Strain identifier

BacDive ID: 5832

Type strain: Yes

Species: Modestobacter marinus

Strain Designation: 42H12-1

Strain history: CGMCC 4.5581 <-- J. Xiao 42H12-1.

NCBI tax ID(s): 477641 (species)

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General

@ref: 15799

BacDive-ID: 5832

DSM-Number: 45201

keywords: genome sequence, 16S sequence, Bacteria, Gram-positive

description: Modestobacter marinus 42H12-1 is a Gram-positive bacterium that was isolated from deep-sea sediment.

NCBI tax id

  • NCBI tax id: 477641
  • Matching level: species

strain history

@refhistory
15799<- J. Xu and Y.-X. Luo, Key Lab. Marine Biogenetic Resources, Third Institute of Oceanography, Xiamen, China; 42H12-1
67770CGMCC 4.5581 <-- J. Xiao 42H12-1.

doi: 10.13145/bacdive5832.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Geodermatophilales
  • family: Geodermatophilaceae
  • genus: Modestobacter
  • species: Modestobacter marinus
  • full scientific name: Modestobacter marinus Xiao et al. 2011

@ref: 15799

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Geodermatophilaceae

genus: Modestobacter

species: Modestobacter marinus

full scientific name: Modestobacter marinus Xiao et al. 2011

strain designation: 42H12-1

type strain: yes

Morphology

colony morphology

@refcolony colormedium used
69378Green brown (8000)suter without tyrosine
69378Black brown (8022)ISP 2
69378Black brown (8022)ISP 6
69378Jet black (9005)ISP 3
69378Khaki grey (7008)ISP 5
69378Khaki grey (7008)ISP 7
69378Olive brown (8008)ISP 4
69378Olive brown (8008)suter with tyrosine

multicellular morphology

@refforms multicellular complexcomplex namemedium name
69378noAerial myceliumISP 2
69378noAerial myceliumISP 3
69378noAerial myceliumISP 4
69378noAerial myceliumISP 5
69378noAerial myceliumISP 6
69378noAerial myceliumISP 7
69378noAerial myceliumsuter with tyrosine
69378noAerial myceliumsuter without tyrosine

pigmentation

@refproductionname
69378noMelanin
69378nosoluble pigment

multimedia

  • @ref: 15799
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45201.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15799GYM 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
15799R2A MEDIUM (DSMZ Medium 830)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium830.pdf

culture temp

@refgrowthtypetemperature
15799positivegrowth28
67770positivegrowth28

Physiology and metabolism

oxygen tolerance

  • @ref: 69480
  • oxygen tolerance: aerobe
  • confidence: 90.04

halophily

  • @ref: 69378
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6937822599arabinose+growth
6937862968cellulose-growth
6937828757fructose+/-growth
6937817234glucose+growth
6937817268inositol-growth
6937837684mannose+/-growth
6937816634raffinose-growth
6937826546rhamnose+/-growth
6937817992sucrose+growth
6937818222xylose+growth
6837917632nitrate-reduction
683794853esculin+hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase-3.2.1.22
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69378---+--+-+----------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69378++++/-+++/---++/--+/--++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic location
15799deep-sea sediment14.7518° N 44.9782° W at a depth of 2983 m
67770Deep-sea sediment from the Atlantic Ocean

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_1976.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_1096;97_1284;98_1546;99_1976&stattab=map
  • Last taxonomy: Modestobacter
  • 16S sequence: EU181225
  • Sequence Identity:
  • Total samples: 31692
  • soil counts: 18491
  • aquatic counts: 2890
  • animal counts: 5702
  • plant counts: 4609

Safety information

risk assessment

  • @ref: 15799
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15799
  • description: Modestobacter marinus strain 42H12-1 16S ribosomal RNA gene, partial sequence
  • accession: EU181225
  • length: 1483
  • database: nuccore
  • NCBI tax ID: 477641

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Modestobacter marinus CGMCC 4.5581GCA_014645755scaffoldncbi477641
66792Modestobacter marinus strain CGMCC 4.5581477641.13wgspatric477641
66792Modestobacter marinus strain DSM 45201477641.12wgspatric477641
66792Modestobacter marinus DSM 452012820994125draftimg477641
67770Modestobacter marinus DSM 45201GCA_011758655contigncbi477641
66792Modestobacter marinus DSM 45201GCA_023383595contigncbi477641

GC content

@refGC-contentmethod
1579972.3
6777071.3-73.3high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingyes88.49no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.067no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes90.04no
69480spore-formingspore-formingAbility to form endo- or exosporesyes60.783no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno97no
69480flagellatedmotile2+Ability to perform flagellated movementno61.833no

External links

@ref: 15799

culture collection no.: DSM 45201, CGMCC 4.5581, JCM 18320

straininfo link

  • @ref: 75314
  • straininfo: 398505

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20802061Modestobacter marinus sp. nov., a psychrotolerant actinobacterium from deep-sea sediment, and emended description of the genus Modestobacter.Xiao J, Luo Y, Xu J, Xie S, Xu JInt J Syst Evol Microbiol10.1099/ijs.0.023085-02010Actinomycetales/*classification/genetics/isolation & purification, Atlantic Ocean, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny23148095Modestobacter roseus sp. nov., an endophytic actinomycete isolated from the coastal halophyte Salicornia europaea Linn., and emended description of the genus Modestobacter.Qin S, Bian GK, Zhang YJ, Xing K, Cao CL, Liu CH, Dai CC, Li WJ, Jiang JHInt J Syst Evol Microbiol10.1099/ijs.0.044412-02012Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Chenopodiaceae/*microbiology, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Salt-Tolerant Plants/microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny27108251Modestobacter caceresii sp. nov., novel actinobacteria with an insight into their adaptive mechanisms for survival in extreme hyper-arid Atacama Desert soils.Busarakam K, Bull AT, Trujillo ME, Riesco R, Sangal V, van Wezel GP, Goodfellow MSyst Appl Microbiol10.1016/j.syapm.2016.03.0072016Actinobacteria/*classification/genetics/isolation & purification/*metabolism, Adaptation, Physiological/genetics, *Bacterial Typing Techniques, Base Sequence, DNA, Bacterial/genetics, *Desert Climate, Fatty Acids/analysis, Genome, Bacterial/genetics, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny27537546Modestobacter lacusdianchii sp. nov., a Phosphate-Solubilizing Actinobacterium with Ability to Promote Microcystis Growth.Zhang BH, Salam N, Cheng J, Li HQ, Yang JY, Zha DM, Zhang YQ, Ai MJ, Hozzein WN, Li WJPLoS One10.1371/journal.pone.01610692016Actinobacteria/genetics/*metabolism, Culture Media, DNA, Bacterial/genetics, Microcystis/genetics/*growth & development, Phosphates/metabolism, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
15799Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45201)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45201
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69378Wink, J.https://cdn.dsmz.de/wink/DSM%2045201.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
75314Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID398505.1StrainInfo: A central database for resolving microbial strain identifiers