Strain identifier

BacDive ID: 132342

Type strain: Yes

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)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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

@refhistory
24131<- L. Tuo, Chinese Acad. Med. Sciences & Peking Union Medical College, Beijing, China; S3Af-1
67770CGMCC 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

@refgram staincell lengthcell widthcell shapemotilityconfidence
44060negative0.5-0.7 µm0.5-0.7 µmcoccus-shapedno
69480no91.699
69480positive100

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

@refnamegrowthlinkcomposition
44060ISP 2 agaryes
44060ISP 3 agaryes
44060ISP 4 agarno
44060ISP 5 agarno
44060ISP 7 agarno
44060LB (Luria-Bertani) MEDIUMno
44060Nutrient agar (NA)yes
44060Reasoner's 2A agar (R2A)yes
44060Trypticase Soy Agar (TSA)yes
24131GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: 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

@refgrowthtypetemperaturerange
44060positivegrowth20-42
44060positiveoptimum28-30mesophilic
44060nogrowth15psychrophilic
44060nogrowth50thermophilic
24131positivegrowth28mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
44060positivegrowth5.0-9.0alkaliphile
44060positiveoptimum7
44060nogrowth4
44060nogrowth10

Physiology and metabolism

oxygen tolerance

  • @ref: 44060
  • oxygen tolerance: aerobe

spore formation

@reftype of sporespore formationconfidence
44060sporeno
69480no99.814

halophily

@refsaltgrowthtested relationconcentrationhalophily level
44060NaClpositivegrowth0-2 %(w/v)
44060NaClpositiveoptimum0 %(w/v)non-halophilic
44060NaClnogrowth3 %(w/v)

observation

@refobservation
44060substrate mycelium
44060primary mycelium
67770quinones: MK-9(H6), MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
44060168082-dehydro-D-gluconate-builds acid from
44060581435-dehydro-D-gluconate-builds acid from
4406015963ribitol-builds acid from
4406018333D-arabitol-builds acid from
4406015824D-fructose-builds acid from
4406028847D-fucose-builds acid from
4406016443D-tagatose-builds acid from
4406065327D-xylose-builds acid from
4406016813galactitol-builds acid from
4406017113erythritol-builds acid from
4406024265gluconate-builds acid from
4406028087glycogen-builds acid from
4406013643glycol-builds acid from
4406017268myo-inositol-builds acid from
4406015443inulin-builds acid from
4406018403L-arabitol-builds acid from
4406018287L-fucose-builds acid from
4406062345L-rhamnose-builds acid from
4406017266L-sorbose-builds acid from
4406065328L-xylose-builds acid from
4406029864mannitol-builds acid from
4406030911sorbitol-builds acid from
4406017151xylitol-builds acid from
440601 % sodium lactate-growth
44060161680aztreonam-growth
4406071321fusidate-growth
4406032735guanidinium chloride-growth
440606472lincomycin-growth
4406048607lithium chloride-growth
4406050694minocycline-growth
4406075273niaproof-growth
4406075229sodium bromate-growth
4406064103sodium butyrate-growth
4406075198tetrazolium blue-growth
4406075193tetrazolium violet-growth
4406045735troleandomycin-growth
4406028001vancomycin-growth
440605291gelatin-hydrolysis
4406053426tween 80-hydrolysis
4406013705acetoacetate-oxidation
4406016523D-serine-oxidation
4406017272propionate-oxidation
4406017632nitrate-reduction
4406027613amygdalin+builds acid from
4406018305arbutin+builds acid from
4406017057cellobiose+builds acid from
4406017108D-arabinose+builds acid from
4406012936D-galactose+builds acid from
4406016988D-ribose+builds acid from
4406065327D-xylose+builds acid from
440604853esculin+builds acid from
4406028066gentiobiose+builds acid from
4406030849L-arabinose+builds acid from
4406017306maltose+builds acid from
440606731melezitose+builds acid from
4406028053melibiose+builds acid from
44060320061methyl alpha-D-glucopyranoside+builds acid from
4406043943methyl alpha-D-mannoside+builds acid from
4406074863methyl beta-D-xylopyranoside+builds acid from
44060506227N-acetylglucosamine+builds acid from
4406016634raffinose+builds acid from
4406017814salicin+builds acid from
4406017992sucrose+builds acid from
4406027082trehalose+builds acid from
4406032528turanose+builds acid from
44060100147nalidixic acid+growth
4406075248potassium tellurite+growth
4406029673rifamycin sv+growth
4406028017starch+hydrolysis
4406053424tween 20+hydrolysis
4406053423tween 40+hydrolysis
4406016651(S)-lactate+oxidation
44060309162-oxoglutarate+oxidation
44060370543-hydroxybutyrate+oxidation
44060739183-O-methyl-D-glucose+oxidation
44060181014-hydroxyphenylacetic acid+oxidation
4406030089acetate+oxidation
4406017925alpha-D-glucose+oxidation
44060645522-hydroxybutyrate+oxidation
4406036219alpha-lactose+oxidation
4406073706bromosuccinate+oxidation
4406017057cellobiose+oxidation
4406016947citrate+oxidation
4406015570D-alanine+oxidation
4406018333D-arabitol+oxidation
4406029990D-aspartate+oxidation
4406015824D-fructose+oxidation
4406078697D-fructose 6-phosphate+oxidation
4406028847D-fucose+oxidation
4406012936D-galactose+oxidation
4406018024D-galacturonic acid+oxidation
440608391D-gluconate+oxidation
4406014314D-glucose 6-phosphate+oxidation
4406015748D-glucuronate+oxidation
4406015588D-malate+oxidation
4406016899D-mannitol+oxidation
4406016024D-mannose+oxidation
4406033801D-saccharate+oxidation
4406017924D-sorbitol+oxidation
4406023652dextrin+oxidation
4406015740formate+oxidation
4406016537galactarate+oxidation
4406016865gamma-aminobutyric acid+oxidation
440605291gelatin+oxidation
4406028066gentiobiose+oxidation
4406032323glucuronamide+oxidation
4406017754glycerol+oxidation
4406070744glycine-proline+oxidation
4406017596inosine+oxidation
4406016467L-arginine+oxidation
4406029991L-aspartate+oxidation
4406018287L-fucose+oxidation
4406029985L-glutamate+oxidation
4406015971L-histidine+oxidation
4406015589L-malate+oxidation
4406018183L-pyroglutamic acid+oxidation
4406062345L-rhamnose+oxidation
4406017115L-serine+oxidation
4406017306maltose+oxidation
4406028053melibiose+oxidation
4406074611methyl (R)-lactate+oxidation
44060320055methyl beta-D-glucopyranoside+oxidation
4406051850methyl pyruvate+oxidation
4406017268myo-inositol+oxidation
4406063153N-acetyl-D-mannosamine+oxidation
4406028037N-acetylgalactosamine+oxidation
44060506227N-acetylglucosamine+oxidation
4406035418n-acetylneuraminate+oxidation
4406017309pectin+oxidation
4406026490quinate+oxidation
4406016634raffinose+oxidation
4406017814salicin+oxidation
4406017164stachyose+oxidation
4406017992sucrose+oxidation
4406027082trehalose+oxidation
4406032528turanose+oxidation
4406053423tween 40+oxidation
4406017634D-glucose+/-builds acid from
4406016024D-mannose+/-builds acid from
4406017716lactose+/-builds acid from
4406028017starch+/-builds acid from
44060casein+/-hydrolysis

