Strain identifier

BacDive ID: 6411

Type strain: Yes

Species: Amylolactobacillus amylophilus

Strain Designation: B-4437

Strain history: CIP <- 1987, DSM <- L.K. Nakamura, NRRL, USA: strain B-4437

NCBI tax ID(s): 1603 (species)

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General

@ref: 8763

BacDive-ID: 6411

DSM-Number: 20533

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, Gram-positive, lactate production

description: Amylolactobacillus amylophilus B-4437 is a facultative anaerobe, Gram-positive bacterium that produces lactate and was isolated from swine waste-corn fermentation.

NCBI tax id

  • NCBI tax id: 1603
  • Matching level: species

strain history

@refhistory
8763<- NRRL <- L.K. Nakamura
67770NRRL B-4437 <-- L. K. Nakamura.
116360CIP <- 1987, DSM <- L.K. Nakamura, NRRL, USA: strain B-4437

doi: 10.13145/bacdive6411.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Amylolactobacillus
  • species: Amylolactobacillus amylophilus
  • full scientific name: Amylolactobacillus amylophilus (Nakamura and Crowell 1981) Zheng et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus amylophilus

@ref: 8763

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Amylolactobacillus

species: Amylolactobacillus amylophilus

full scientific name: Amylolactobacillus amylophilus (Nakamura and Crowell 1981) Zheng et al. 2020

strain designation: B-4437

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
116360positiverod-shapedno
69480positive95.19
69480no90.833

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8763MRS MEDIUM (DSMZ Medium 11)yeshttps://mediadive.dsmz.de/medium/11Name: MRS MEDIUM (DSMZ Medium 11) Composition: Glucose 20.0 g/l Casein peptone 10.0 g/l Meat extract 10.0 g/l Na-acetate 5.0 g/l Yeast extract 5.0 g/l (NH4)3 citrate 2.0 g/l K2HPO4 2.0 g/l Tween 80 1.0 g/l MgSO4 x 7 H2O 0.2 g/l MnSO4 x H2O 0.05 g/l Distilled water
40497MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
116360CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperature
8763positivegrowth28
40497positivegrowth30
49931positivegrowth28
67770positivegrowth30
116360positivegrowth15-37
116360nogrowth45

Physiology and metabolism

oxygen tolerance

  • @ref: 116360
  • oxygen tolerance: facultative anaerobe

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 100

compound production

  • @ref: 8763
  • compound: L(+) lactic acid

murein

  • @ref: 8763
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
116360nitrate-reduction17632
116360nitrite-reduction16301
116360nitrate+respiration17632

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11636015688acetoin-
11636017234glucose+

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
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase-3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
116360oxidase-
116360alcohol dehydrogenase-1.1.1.1
116360catalase-1.11.1.6
116360lysine decarboxylase-4.1.1.18
116360ornithine decarboxylase-4.1.1.17

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    49931C12:00.512
    49931C14:03.514
    49931C15:00.515
    49931C16:026.716
    49931C18:03.918
    49931C16:1 ω7c3.315.819
    49931C16:1 ω9c0.615.774
    49931C17:1 ω8c0.516.792
    49931C18:1 ω9c27.317.769
    49931C18:2 ω6,9c/C18:0 ANTE32.417.724
    49931Unidentified0.513.242
    49931Unidentified0.519.407
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116360-++-------++--------

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8763----------++++--------+-----+-------++------------
8763----------++++--------+--+/---+-------++------------
116360----------+/-+/----------+/----------------------------

Isolation, sampling and environmental information

isolation

@refsample type
8763swine waste-corn fermentation
49931Swine waste-corn fermentation
67770Swine waste-corn fermentation
116360Environment, Swine, waste-corn fermentation

isolation source categories

Cat1Cat2Cat3
#Engineered#Waste
#Host#Mammals#Suidae (Pig,Swine)

taxonmaps

  • @ref: 69479
  • File name: preview.99_3392.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_46;96_1770;97_2120;98_2600;99_3392&stattab=map
  • Last taxonomy: Amylolactobacillus
  • 16S sequence: LC145552
  • Sequence Identity:
  • Total samples: 1624
  • soil counts: 122
  • aquatic counts: 136
  • animal counts: 1297
  • plant counts: 69

