Strain identifier

BacDive ID: 141137

Type strain: Yes

Species: Lacimicrobium alkaliphilum

Strain Designation: X13M-12

NCBI tax ID(s): 1526571 (species)

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General

@ref: 44053

BacDive-ID: 141137

keywords: genome sequence, 16S sequence, Bacteria, facultative aerobe, Gram-negative, motile, curved-shaped, colony-forming

description: Lacimicrobium alkaliphilum X13M-12 is a facultative aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from surface water sample of a salt lake.

NCBI tax id

  • NCBI tax id: 1526571
  • Matching level: species

doi: 10.13145/bacdive141137.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Alteromonadales
  • family: Alteromonadaceae
  • genus: Lacimicrobium
  • species: Lacimicrobium alkaliphilum
  • full scientific name: Lacimicrobium alkaliphilum Zhong et al. 2016

@ref: 44053

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Alteromonadaceae

genus: Lacimicrobium

species: Lacimicrobium alkaliphilum

strain designation: X13M-12

type strain: yes

Morphology

cell morphology

  • @ref: 44053
  • gram stain: negative
  • cell length: 1.2-2.3 µm
  • cell width: 0.5-0.8 µm
  • cell shape: curved-shaped
  • motility: yes
  • flagellum arrangement: polar

colony morphology

  • @ref: 44053
  • colony size: 2.0-3.0 mm
  • colony color: yellow
  • colony shape: circular
  • incubation period: 3 days
  • medium used: MA agar

Culture and growth conditions

culture medium

@refnamegrowth
44053LB (Luria-Bertani) MEDIUMno
44053Marine agar (MA)yes
44053MByes
44053trypticase soy broth (TSB)no

culture temp

@refgrowthtypetemperaturerange
44053positivegrowth4-40
44053positiveoptimum25-30mesophilic

culture pH

@refabilitytypepHPH range
44053positivegrowth6.0-11.0alkaliphile
44053positiveoptimum8.5

Physiology and metabolism

oxygen tolerance

  • @ref: 44053
  • oxygen tolerance: facultative aerobe

halophily

@refsaltgrowthtested relationconcentration
44053NaClpositivegrowth0-15.0 %(w/v)
44053NaClpositiveoptimum3.0-5.0 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4405315824D-fructose-carbon source
4405312936D-galactose-carbon source
4405316024D-mannose-carbon source
4405365327D-xylose-carbon source
4405329987glutamate-carbon source
4405315428glycine-carbon source
4405317561L-cysteine-carbon source
4405318019L-lysine-carbon source
4405317716lactose-carbon source
4405317306maltose-carbon source
4405330031succinate-carbon source
4405315824D-fructose-energy source
4405312936D-galactose-energy source
4405316024D-mannose-energy source
4405365327D-xylose-energy source
4405329987glutamate-energy source
4405315428glycine-energy source
4405317561L-cysteine-energy source
4405318019L-lysine-energy source
4405317716lactose-energy source
4405317306maltose-energy source
4405330031succinate-energy source
44053casein-hydrolysis
4405316467L-arginine-hydrolysis
4405328017starch-hydrolysis
4405316947citrate+carbon source
4405317634D-glucose+carbon source
4405317924D-sorbitol+carbon source
4405317790methanol+carbon source
4405315361pyruvate+carbon source
4405317992sucrose+carbon source
4405327082trehalose+carbon source
4405316947citrate+energy source
4405317634D-glucose+energy source
4405317924D-sorbitol+energy source
4405317790methanol+energy source
4405315361pyruvate+energy source
4405317992sucrose+energy source
4405327082trehalose+energy source
4405317634D-glucose+fermentation
440534853esculin+hydrolysis
440535291gelatin+hydrolysis
4405317895L-tyrosine+hydrolysis
4405353424tween 20+hydrolysis
4405353423tween 40+hydrolysis
4405353425tween 60+hydrolysis
4405353426tween 80+hydrolysis
4405317632nitrate+reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
4405348923erythromycinyesyes15 µg (disc)
4405317698chloramphenicolyesyes30 µg (disc)
4405317076streptomycinyesyes10 µg (disc)
4405328971ampicillinyesyes10 µg (disc)
440533732clarithromycinyesyes15 µg (disc)
4405317833gentamicinyesyes10 µg (disc)
44053100246norfloxacinyesyes10 µg (disc)
440539332sulfamethoxazoleyesyes300 µg (disc)
4405327902tetracyclineyesyes30 µg (disc)
440536104kanamycinyesyes30 µg (disc)
440533745clindamycinyesyes2 µg (disc)
4405328001vancomycinyesyes30 µg (disc)

