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BacDive ID 140509
Type strain
Culture col. no. LMG 3411 CCUG 62454
NCBI tax ID(s) 1353888
Links
For citation purpose refer to the digital object identifier (doi) of the current version.

Archive

version 9.3 (current version):
version 9.3 (current version)

General

@ref: 43168

BacDive-ID: 140509

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Achromobacter agilis LMG 3411 is an aerobe, mesophilic, Gram-negative bacterium of the family Alcaligenaceae.

NCBI tax id

  • NCBI tax id: 1353888
  • Matching level: species

doi: 10.13145/bacdive140509.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Alcaligenaceae
  • genus: Achromobacter
  • species: Achromobacter agilis
  • full scientific name: Achromobacter agilis Vandamme et al. 2016

@ref: 43168

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Alcaligenaceae

genus: Achromobacter

species: Achromobacter agilis

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43168negative0.9-1.5 µm0.4-0.7 µmrod-shapedyes
125439negative97
125438negative96.932

colony morphology

  • @ref: 43168
  • colony size: 1-1.5 mm
  • colony color: non-pigmented
  • incubation period: 2 days
  • medium used: tryptic soy agar (TSA)

Culture and growth conditions

culture medium

@refnamegrowth
43168tryptic soy agar (TSA)yes
43168cetrimide agaryes
43168Drigalsky agaryes
43168blood agaryes

culture temp

@refgrowthtypetemperature
43168positivegrowth37
43168positivegrowth30

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
43168aerobe
125438aerobe91.138
125439obligate aerobe94.8

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 97.9

halophily

@refsaltgrowthtested relationconcentration
43168NaClpositivegrowth3 %
43168NaClnogrowth4.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4316816301nitrite+reduction
4316817632nitrate+reduction
4316827856acetamide+growth
4316830849L-arabinose-assimilation
4316816024D-mannose-assimilation
43168506227N-acetylglucosamine-assimilation
4316817306maltose-assimilation
431688391D-gluconate-assimilation
4316827689decanoate-assimilation
4316817128adipate+/-assimilation
4316815589L-malate-assimilation
4316816947citrate-assimilation
4316818401phenylacetate-assimilation
4316816004(R)-lactate-assimilation
4316817634D-glucose-assimilation
431684853esculin-hydrolysis
4316853426tween 80-hydrolysis
431685291gelatin-hydrolysis
4316817234glucose-assimilation
4316827082trehalose-assimilation
4316816467L-arginine-assimilation
4316836405norleucine-assimilation
4316816899D-mannitol-assimilation
4316817992sucrose-assimilation

metabolite production

@refChebi-IDmetaboliteproduction
4316835581indoleno
4316816136hydrogen sulfideno

enzymes

@refvalueactivityec
43168alkaline phosphatase-3.1.3.1
43168acid phosphatase-3.1.3.2
43168phosphoamidase-3.9.1.1
43168beta-glucosidase-3.2.1.21
43168esterase (C 4)+
43168cytochrome oxidase+1.9.3.1
43168catalase+1.11.1.6
43168leucine arylamidase+3.4.11.1
43168amylase-
43168lysine decarboxylase-4.1.1.18
43168ornithine decarboxylase-4.1.1.17
43168arginine dihydrolase-3.5.3.6
43168urease-3.5.1.5
43168DNase-
43168tryptophanase-4.1.99.1
43168esterase Lipase (C 8)-
43168lipase (C 14)-
43168valine arylamidase-
43168cystine arylamidase-3.4.11.3
43168trypsin-3.4.21.4
43168chymotrypsin-3.4.4.5
43168alpha-galactosidase-3.2.1.22
43168beta-galactosidase-3.2.1.23
43168beta-glucuronidase-3.2.1.31
43168alpha-glucosidase-3.2.1.20
43168N-acetyl-beta-glucosaminidase-3.2.1.52
43168alpha-mannosidase-3.2.1.24
43168alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43168C12:01.37
    43168C12:0 2OH2.42
    43168C14:04.35
    43168C16:031.66
    43168C17:0 cyclo1.63
    43168C18:01.95
    43168C18:1ω7c9.6
    43168C16:1 iso I / C14:0 3OH7.85
    43168C15:0 iso 2OH / C16:1ω7c37.61
  • type of FA analysis: whole cell analysis
  • incubation medium: trypticase soy agar (TSA; BBL)
  • incubation temperature: 28
  • incubation time: 1
  • system: MIS MIDI
  • cutoff value:

Sequence information

16S sequences

  • @ref: 43168
  • description: Achromobacter agilis partial 16S rRNA gene, strain LMG 3411
  • accession: HG324050
  • length: 1483
  • database: nuccore
  • NCBI tax ID: 1353888

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Achromobacter agilis LMG 3411GCA_900496965contigncbi1353888
66792Achromobacter agilis strain LMG 34111353888.3wgspatric1353888
66792Achromobacter agilis LMG 34112882181859draftimg1353888

GC content

  • @ref: 43168
  • GC-content: 66.4
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno96.932yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.853no
125438spore-formingspore-formingAbility to form endo- or exosporesno87.872no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes91.138yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97.485yes
125438motile2+flagellatedAbility to perform flagellated movementyes84.159no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno97.9
125439BacteriaNetmotilityAbility to perform movementyes83.1
125439BacteriaNetgram_stainReaction to gram-stainingnegative97
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe94.8

External links

@ref: 43168

culture collection no.: LMG 3411, CCUG 62454

straininfo link

  • @ref: 96736
  • straininfo: 817

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27373279Taxonomic dissection of Achromobacter denitrificans Coenye et al. 2003 and proposal of Achromobacter agilis sp. nov., nom. rev., Achromobacter pestifer sp. nov., nom. rev., Achromobacter kerstersii sp. nov. and Achromobacter deleyi sp. nov.Vandamme PA, Peeters C, Inganas E, Cnockaert M, Houf K, Spilker T, Moore ERB, LiPuma JJInt J Syst Evol Microbiol10.1099/ijsem.0.0012542016Achromobacter/*classification, Achromobacter denitrificans/*classification, Bacterial Typing Techniques, DNA, Bacterial/genetics, Genes, Bacterial, Multilocus Sequence Typing, *Phylogeny, Sequence Analysis, DNATranscriptome
Phylogeny31613739Achromobacter veterisilvae sp. nov., from a mixed hydrogen-oxidizing bacteria enrichment reactor for microbial protein production.Dumolin C, Peeters C, Ehsani E, Tahon G, De Canck E, Cnockaert M, Boon N, Vandamme PInt J Syst Evol Microbiol10.1099/ijsem.0.0037862020Achromobacter/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Belgium, Bioreactors/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Forests, Hydrogen, Multilocus Sequence Typing, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome

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
43168Peter A. Vandamme, Charlotte Peeters, Elisabeth Inganäs, Margo Cnockaert, Kurt Houf, Theodore Spilker, Edward R. B. Moore, John J. LiPumaTaxonomic dissection of Achromobacter denitrificans Coenye et al. 2003 and proposal of Achromobacter agilis sp. nov., nom. rev., Achromobacter pestifer sp. nov., nom. rev., Achromobacter kerstersii sp. nov. and Achromobacter deleyi sp. nov.10.1099/ijsem.0.001254IJSEM 66: 3708-3717 201627373279
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
96736Reimer, 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-ID817.1
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG

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