
44060 | urease | - | 3.5.1.5 |
44060 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
44060 | acid phosphatase | + | 3.1.3.2 |
44060 | alpha-chymotrypsin | + | 3.4.21.1 |
44060 | cystine arylamidase | + | 3.4.11.3 |
44060 | esterase (C 4) | + | |
44060 | esterase Lipase (C 8) | + | |
44060 | alpha-fucosidase | + | 3.2.1.51 |
44060 | alpha-galactosidase | + | 3.2.1.22 |
44060 | beta-galactosidase | + | 3.2.1.23 |
44060 | alpha-glucosidase | + | 3.2.1.20 |
44060 | beta-glucosidase | + | 3.2.1.21 |
44060 | leucine arylamidase | + | 3.4.11.1 |
44060 | alpha-mannosidase | + | 3.2.1.24 |
44060 | naphthol-AS-BI-phosphohydrolase | + | |
44060 | valine arylamidase | + | |
44060 | alkaline phosphatase | - | 3.1.3.1 |
44060 | beta-glucuronidase | - | 3.2.1.31 |
44060 | lipase (C 14) | - | |
44060 | trypsin | - | 3.4.21.4 |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | geographic location | country | origin.country | continent | latitude | longitude | enrichment culture | enrichment culture composition | enrichment culture duration | enrichment culture temperature | isolation procedure |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
24131 | surface-sterilized bark of Bruguiera sexangula | Bruguiera sexangula | Hainan, Dongzhaigang National Nature Reserve (19° 56' 59'' N 110° 34' 32'' E) | China | CHN | Asia | 19.9497 | 110.576 | |||||
44060 | surface-sterilized bark of Bruguiera sexangula | Dongzhaigang National Nature Reserve, Hainan | China | CHN | Asia | 19.9497 | 110.576 | chitin agar | containing, per litre distilled water: 2.0 g chitin, 0.7 g K2HPO4 , 0.3 g KH2PO4 , 0.5 g MgSO4 . 7H2O, 0.01 g FeSO4 . 7H2O, 0.001 g ZnSO4 , 0.001 g MnCl2 and 15.0 g agar, pH 7.2 | 28 days | 28 | The plant samples of Bruguiera sexangula were washed in running tap water to remove adherent epiphytes and surface-sterilized according to the ve-step sterilization procedure (Qin et al., 2008). After drying under a hood, the surface-sterilized bark was ground into powder by using a micromill and distributed on different media plates. | |
67770 | Surface-sterilized bark of Bruguiera sexangula from Dongzhaigang National Nature Reserve | Bruguiera sexangula | Hainan | China | CHN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host Body-Site | #Plant | #Sterilized plant part |
#Host | #Plants | #Shrub (Scrub) |
#Host Body-Site | #Plant | #Bark |
taxonmaps
- @ref: 69479
- File name: preview.99_162990.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_72;96_19542;97_24243;98_30668;99_162990&stattab=map
- Last taxonomy: Microlunatus endophyticus
- 16S sequence: KT749873
- Sequence Identity:
- Total samples: 758
- soil counts: 595
- aquatic counts: 31
- animal counts: 106
- plant counts: 26
Safety information
risk assessment
- @ref: 24131
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 24131
- description: Microlunatus endophyticus 16S ribosomal RNA gene, partial sequence
- accession: KT749873
- length: 1478
- database: ena
- NCBI tax ID: 1716077
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Microlunatus endophyticus CGMCC 4.7306 | GCA_014646195 | contig | ncbi | 1716077 |
66792 | Microlunatus endophyticus strain CGMCC 4.7306 | 1716077.3 | wgs | patric | 1716077 |
GC content
- @ref: 24131
- GC-content: 67.1
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 57 | no |
motile | no | 95.309 | yes |
gram-positive | yes | 86.567 | yes |
anaerobic | no | 99.06 | yes |
aerobic | yes | 86.685 | yes |
halophile | no | 93.593 | yes |
spore-forming | no | 83.42 | yes |
glucose-util | yes | 86.362 | no |
flagellated | no | 98.882 | yes |
thermophile | no | 99.247 | no |
glucose-ferment | no | 82.029 | no |
External links
@ref: 24131
culture collection no.: DSM 100019, CGMCC 4.7306, JCM 31774
straininfo link
- @ref: 90688
- straininfo: 399010
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 26585772 | Microlunatus endophyticus sp. nov., an endophytic actinobacterium isolated from bark of Bruguiera sexangula. | Tuo L, Li J, Liu SW, Liu Y, Hu L, Chen L, Jiang MG, Sun CH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000779 | 2015 | Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Bark/*microbiology, Propionibacteriaceae/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Rhizophoraceae/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
Phylogeny | 32886594 | Microlunatus elymi sp. nov., a novel actinobacterium isolated from rhizospheric soil of the wild plant Elymus tsukushiensis. | Son JS, Lee SY, Hwang YJ, Shin JH, Ghim SY | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004428 | 2020 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Elymus/*microbiology, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Propionibacteriaceae/*classification/isolation & purification, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/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 | |||
24131 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-100019 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100019) | |||
44060 | Li Tuo, Jing Li, Shao-Wei Liu, Yang Liu, Lin Hu, Li Chen, Ming-Guo Jiang and Cheng-Hang Sun | Microlunatus endophyticus sp. nov., an endophytic actinobacterium isolated from bark of Bruguiera sexangula | 10.1099/ijsem.0.000779 | IJSEM 66: 481-486 2016 | 26585772 | |
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 | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
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 | |||
90688 | 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-ID399010.1 |