Strain identifier

BacDive ID: 158376

Type strain: Yes

Species: Aminipila butyrica

Strain Designation: FH042

Strain history: A. Ueki; Fac. of Agric., Yamagata Univ., Japan; FH042.

NCBI tax ID(s): 433296 (species)

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General

@ref: 65052

BacDive-ID: 158376

DSM-Number: 103574

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

description: Aminipila butyrica FH042 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from Methanogenic reactor of cattlefarms.

NCBI tax id

  • NCBI tax id: 433296
  • Matching level: species

strain history

@refhistory
65052<- A. Ueki, Yamagata Univ., Tsuruoka, Japan; FH042 <- A. Ueki {2004}
67770A. Ueki; Fac. of Agric., Yamagata Univ., Japan; FH042.

doi: 10.13145/bacdive158376.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Anaerovoracaceae
  • genus: Aminipila
  • species: Aminipila butyrica
  • full scientific name: Aminipila butyrica Ueki et al. 2018

@ref: 65052

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Eubacteriales

family: Eubacteriales, not assigned to family

genus: Aminipila

species: Aminipila butyrica

full scientific name: Aminipila butyrica Ueki et al. 2018

strain designation: FH042

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
65320positive3-8 µm0.7-1 µmrod-shapedyespolar
69480positive100

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
65052PY + X MEDIUM (N2/CO2) (DSMZ Medium 104c)yeshttps://mediadive.dsmz.de/medium/104cName: PY + X MEDIUM (N2/CO2) (DSMZ Medium 104c; with strain-specific modifications) Composition: Yeast extract 10.0 g/l Trypticase peptone 5.0 g/l Meat peptone 5.0 g/l Casamino acids 3.0 g/l Na2CO3 1.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Sodium resazurin 0.0005 g/l Distilled water
65320PY4Syes
65320chopped meat brothno

culture temp

@refgrowthtypetemperaturerange
65052positivegrowth30mesophilic
65320positivegrowth10-35
65320positiveoptimum30mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepH
65320positivegrowth5.3-8.2
65320positiveoptimum6.1-6.8

Physiology and metabolism

oxygen tolerance

  • @ref: 69480
  • oxygen tolerance: anaerobe
  • confidence: 99.999

spore formation

  • @ref: 65320
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
65320NaClpositivegrowth0-20 g/L
65320NaClpositiveoptimum0 g/L

observation

@refobservation
65320Longer rods up to 40 µm often occur.
65320B-vitamins are not required for growth.

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6532027613amygdalin-assimilation
6532022599arabinose-assimilation
6532085146carboxymethylcellulose-assimilation
65320casamino acids+assimilation
6532017057cellobiose-assimilation
6532062968cellulose-assimilation
6532023652dextrin-assimilation
6532016813galactitol-assimilation
653204853esculin-assimilation
653204853esculin-hydrolysis
6532028757fructose-assimilation
6532029806fumarate-assimilation
6532028260galactose-assimilation
6532016865gamma-aminobutyric acid-assimilation
653205291gelatin-hydrolysis
6532017234glucose-assimilation
6532017754glycerol-assimilation
6532015428glycine-assimilation
6532028087glycogen-assimilation
6532017268myo-inositol-assimilation
6532015443inulin-assimilation
6532016977L-alanine-assimilation
6532016467L-arginine+assimilation
6532017196L-asparagine-assimilation
6532029985L-glutamate-assimilation
6532015971L-histidine-assimilation
6532017191L-isoleucine-assimilation
6532015603L-leucine-assimilation
6532018019L-lysine+assimilation
6532016643L-methionine-assimilation
6532017295L-phenylalanine-assimilation
6532017203L-proline-assimilation
6532017115L-serine+assimilation
6532016857L-threonine-assimilation
6532016828L-tryptophan-assimilation
6532017895L-tyrosine-assimilation
6532016414L-valine-assimilation
6532024996lactate-assimilation
6532017716lactose-assimilation
6532025115malate-assimilation
6532017306maltose-assimilation
6532029864mannitol-assimilation
6532037684mannose-assimilation
653206731melezitose-assimilation
6532028053melibiose-assimilation
65320milk-assimilation
6532017632nitrate-reduction
6532017309pectin-assimilation
6532015361pyruvate-assimilation
6532016634raffinose-assimilation
6532026546rhamnose-assimilation
6532033942ribose-assimilation
6532017814salicin-assimilation
6532030911sorbitol-assimilation
6532027922sorbose-assimilation
6532028017starch-assimilation
6532028017starch-hydrolysis
6532030031succinate-assimilation
6532017992sucrose-assimilation
6532027082trehalose-assimilation
6532037166xylan-assimilation
6532018222xylose-assimilation