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
87631Risk group (German classification)
1163601Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lactobacillus amylophilus partial 16S rRNA gene, type strain CIP 102988THE5739131530nuccore1603
20218Lactobacillus amylophilus strain DSM 20533 16S ribosomal RNA gene, partial sequenceM588061516nuccore1603
20218Lactobacillus amylophilus gene for 16S rRNA, partial sequence, strain: JCM 1125AB289028688nuccore1423721
20218Lactobacillus amylophilus gene for 16S ribosomal RNA, partial sequenceD31678178nuccore1423721
20218Lactobacillus amylophilus gene for 16S rRNA, partial sequence, strain: NBRC 15881AB6809881499nuccore1603
67770Lactobacillus amylophilus gene for 16S ribosomal RNA, partial sequence, strain: JCM 1125LC1455521459nuccore1423721

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Amylolactobacillus amylophilus DSM 20533 = JCM 1125GCA_001936335completencbi1423721
66792Lactobacillus amylophilus DSM 20533 = JCM 11251423721.4wgspatric1423721
66792Lactobacillus amylophilus DSM 20533 = JCM 11251423721.7completepatric1423721
66792Lactobacillus amylophilus DSM 20533 = JCM 11251423721.3wgspatric1423721
66792Lactobacillus amylophilus strain NBRC 158811603.4wgspatric1603
66792Amylolactobacillus amylophilus DSM 205332721755795completeimg1423721
66792Amylolactobacillus amylophilus JCM 11252728369694draftimg1423721
66792Amylolactobacillus amylophilus DSM 205332695420657draftimg1423721
67770Amylolactobacillus amylophilus DSM 20533 = JCM 1125GCA_001436185scaffoldncbi1423721
67770Amylolactobacillus amylophilus DSM 20533 = JCM 1125GCA_001311665contigncbi1423721
67770Amylolactobacillus amylophilus NBRC 15881GCA_006540265contigncbi1603

GC content

@refGC-contentmethod
876345.5
6777045.5thermal denaturation, midpoint method (Tm)
6777043.6genome sequence analysis

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes95.19no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no85.331yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no95.692yes
69480spore-formingspore-formingAbility to form endo- or exosporesno88.267no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno96yes
69480flagellatedmotile2+Ability to perform flagellated movementno90.833no

External links

@ref: 8763

culture collection no.: CCUG 30137, NCIMB 11546, JCM 1125, DSM 20533, ATCC 49845, LMG 6900, NRRL B-4437, VKM B-2234, BCRC 14055, CCM 7001, CECT 4133, CGMCC 1.3394, CIP 102988, IFO 15881, KCTC 3161, NBRC 15881, NCAIM B.01457, NCFB 2503, NRRL B-4476, VTT E-95574, NCDO 2503

straininfo link

@refstraininfo
758843208
75885312264

literature

  • topic: Phylogeny
  • Pubmed-ID: 17082384
  • title: Reclassification of Lactobacillus amylophilus LMG 11400 and NRRL B-4435 as Lactobacillus amylotrophicus sp. nov.
  • authors: Naser SM, Vancanneyt M, Snauwaert C, Vrancken G, Hoste B, De Vuyst L, Swings J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64463-0
  • year: 2006
  • mesh: Animal Husbandry, Bacterial Proteins/genetics, Bacterial Typing Techniques, Carbohydrate Metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, DNA-Directed RNA Polymerases/genetics, Electrophoresis, Polyacrylamide Gel, Genes, rRNA, Industrial Waste, Lactobacillus/*classification/cytology/isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenylalanine-tRNA Ligase/genetics, Phylogeny, Protein Subunits/genetics, Proteome/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8763Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20533)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20533
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
40497Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14735
49931Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 30137)https://www.ccug.se/strain?id=30137
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/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
75884Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3208.1StrainInfo: A central database for resolving microbial strain identifiers
75885Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID312264.1StrainInfo: A central database for resolving microbial strain identifiers
116360Curators of the CIPCollection of Institut Pasteur (CIP 102988)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102988