Strain identifier

BacDive ID: 140570

Type strain: Yes

Species: Anaeromicrobium sediminis

Strain Designation: DY2726D

Strain history: X. Zhang; Key Lab. of Mar. Biogenet. Resour., State Oceanic Admin., China; DY2726D.

NCBI tax ID(s): 1478221 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 8.1 (current version)

General

@ref: 43340

BacDive-ID: 140570

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, heterotroph, mesophilic, Gram-variable, motile, rod-shaped

description: Anaeromicrobium sediminis DY2726D is an anaerobe, heterotroph, mesophilic bacterium that was isolated from deep-sea sediment sample of the West Pacific Ocean at a depth of 5445 m.

NCBI tax id

  • NCBI tax id: 1478221
  • Matching level: species

strain history

  • @ref: 67770
  • history: X. Zhang; Key Lab. of Mar. Biogenet. Resour., State Oceanic Admin., China; DY2726D.

doi: 10.13145/bacdive140570.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Clostridiaceae
  • genus: Anaeromicrobium
  • species: Anaeromicrobium sediminis
  • full scientific name: Anaeromicrobium sediminis Zhang et al. 2017

@ref: 43340

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Eubacteriales

family: Clostridiaceae

genus: Anaeromicrobium

species: Anaeromicrobium sediminis

strain designation: DY2726D

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43340variable4-15 µm0.5-0.8 µmrod-shapedyes
69480yes96.959
69480positive100

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
43340positiveoptimum37mesophilic
43340positivegrowth25-40
67770positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
43340positivegrowth6.5-9.0alkaliphile
43340positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
43340anaerobe
69480anaerobe98.105

nutrition type

  • @ref: 43340
  • type: heterotroph

spore formation

@reftype of sporespore formationconfidence
43340endosporeno
69480yes99.999

halophily

@refsaltgrowthtested relationconcentration
43340Marine saltspositivegrowth10-30 g/L
43340Marine saltspositiveoptimum20 g/L

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
43340peptone+assimilation
43340tryptone+assimilation
43340yeast extract+assimilation
43340cellobiose+carbon source17057
43340dextrin+carbon source23652
43340D-fructose+carbon source15824
43340L-fucose+carbon source18287
43340D-galactose+carbon source12936
43340D-galacturonic acid+carbon source18024
43340D-glucosaminic acid+carbon source17784
43340gentiobiose+carbon source28066
43340D-glucose+carbon source17634
43340D-glucose 6-phosphate+carbon source14314
43340D-mannose+carbon source16024
43340melibiose+carbon source28053
433403-O-methyl-D-glucose+carbon source73918
43340palatinose+carbon source18394
43340L-rhamnose+carbon source62345
433402-oxobutanoate+carbon source16763
433402-oxopentanoate+carbon source28644
43340elemental sulfur-reduction33403
43340sulfite-reduction17359
43340sulfate-reduction16189
43340thiosulfate-reduction16094
43340nitrate-reduction17632
43340amorphous fe(iii) oxyhydroxid+reduction
43340amorphous iron (iii) oxide+reduction
43340goethite+reduction
43340lactate-carbon source24996
43340malate-carbon source25115
43340maltose-carbon source17306
43340sucrose-carbon source17992
43340tartrate-carbon source30929
43340trehalose-carbon source27082
43340acetate-carbon source30089
43340formate-carbon source15740
43340fumarate-carbon source29806
43340glyoxylate-carbon source36655
43340succinate-carbon source30031
43340L-alaninamide-carbon source21217

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43340C16:142
    43340C14:031.9
    43340C16:012.8
  • type of FA analysis: whole cell analysis
  • incubation medium: YTG
  • agar/liquid: liquid
  • incubation temperature: 37
  • incubation time: 1
  • system: MIS MIDI

Isolation, sampling and environmental information

isolation

@refsample typesampling dategeographic locationlatitudelongitude
43340deep-sea sediment sample of the West Pacific Ocean at a depth of 5445 m2012-07Pacific Ocean16154
67770West Pacific Ocean sediments

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_42785.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15791;96_19793;97_24562;98_31080;99_42785&stattab=map
  • Last taxonomy: Anaeromicrobium sediminis subclade
  • 16S sequence: KJ137882
  • Sequence Identity:
  • Total samples: 4466
  • soil counts: 197
  • aquatic counts: 3707
  • animal counts: 524
  • plant counts: 38

Sequence information

16S sequences

  • @ref: 43340
  • description: 16S rRNA gene sequences
  • accession: KJ137882
  • length: 1414
  • database: ena
  • NCBI tax ID: 1478221

Genome sequences

  • @ref: 67770
  • description: Anaeromicrobium sediminis DY2726D
  • accession: GCA_002270055
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 1478221

GC content

  • @ref: 43340
  • GC-content: 33.4
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno72no
flagellatedyes65.755no
gram-positiveno58.208yes
anaerobicyes96.291no
aerobicno97.472yes
halophileno86.378no
spore-formingyes94.684no
glucose-utilyes88.22yes
thermophileno80.063no
motileyes87.979yes
glucose-fermentno62.796no

External links

@ref: 43340

culture collection no.: JCM 30224, MCCC 1A00776

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27974087Anaeromicrobium sediminis gen. nov., sp. nov., a fermentative bacterium isolated from deep-sea sediment.Zhang X, Zeng X, Li X, Alain K, Jebbar M, Shao ZInt J Syst Evol Microbiol10.1099/ijsem.0.0017392017Bacterial Typing Techniques, Base Composition, Clostridiales/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Pacific Ocean, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNATranscriptome
Genetics29439028Draft Genome Sequence of Anaerobic Fermentative Bacterium Anaeromicrobium sediminis DY2726D.Zhang J, Hu J, Zhang X, Zeng XGenome Announc10.1128/genomeA.00002-182018

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
43340Xiaobo Zhang, Xiang Zeng, Xi Li, Karine Alain, Mohamed Jebbar, Zongze ShaoAnaeromicrobium sediminis gen. nov., sp. nov., a fermentative bacterium isolated from deep-sea sediment10.1099/ijsem.0.001739IJSEM 67: 1462-1467 201727974087
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
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