metabolite production

@refChebi-IDmetaboliteproduction
6532016136hydrogen sulfideyes
6532035581indoleno

enzymes

@refvalueactivityec
65320catalase-1.11.1.6
65320cytochrome oxidase-1.9.3.1
65320lecithinase-
65320lipase-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation procedure
65052Methanogenic reactor of cattlefarmsHokkaidoJapanJPNAsia
65320methanogenic reactor treating waste from cattle farmsBetsukai-machi, HokkaidoJapanJPNAsiaanaerobic roll-tube method
67770Methanogenic reactor treating waste from cattle farmsBetsukai-machi, HokkaidoJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Waste#Solid animal waste
#Engineered#Waste#Solid waste
#Engineered#Bioreactor

taxonmaps

  • @ref: 69479
  • File name: preview.99_114297.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_184;96_45475;97_58320;98_77378;99_114297&stattab=map
  • Last taxonomy: Aminipila butyrica subclade
  • 16S sequence: AB298771
  • Sequence Identity:
  • Total samples: 142
  • soil counts: 15
  • aquatic counts: 14
  • animal counts: 90
  • plant counts: 23

Safety information

risk assessment

  • @ref: 65052
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 65052
  • description: Aminipila butyrica gene for 16S rRNA, partial sequence
  • accession: AB298771
  • length: 1460
  • database: ena
  • NCBI tax ID: 433296

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Aminipila butyrica DSM 103574GCA_010669305completencbi433296
66792Aminipila butyrica strain DSM 103574433296.3completepatric433296
66792Aminipila butyrica DSM 1035742883526296completeimg433296

GC content

@refGC-contentmethod
6505244.7
6532044.5-44.9high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno67no
motileyes89.24yes
flagellatedyes54.131yes
gram-positiveno66.749no
anaerobicyes99.44no
aerobicno97.819no
halophileno96.173yes
spore-formingyes80.29yes
thermophileno99.052yes
glucose-utilyes56.457yes
glucose-fermentyes54.463no

External links

@ref: 65052

culture collection no.: DSM 103574, JCM 31555

straininfo link

  • @ref: 111181
  • straininfo: 396548

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny29235979Aminipila butyrica gen. nov., sp. nov., a strictly anaerobic, arginine-decomposing bacterium isolated from a methanogenic reactor of cattle waste.Ueki A, Goto K, Kaku N, Ueki KInt J Syst Evol Microbiol10.1099/ijsem.0.0025342017Animals, Arginine/*metabolism, Bacteria, Anaerobic/classification, Bacterial Typing Techniques, Base Composition, Bioreactors/*microbiology, Cattle, Clostridiales/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Japan, Manure/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome
Phylogeny33821299Aminipila terrae sp. nov., a strictly anaerobic bacterium isolated from river sediment.Kim YB, Kim JY, Kim J, Song HS, Whon TW, Lee SH, Yoo S, Myoung J, Son HS, Roh SWArch Microbiol10.1007/s00203-021-02301-x2021Anaerobiosis, Base Composition, *Clostridiales/classification/genetics/isolation & purification, Fatty Acids/analysis, *Geologic Sediments/microbiology, *Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, *Rivers/microbiologyEnzymology
Phylogeny34662267Aminipila luticellarii sp. nov., an anaerobic bacterium isolated from the pit mud of strong aromatic Chinese liquor, and emended description of the genus Aminipila.Wei Z, Ma S, Chen R, Wu W, Fan H, Dai L, Deng YInt J Syst Evol Microbiol10.1099/ijsem.0.0047102021*Alcoholic Beverages, Anaerobiosis, Bacterial Typing Techniques, Base Composition, China, Clostridiales/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome

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
65052Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103574Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103574)
65320Atsuko Ueki, Kazushi Goto, Nobuo Kaku, Katsuji UekiAminipila butyrica gen. nov., sp. nov., a strictly anaerobic, arginine-decomposing bacterium isolated from a methanogenic reactor of cattle waste10.1099/ijsem.0.002534IJSEM 68: 443-448 201829235979
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
111181Reimer, 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-ID396548.1