Strain identifier

BacDive ID: 2287

Type strain: Yes

Species: Lacticigenium naphthae

Strain Designation: MIC1-18

Strain history: <- T. Iino, NBRC; MIC1-18

NCBI tax ID(s): 1122143 (strain), 515351 (species)

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General

@ref: 8236

BacDive-ID: 2287

DSM-Number: 19658

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

description: Lacticigenium naphthae MIC1-18 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from spilled crude oil, oil-water well.

NCBI tax id

NCBI tax idMatching level
515351species
1122143strain

strain history

  • @ref: 8236
  • history: <- T. Iino, NBRC; MIC1-18

doi: 10.13145/bacdive2287.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Carnobacteriaceae
  • genus: Lacticigenium
  • species: Lacticigenium naphthae
  • full scientific name: Lacticigenium naphthae corrig. Iino et al. 2009

  • synonyms

    • @ref: 20215
    • synonym: Lacticigenium naphtae

@ref: 8236

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Carnobacteriaceae

genus: Lacticigenium

species: Lacticigenium naphthae

full scientific name: Lacticigenium naphthae Iino et al. 2009

strain designation: MIC1-18

type strain: yes

Morphology

cell morphology

  • @ref: 28990
  • gram stain: negative
  • cell length: 2.15 µm
  • cell width: 0.65 µm
  • cell shape: rod-shaped
  • motility: yes

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_19658_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_19658_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_19658_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_19658_4.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

  • @ref: 8236
  • name: METHANOGENIUM MEDIUM (H2/CO2) (DSMZ Medium 141)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/141
  • composition: Name: METHANOGENIUM MEDIUM (H2/CO2) (DSMZ Medium 141) Composition: NaHCO3 4.89237 g/l MgCl2 x 6 H2O 3.91389 g/l Yeast extract 1.95695 g/l Trypticase peptone 1.95695 g/l Na-acetate 0.978474 g/l Na2S x 9 H2O 0.489237 g/l L-Cysteine HCl x H2O 0.489237 g/l KCl 0.332681 g/l NH4Cl 0.244618 g/l K2HPO4 0.136986 g/l MgSO4 x 7 H2O 0.0293542 g/l Nitrilotriacetic acid 0.0146771 g/l NaCl 0.00978474 g/l MnSO4 x H2O 0.00489237 g/l Fe(NH4)2(SO4)2 x 6 H2O 0.00195695 g/l CoSO4 x 7 H2O 0.00176125 g/l ZnSO4 x 7 H2O 0.00176125 g/l FeSO4 x 7 H2O 0.000978474 g/l CaCl2 x 2 H2O 0.000978474 g/l Sodium resazurin 0.000489237 g/l NiCl2 x 6 H2O 0.000293542 g/l AlK(SO4)2 x 12 H2O 0.000195695 g/l CuSO4 x 5 H2O 9.78474e-05 g/l Pyridoxine hydrochloride 9.78474e-05 g/l Na2MoO4 x 2 H2O 9.78474e-05 g/l H3BO3 9.78474e-05 g/l Nicotinic acid 4.89237e-05 g/l Riboflavin 4.89237e-05 g/l (DL)-alpha-Lipoic acid 4.89237e-05 g/l Thiamine HCl 4.89237e-05 g/l Calcium D-(+)-pantothenate 4.89237e-05 g/l p-Aminobenzoic acid 4.89237e-05 g/l Folic acid 1.95695e-05 g/l Biotin 1.95695e-05 g/l Na2WO4 x 2 H2O 3.91389e-06 g/l Na2SeO3 x 5 H2O 2.93542e-06 g/l Vitamin B12 9.78474e-07 g/l Distilled water

culture temp

@refgrowthtypetemperature
8236positivegrowth30
28990positivegrowth04-30
28990positiveoptimum30

culture pH

@refabilitytypepHPH range
28990positivegrowth6.5-8.5alkaliphile
28990positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
8236anaerobe
28990facultative anaerobe

spore formation

  • @ref: 28990
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
28990NaClpositivegrowth<17 %
28990NaClpositiveoptimum3 %

murein

  • @ref: 8236
  • murein short key: A11.33
  • type: A4alpha L-Lys-D-Glu

observation

  • @ref: 28990
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2899016449alanine+carbon source
2899022599arabinose+carbon source
2899017057cellobiose+carbon source
2899028757fructose+carbon source
2899017234glucose+carbon source
2899029987glutamate+carbon source
2899017306maltose+carbon source
2899037684mannose+carbon source
28990506227N-acetylglucosamine+carbon source
2899033942ribose+carbon source
2899017814salicin+carbon source
2899017992sucrose+carbon source
2899027082trehalose+carbon source
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin+builds acid from
6837159640N-acetylglucosamine-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837117634D-glucose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8236-------------------------+------------------------

Isolation, sampling and environmental information

isolation

  • @ref: 8236
  • sample type: spilled crude oil, oil-water well
  • geographic location: Akita
  • country: Japan
  • origin.country: JPN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial#Oil reservoir
#Environmental#Aquatic

taxonmaps

  • @ref: 69479
  • File name: preview.99_184495.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_13;96_67931;97_88298;98_120071;99_184495&stattab=map
  • Last taxonomy: Lacticigenium naphthae subclade
  • 16S sequence: AB430339
  • Sequence Identity:
  • Total samples: 4838
  • soil counts: 292
  • aquatic counts: 949
  • animal counts: 3390
  • plant counts: 207

Safety information

risk assessment

  • @ref: 8236
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8236
  • description: Lacticigenium naphtae gene for 16S rRNA, partial sequence
  • accession: AB430339
  • length: 1446
  • database: nuccore
  • NCBI tax ID: 515351

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lacticigenium naphthae DSM 19658GCA_000425865scaffoldncbi1122143
66792Lacticigenium naphtae DSM 196581122143.3wgspatric1122143
66792Lacticigenium naphtae DSM 196582524023191draftimg1122143

GC content

  • @ref: 8236
  • GC-content: 37.8

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthfacultative anaerobe79.4
125439BacteriaNetgram_stainReaction to gram-stainingvariable84
125439BacteriaNetmotilityAbility to perform movementyes69.7
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes74.9
125438gram-positivegram-positivePositive reaction to Gram-stainingyes77.236yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no88.633no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no88.759yes
125438spore-formingspore-formingAbility to form endo- or exosporesno74.424no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno91.988no
125438motile2+flagellatedAbility to perform flagellated movementyes65.425no

External links

@ref: 8236

culture collection no.: DSM 19658, NBRC 101988

straininfo link

  • @ref: 71845
  • straininfo: 397742

literature

  • topic: Phylogeny
  • Pubmed-ID: 19329605
  • title: Lacticigenium naphtae gen. nov., sp. nov., a halotolerant and motile lactic acid bacterium isolated from crude oil.
  • authors: Iino T, Suzuki K, Harayama S
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.003293-0
  • year: 2009
  • mesh: Anaerobiosis, Bacterial Typing Techniques, Base Composition, Carbohydrate Metabolism, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, *Environmental Microbiology, Fatty Acids/analysis, Gram-Positive Bacteria/*classification/genetics/*isolation & purification/physiology, Hydrogen-Ion Concentration, Japan, Lactic Acid/metabolism, Locomotion, Molecular Sequence Data, Peptidoglycan/analysis, *Petroleum, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, Temperature
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
8236Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19658)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19658
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
28990Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2542328776041
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life28604660 35: 676-683 2017
68371Automatically annotated from API 50CH acid
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
71845Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID397742.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1