metabolite production

  • @ref: 44060
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: no

enzymes

@refvalueactivityec
44060catalase+1.11.1.6
44060cytochrome oxidase+1.9.3.1
44060urease-3.5.1.5
44060N-acetyl-beta-glucosaminidase+3.2.1.52
44060acid phosphatase+3.1.3.2
44060alpha-chymotrypsin+3.4.21.1
44060cystine arylamidase+3.4.11.3
44060esterase (C 4)+
44060esterase Lipase (C 8)+
44060alpha-fucosidase+3.2.1.51
44060alpha-galactosidase+3.2.1.22
44060beta-galactosidase+3.2.1.23
44060alpha-glucosidase+3.2.1.20
44060beta-glucosidase+3.2.1.21
44060leucine arylamidase+3.4.11.1
44060alpha-mannosidase+3.2.1.24
44060naphthol-AS-BI-phosphohydrolase+
44060valine arylamidase+
44060alkaline phosphatase-3.1.3.1
44060beta-glucuronidase-3.2.1.31
44060lipase (C 14)-
44060trypsin-3.4.21.4

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperatureisolation procedure
24131surface-sterilized bark of Bruguiera sexangulaBruguiera sexangulaHainan, Dongzhaigang National Nature Reserve (19° 56' 59'' N 110° 34' 32'' E)ChinaCHNAsia19.9497110.576
44060surface-sterilized bark of Bruguiera sexangulaDongzhaigang National Nature Reserve, HainanChinaCHNAsia19.9497110.576chitin agarcontaining, 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 7.228 days28The 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.
67770Surface-sterilized bark of Bruguiera sexangula from Dongzhaigang National Nature ReserveBruguiera sexangulaHainanChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microlunatus endophyticus CGMCC 4.7306GCA_014646195contigncbi1716077
66792Microlunatus endophyticus strain CGMCC 4.73061716077.3wgspatric1716077

GC content

  • @ref: 24131
  • GC-content: 67.1
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno57no
motileno95.309yes
gram-positiveyes86.567yes
anaerobicno99.06yes
aerobicyes86.685yes
halophileno93.593yes
spore-formingno83.42yes
glucose-utilyes86.362no
flagellatedno98.882yes
thermophileno99.247no
glucose-fermentno82.029no

External links

@ref: 24131

culture collection no.: DSM 100019, CGMCC 4.7306, JCM 31774

straininfo link

  • @ref: 90688
  • straininfo: 399010

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny26585772Microlunatus 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 CHInt J Syst Evol Microbiol10.1099/ijsem.0.0007792015Bacterial 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/chemistryGenetics
Phylogeny32886594Microlunatus 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 SYInt J Syst Evol Microbiol10.1099/ijsem.0.0044282020Bacterial 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/chemistryTranscriptome

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
24131Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100019Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100019)
44060Li Tuo, Jing Li, Shao-Wei Liu, Yang Liu, Lin Hu, Li Chen, Ming-Guo Jiang and Cheng-Hang SunMicrolunatus endophyticus sp. nov., an endophytic actinobacterium isolated from bark of Bruguiera sexangula10.1099/ijsem.0.000779IJSEM 66: 481-486 201626585772
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69479João 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 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions 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
90688Reimer, 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-ID399010.1