Strain identifier

BacDive ID: 132584

Type strain: Yes

Species: Anaerocolumna cellulosilytica

Strain history: A. Ueki; Fac. of Agric., Yamagata Univ., Japan; SN021.

NCBI tax ID(s): 433286 (species)

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General

@ref: 24373

BacDive-ID: 132584

DSM-Number: 100423

keywords: genome sequence, 16S sequence, Bacteria, obligate anaerobe, chemoorganotroph, spore-forming, mesophilic, Gram-positive, motile, rod-shaped

description: Anaerocolumna cellulosilytica DSM 100423 is an obligate anaerobe, chemoorganotroph, spore-forming bacterium that was isolated from decomposed rice straw in a methanogenic reactor treating waste from cattle farms.

NCBI tax id

  • NCBI tax id: 433286
  • Matching level: species

strain history

@refhistory
24373<- A. Ueki, Yamagata Univ., Tsuruoka, Japan; SN021 <- A. Ueki {2004}
67770A. Ueki; Fac. of Agric., Yamagata Univ., Japan; SN021.

doi: 10.13145/bacdive132584.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Lachnospiraceae
  • genus: Anaerocolumna
  • species: Anaerocolumna cellulosilytica
  • full scientific name: Anaerocolumna cellulosilytica Ueki et al. 2016

@ref: 24373

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Lachnospiraceae

genus: Anaerocolumna

species: Anaerocolumna cellulosilytica

full scientific name: Anaerocolumna cellulosilytica Ueki et al. 2016

type strain: yes

Morphology

cell morphology

  • @ref: 43082
  • gram stain: positive
  • cell length: 9.5-12.0 µm
  • cell width: 0.8 µm
  • cell shape: rod-shaped
  • motility: yes
  • flagellum arrangement: peritrichous

colony morphology

  • @ref: 43082
  • colony color: translucent
  • medium used: PY4S agar

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
43082PY4S agaryespeptone/yeast extract (PY) basal medium supplemented with glucose, cellobiose, maltose and soluble starch
43082chopped meat brothno
43082PYGyes
24373WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339)yesName: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339) Composition: dehydrated Wilkins-Chalgren medium 33.0 g/l L-Cysteine HCl 0.3 g/l Sodium resazurin 0.0005 g/l Distilled waterhttps://mediadive.dsmz.de/medium/339

culture temp

@refgrowthtypetemperaturerange
43082positiveoptimum35mesophilic
43082positivegrowth15-40
24373positivegrowth35mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
43082positivegrowth6.2-8.5alkaliphile
43082positiveoptimum7.6

Physiology and metabolism

oxygen tolerance

  • @ref: 43082
  • oxygen tolerance: obligate anaerobe

nutrition type

  • @ref: 43082
  • type: chemoorganotroph

spore formation

  • @ref: 43082
  • spore description: terminal, spherical spores from swollen cells
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
43082NaClpositivegrowth0-30 g/L
43082NaClpositiveoptimum0 g/L

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4308222599arabinose+assimilation
4308218222xylose+assimilation
4308228757fructose+assimilation
4308228260galactose+assimilation
4308217234glucose+assimilation
4308237684mannose+assimilation
4308217057cellobiose+assimilation
4308217716lactose+assimilation
4308217306maltose+assimilation
4308228053melibiose+assimilation
4308262968cellulose+assimilation
4308223652dextrin+assimilation
4308228087glycogen+assimilation
4308217309pectin+assimilation
4308228017starch+assimilation
4308237166xylan+assimilation
4308227613amygdalin+assimilation
430824853esculin+assimilation
4308217814salicin+assimilation
4308285146carboxymethylcellulose+assimilation
43082288162-deoxy-d-ribose-assimilation
4308226546rhamnose-assimilation
4308227922sorbose-assimilation
4308217992sucrose-assimilation
4308227082trehalose-assimilation
430826731melezitose-assimilation
4308216634raffinose-assimilation
4308215443inulin-assimilation
4308216813galactitol-assimilation
4308217754glycerol-assimilation
4308217268myo-inositol-assimilation
4308229864mannitol-assimilation
4308230911sorbitol-assimilation
4308229806fumarate-assimilation
4308224996lactate-assimilation
4308225115malate-assimilation
4308215361pyruvate-assimilation
4308230031succinate-assimilation
4308217632nitrate-reduction
430824853esculin+hydrolysis
4308228017starch+hydrolysis
430825291gelatin-hydrolysis
43082milk+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
4308216236ethanolyes
4308218276dihydrogenyes
4308216526carbon dioxideyes
4308224996lactateno
4308230031succinateno
4308216136hydrogen sulfideyes
4308235581indoleno
4308230089acetateyes

enzymes

@refvalueactivityec
43082cytochrome oxidase-1.9.3.1
43082lecithinase-
43082lipase-
43082catalase-1.11.1.6