metabolite production

  • @ref: 44053
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

enzymes

@refvalueactivityec
44053cytochrome oxidase+1.9.3.1
44053catalase+1.11.1.6
44053alkaline phosphatase+3.1.3.1
44053esterase (C 4)+
44053esterase Lipase (C 8)+
44053leucine arylamidase+3.4.11.1
44053valine arylamidase+
44053alpha-chymotrypsin+3.4.21.1
44053acid phosphatase+3.1.3.2
44053naphthol-AS-BI-phosphohydrolase+
44053N-acetyl-beta-glucosaminidase+3.2.1.52
44053lipase (C 14)-
44053cystine arylamidase-3.4.11.3
44053trypsin-3.4.21.4
44053alpha-galactosidase-3.2.1.22
44053beta-galactosidase-3.2.1.23
44053beta-glucuronidase-3.2.1.31
44053alpha-glucosidase-3.2.1.20
44053beta-glucosidase-3.2.1.21
44053alpha-mannosidase-3.2.1.24
44053alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    44053C11:0-3-OH1.4
    44053C12:01.5
    44053C12:0 3OH9.6
    44053C12:1 3OH2
    44053C14:01.8
    44053C16:016.5
    44053C16:0-3-OH3.1
    44053C16:1ω7c / C16:1ω6c21
    44053C17:01.8
    44053C17:0-cyclo3.8
    44053C17:1ω8c6
    44053C18:1ω6c / C18:1ω7c16.1
    4405310-methyl C19:04.7
  • type of FA analysis: whole cell analysis
  • incubation medium: MA
  • incubation time: 2
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

  • @ref: 44053
  • sample type: surface water sample of a salt lake
  • geographic location: Lake Xiaochaidan, Qaidam basin, Qinghai Province
  • country: China
  • origin.country: CHN
  • continent: Asia
  • latitude: 37.4944
  • longitude: 95.5239
  • enrichment culture: marine agar 2216 (MA, Difco)
  • enrichment culture temperature: 30

isolation source categories

Cat1Cat2Cat3
#Condition#Saline
#Environmental#Aquatic#Lake (large)
#Environmental#Aquatic#Surface water

taxonmaps

  • @ref: 69479
  • File name: preview.99_7764.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_98;96_3606;97_4429;98_5677;99_7764&stattab=map
  • Last taxonomy: Lacimicrobium alkaliphilum
  • 16S sequence: KJ782426
  • Sequence Identity:
  • Total samples: 3779
  • soil counts: 179
  • aquatic counts: 2054
  • animal counts: 1411
  • plant counts: 135

Sequence information

16S sequences

  • @ref: 44053
  • description: 16S rRNA gene sequence
  • accession: KJ782426
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lacimicrobium alkaliphilum X13M-12GCA_002591895contigncbi1526571
66792Lacimicrobium alkaliphilum CGMCC 1.12923GCA_014640135scaffoldncbi1526571
66792Lacimicrobium alkaliphilum strain CGMCC 1.129231526571.11wgspatric1526571
66792Lacimicrobium alkaliphilum X13M-122832081228draftimg1526571

GC content

  • @ref: 44053
  • GC-content: 49
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes83.79no
gram-positiveno99.135yes
anaerobicno97.48yes
aerobicyes69.959yes
halophileno73.252no
spore-formingno96.301no
glucose-utilyes91.907yes
thermophileno99.238no
motileyes90.29yes
glucose-fermentno66.676yes

External links

@ref: 44053

culture collection no.: CGMCC 1.12923, KCTC 42674

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny26537772Lacimicrobium alkaliphilum gen. nov., sp. nov., a member of the family Alteromonadaceae isolated from a salt lake.Zhong ZP, Liu Y, Wang F, Zhou YG, Liu HC, Liu ZPInt J Syst Evol Microbiol10.1099/ijsem.0.0007352015Alteromonadaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lakes/*microbiology, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Saline Waters, Sequence Analysis, DNA, Ubiquinone/chemistryGenetics
Phylogeny31622231Saliniradius amylolyticus gen. nov., sp. nov., isolated from solar saltern sediment.Kang H, Cha I, Kim H, Joh KInt J Syst Evol Microbiol10.1099/ijsem.0.0037482020Alteromonadaceae/*classification/isolation & purification, Alteromonas/genetics, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Glycolipids/chemistry, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Salinity, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome

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
44053Zhi-Ping Zhong, Ying Liu, Fang Wang, Yu-Guang Zhou, Hong-Can Liu and Zhi-Pei LiuLacimicrobium alkaliphilum gen. nov., sp. nov., a member of the family Alteromonadaceae isolated from a salt lake10.1099/ijsem.0.000735IJSEM 66: 422-429 201626537772
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
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/