Strain identifier

BacDive ID: 158677

Type strain: Yes

Species: Marmoricola endophyticus

Strain Designation: 8BXZ-J1

Strain history: <- Zhong-ke Jiang, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College

NCBI tax ID(s): 2040280 (species)

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General

@ref: 65409

BacDive-ID: 158677

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-positive, rod-shaped, colony-forming

description: Marmoricola endophyticus 8BXZ-J1 is an aerobe, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from surface-sterilized branches of Thespesia populnea.

NCBI tax id

  • NCBI tax id: 2040280
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Zhong-ke Jiang, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College

doi: 10.13145/bacdive158677.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Nocardioidaceae
  • genus: Marmoricola
  • species: Marmoricola endophyticus
  • full scientific name: Marmoricola endophyticus Jiang et al. 2017

  • synonyms

    • @ref: 20215
    • synonym: Nocardioides marmoriendophyticus

@ref: 65409

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Propionibacteriales

family: Nocardioidaceae

genus: Marmoricola

species: Marmoricola endophyticus

strain designation: 8BXZ-J1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
65409positive0.80-1.6 µm0.55-0.75 µmrod-shapedno
69480no97.281
69480positive100

colony morphology

  • @ref: 65409
  • colony color: yellowish white
  • colony shape: circular

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
65409positivegrowth10-35
65409positiveoptimum28-30mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepH
65409positivegrowth6-8
65409positiveoptimum7.0

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
65409aerobe
67771aerobe

spore formation

@refspore formationconfidence
65409no
69480no99.765

halophily

@refsaltgrowthtested relationconcentration
65409NaClpositivegrowth0-10.0 %(w/v)
65409NaClpositiveoptimum0-5.0 %(w/v)

observation

@refobservation
65409the cell-wall peptidoglycan contains LL-DAP as the diagnostic diaminoacid
65409predominant menaquinone is MK-8(H 4)
65409polar lipids comprise diphosphatidylglycerol, phosphatidyl-glycerol, phosphatidylinositol, phosphatidylcholine and two unknown lipids

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6540916899D-mannitol+assimilation
65409370543-hydroxybutyrate-assimilation
65409167244-hydroxybutyrate-assimilation
6540917128adipate-assimilation
6540927689decanoate-assimilation
65409casein+hydrolysis
6540962968cellulose-hydrolysis
6540917029chitin-hydrolysis
6540917634D-glucose+assimilation
6540916988D-ribose-assimilation
6540917924D-sorbitol-assimilation
65409esculin ferric citrate+hydrolysis
654095291gelatin+hydrolysis
6540917234glucose-fermentation
6540928087glycogen-assimilation
6540917240itaconate-assimilation
65409L-alanine 4-nitroanilide-assimilation
6540930849L-arabinose+assimilation
6540918287L-fucose-assimilation
6540915971L-histidine-assimilation
6540917203L-proline-assimilation
6540962345L-rhamnose-assimilation
6540917115L-serine-assimilation
6540924996lactate-assimilation
6540925115malate+assimilation
6540917306maltose+assimilation
6540928053melibiose-assimilation
6540917268myo-inositol-assimilation
65409506227N-acetylglucosamine+assimilation
6540917632nitrate-reduction
6540918401phenylacetate-assimilation
65409potassium 2-dehydro-D-gluconate-assimilation
65409potassium 5-dehydro-D-gluconate-assimilation
6540917272propionate-assimilation
6540917814salicin-assimilation
6540953258sodium citrate-assimilation
6540962983sodium malonate-assimilation
6540928017starch+hydrolysis
6540917992sucrose+assimilation
6540953426tween 80+hydrolysis
6540918186tyrosine-hydrolysis
6540931011valerate-assimilation
6540915318xanthine-hydrolysis

metabolite production

  • @ref: 65409
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
65409cytochrome oxidase-1.9.3.1
65409catalase+1.11.1.6
65409esterase (C 4)+
65409esterase Lipase (C 8)+
65409leucine arylamidase+3.4.11.1
65409acid phosphatase+3.1.3.2
65409naphthol-AS-BI-phosphohydrolase+
65409alpha-glucosidase+3.2.1.20
65409alkaline phosphatase+3.1.3.1
65409lipase (C 14)-
65409valine arylamidase-
65409cystine arylamidase-3.4.11.3
65409trypsin-3.4.21.4
65409alpha-chymotrypsin-3.4.21.1
65409alpha-galactosidase-3.2.1.22
65409beta-galactosidase-3.2.1.23
65409beta-glucuronidase-3.2.1.31
65409beta-glucosidase-3.2.1.21
65409N-acetyl-beta-glucosaminidase-3.2.1.52
65409alpha-mannosidase-3.2.1.24
65409alpha-fucosidase-3.2.1.51
65409arginine dihydrolase-3.5.3.6
65409urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    65409C15:03.6
    65409C16:012.3
    65409C18:06
    65409C17:1ω8c1.5
    65409C18:1ω5c4.3
    65409C15:0 iso6.7
    65409C16:0 iso21.2
    65409C16:0 10-methyl4.6
    65409C17:0 iso4.9
    65409C17:0 10-methyl1.1
    65409C18:0 10-methyl (TBSA)22.5
    65409C16:0 2OH2.8
    65409C16:0 iso 2OH7.9
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A agar
  • incubation temperature: 28
  • incubation time: 3
  • system: MIS MIDI
  • instrument: Agilent 7890A gas chromatograph coupled with an Agilent 5975C single quadrupole mass spectrometer equipped with Nist08 Library software database
  • method/protocol: Sasser, 1990
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
65409surface-sterilized branches of Thespesia populneaBeilun Estuary National Nature ReserveChinaCHNAsia21.6038108.207
67771from surface-sterilized branches of Thespesia populnea collected from Beilun Estuary Mangrove Forest National Nature Reserve in GuangxiChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Host Body-Site#Plant#Stem (Branch)
#Engineered#Treatment#Sterilized (Desinfected)
#Host#Plants#Tree

Sequence information

16S sequences

  • @ref: 65409
  • description: 16S rRNA gene sequence
  • accession: KY921599
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Marmoricola endophyticus CGMCC 1.16067GCA_014644415scaffoldncbi2040280
66792Marmoricola endophyticus strain CGMCC 1.160672040280.3wgspatric2040280

GC content

  • @ref: 65409
  • GC-content: 68.7
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno67no
flagellatedno98.644yes
gram-positiveyes93.573no
anaerobicno99.395yes
aerobicyes94.634no
halophileno81.205no
spore-formingno85.703no
glucose-utilyes88.173yes
thermophileno98.603yes
motileno95.956yes
glucose-fermentno91.839yes

External links

@ref: 65409

culture collection no.: KCTC 39789, CGMCC 1.16067

literature

  • topic: Phylogeny
  • Pubmed-ID: 28920827
  • title: Marmoricola endophyticus sp. nov., an endophytic actinobacterium isolated from Thespesia populnea.
  • authors: Jiang ZK, Pan Z, Li FN, Li XJ, Liu SW, Tuo L, Jiang MG, Sun CH
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002297
  • year: 2017
  • mesh: Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournalpubmed
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
65409Zhong-Ke Jiang, Zhen Pan, Fei-Na Li, Xiao-Jun Li ,Shao-Wei Liu, Li Tuo, Ming-Guo Jiang, Cheng-Hang SunMarmoricola endophyticus sp. nov., an endophytic actinobacterium isolated from Thespesia populnea10.1099/ijsem.0.002297IJSEM 67: 4379-4384 201728920827
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
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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