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    43082C14:00.6
    43082C14:0 DMA1.8
    43082Unknown 14.762 / C15:25.6
    43082C16:0 ALDE20.6
    43082C16:05.5
    43082C16:1ω7c DMA3.8
    43082C16:0 DMA17.4
    43082C17:1ω8c / C17:212.3
    43082C16:0 3OH1.2
    43082C18:1ω9c DMA3.1
    43082C18:1ω7c DMA9
    43082C19:0 cyclo 11,12 DMA1.4
    43082C17:2 / C17:1ω9c4.216758
  • type of FA analysis: whole cell analysis
  • incubation medium: PYG
  • agar/liquid: liquid
  • incubation time: 3
  • system: MIS MIDI
  • method/protocol: Miller 1982
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture compositionenrichment culture temperatureisolation procedure
24373decomposed rice straw in a methanogenic reactor treating waste from cattle farmsHokkaido, Betsukai-machiJapanJPNAsia
43082methanogenic reactor treating waste from cattle farms (samples of small pieces of decomposed rice straw)Betsukai-machi, HokkaidoJapanJPNAsiapeptone/yeast extract (PY) basal medium10 g/l trypticase, 5 g/l yeast extract, 0.2 g Na2CO3, 0.3 g/l L-cysteine hydrochloride dihydrate, 1 mg/l sodium resazurin, salt solutions30anaerobic roll-tube method
67770Methanogenic reactorJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Bioreactor
#Engineered#Waste#Solid waste
#Host#Plants#Decomposing plant
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_54165.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_33;96_24172;97_30251;98_38709;99_54165&stattab=map
  • Last taxonomy: Anaerocolumna cellulosilytica subclade
  • 16S sequence: AB298755
  • Sequence Identity:
  • Total samples: 1152
  • soil counts: 436
  • aquatic counts: 89
  • animal counts: 199
  • plant counts: 428

Safety information

risk assessment

  • @ref: 24373
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24373
  • description: Anaerocolumna cellulosilytica gene for 16S rRNA, partial sequence
  • accession: AB298755
  • length: 1478
  • database: ena
  • NCBI tax ID: 433286

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Anaerocolumna cellulosilytica DSM 100423GCA_014202875scaffoldncbi433286
66792Anaerocolumna cellulosilytica strain DSM 100423433286.3wgspatric433286
66792Anaerocolumna cellulosilytica DSM 1004232861627031draftimg433286

GC content

  • @ref: 24373
  • GC-content: 38.1
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes61.741yes
gram-positiveyes87.217yes
anaerobicyes98.088no
aerobicno97.398yes
halophileno95.791yes
spore-formingyes93.899yes
glucose-utilyes89.115yes
thermophileno98.467yes
motileyes82.899yes
glucose-fermentyes64.848no

External links

@ref: 24373

culture collection no.: DSM 100423, JCM 30819, SN 021

straininfo link

  • @ref: 90901
  • straininfo: 402717

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27126251Descriptions of Anaerotaenia torta gen. nov., sp. nov. and Anaerocolumna cellulosilytica gen. nov., sp. nov. isolated from a methanogenic reactor of cattle waste and reclassification of Clostridium aminovalericum, Clostridium jejuense and Clostridium xylanovorans as Anaerocolumna species.Ueki A, Ohtaki Y, Kaku N, Ueki KInt J Syst Evol Microbiol10.1099/ijsem.0.0011232016Animals, Bacteria, Anaerobic/classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Bioreactors/*microbiology, Cattle, Cellulose/metabolism, Clostridiales/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fermentation, Manure/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAEnzymology
Phylogeny33730291Anaerocolumna sedimenticola sp. nov., isolated from fresh water sediment.Kim J, Kim JY, Song HS, Kim YB, Whon TW, Ahn SW, Lee SH, Yoo S, Kim YJ, Myoung J, Choi YE, Son HS, Roh SWAntonie Van Leeuwenhoek10.1007/s10482-021-01536-42021Bacterial Typing Techniques, Base Composition, Clostridiales, DNA, Bacterial/genetics, Fatty Acids/analysis, *Fresh Water, *Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

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
24373Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100423Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100423)
43082Atsuko Ueki, Yoshimi Ohtaki, Nobuo Kaku, Katsuji UekiDescriptions of Anaerotaenia torta gen. nov., sp. nov. and Anaerocolumna cellulosilytica gen. nov., sp. nov. isolated from a methanogenic reactor of cattle waste and reclassification of Clostridium aminovalericum, Clostridium jejuense and Clostridium xylanovorans as Anaerocolumna species10.1099/ijsem.0.001123IJSEM 66: 2936-2943 201627126251
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/
90901Reimer, 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-ID402717.1