Strain identifier

BacDive ID: 133336

Type strain: Yes

Species: Saccharicrinis aurantiacus

Strain Designation: HQYD1

Strain history: <- Zong-Jun Du, Shandong Univ..

NCBI tax ID(s): 1849719 (species)

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General

@ref: 25189

BacDive-ID: 133336

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

description: Saccharicrinis aurantiacus HQYD1 is a facultative anaerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from sea squirt .

NCBI tax id

  • NCBI tax id: 1849719
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Zong-Jun Du, Shandong Univ..

doi: 10.13145/bacdive133336.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Marinilabiliaceae
  • genus: Saccharicrinis
  • species: Saccharicrinis aurantiacus
  • full scientific name: Saccharicrinis aurantiacus (Lu et al. 2017) García-López et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Labilibacter aurantiacus

@ref: 25189

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Marinilabiliaceae

genus: Labilibacter

species: Labilibacter aurantiacus

strain designation: HQYD1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangement
25189negative1.5-20.0 µm0.3-0.5 µmrod-shapedyes
25189negative2.0-17.0 µm0.3-0.5 µmrod-shapedyes
67771rod-shapedgliding
67771negative

colony morphology

@refcolony sizecolony colorcolony shapeincubation periodmedium used
251890.5 mmorangecircular3 daysmarine agar (MA)
25189yellow

Culture and growth conditions

culture medium

  • @ref: 25189
  • name: marine agar (MA)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
25189positivegrowth4.0-37.0
25189positiveoptimum28mesophilic
25189positivegrowth10psychrophilic
25189nogrowth40thermophilic
25189positivegrowth4.0-33.0
25189positiveoptimum28.0-30.0mesophilic
67771positivegrowth28-30mesophilic

culture pH

@refabilitytypepHPH range
25189positivegrowth6.0-8.5alkaliphile
25189positiveoptimum7.0-7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
25189facultative anaerobe
67771facultative anaerobe

halophily

@refsaltgrowthtested relationconcentration
25189NaClpositivegrowth1.0-5.0 %(w/v)
25189NaCloptimum2.0-3.0 %(w/v)

observation

  • @ref: 67771
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
251895291gelatin-hydrolysis
2518917632nitrate-reduction
2518928017starch-hydrolysis
2518927897tryptophan-energy source
2518953426tween 80-hydrolysis
2518916199urea-hydrolysis
25189309162-oxoglutarate+oxidation
25189581435-dehydro-D-gluconate+builds acid from
251892509agar+hydrolysis
2518958187alginate+hydrolysis
2518936219alpha-lactose+oxidation
2518927613amygdalin+builds acid from
2518917057cellobiose+builds acid from
2518917057cellobiose+oxidation
2518916947citrate+oxidation
2518912936D-galactose+builds acid from
2518918024D-galacturonic acid+oxidation
2518917634D-glucose+builds acid from
2518916899D-mannitol+oxidation
2518916024D-mannose+oxidation
2518916988D-ribose+builds acid from
2518965327D-xylose+builds acid from
251894853esculin+builds acid from
251895291gelatin+hydrolysis
251895291gelatin+oxidation
2518928066gentiobiose+builds acid from
2518928066gentiobiose+oxidation
2518928087glycogen+builds acid from
2518917268myo-inositol+oxidation
2518915971L-histidine+oxidation
2518917716lactose+builds acid from
2518917306maltose+oxidation
2518963154N-acetyl-beta-D-mannosamine+oxidation
2518917632nitrate+reduction
2518928017starch+builds acid from
2518927897tryptophan+energy source

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitive
2518948923erythromycinyesyes
2518917334penicillinyesyes
25189204928cefotaximeyesyes
2518929007ceftriaxoneyesyes
251893745clindamycinyesyes
251896472lincomycinyesyes
2518917698chloramphenicolyesyes
2518928077rifampicinyesyes
2518931168acetylspiramycinyesyes
2518953727sulfamethoxydiazineyesyes

metabolite production

@refChebi-IDmetaboliteproduction
2518916136hydrogen sulfideno
2518935581indoleno
2518935581indoleyes

metabolite tests

@refChebi-IDmetaboliteindole test
2518935581indole-
2518935581indole+

enzymes

@refvalueactivityec
25189acid phosphatase+3.1.3.2
25189alkaline phosphatase+3.1.3.1
25189alpha-chymotrypsin-3.4.21.1
25189alpha-fucosidase-3.2.1.51
25189alpha-galactosidase-3.2.1.22
25189alpha-glucosidase-3.2.1.20
25189alpha-mannosidase-3.2.1.24
25189beta-galactosidase-3.2.1.23
25189beta-glucosidase-3.2.1.21
25189beta-glucuronidase-3.2.1.31
25189catalase+1.11.1.6
25189cystine arylamidase-3.4.11.3
25189cytochrome oxidase-1.9.3.1
25189leucine arylamidase-3.4.11.1
25189lipase (C 14)-
25189N-acetyl-beta-glucosaminidase-3.2.1.52
25189naphthol-AS-BI-phosphohydrolase+
25189trypsin-3.4.21.4
25189tryptophan deaminase-4.1.99.1
25189valine arylamidase+
25189catalase-1.11.1.6
25189cytochrome oxidase+1.9.3.1
25189esterase (C 4)+
25189esterase Lipase (C 8)-
25189tryptophan deaminase+4.1.99.1
25189valine arylamidase-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperature
25189sea squirt (Styela clava)coastal area of WeihaiChinaCHNAsia37122marine agar 2216 (MA; Difco)7 days28
67771From sea squirt, `Styela clava`coastal area of WeihaiChinaCHNAsia

isolation source categories

  • Cat1: #Host
  • Cat2: #Invertebrates (Other)
  • Cat3: #Tunicata

taxonmaps

  • @ref: 69479
  • File name: preview.99_4533.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16198;96_2265;97_2745;98_3408;99_4533&stattab=map
  • Last taxonomy: Saccharicrinis aurantiacus subclade
  • 16S sequence: JF721990
  • Sequence Identity:
  • Total samples: 1191
  • soil counts: 15
  • aquatic counts: 1033
  • animal counts: 99
  • plant counts: 44

Sequence information

16S sequences

  • @ref: 25189
  • description: Cytophaga sp. HQYD1 16S ribosomal RNA gene, partial sequence
  • accession: JF721990
  • length: 1442
  • database: nuccore
  • NCBI tax ID: 1849719

Genome sequences

  • @ref: 66792
  • description: Saccharicrinis aurantiacus HQYD1
  • accession: GCA_001660705
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 1849719

GC content

@refGC-contentmethod
2518935.1high performance liquid chromatography (HPLC)
2518936.1high performance liquid chromatography (HPLC)
6777135.1

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno91.716yes
flagellatedno91.716yes
gram-positiveno98.592yes
gram-positiveno98.592yes
anaerobicno71.257yes
anaerobicno71.257yes
aerobicno77.893yes
aerobicno77.893yes
halophileno78.45no
halophileno78.45no
spore-formingno91.881no
spore-formingno91.881no
glucose-utilyes90.483no
glucose-utilyes90.483no
motileno76.291yes
motileno76.291yes
thermophileno99.479no
glucose-fermentno63.422no
glucose-fermentno63.422no
thermophileno99.479no

External links

@ref: 25189

culture collection no.: MCCC 1K02304, KCTC 42583

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
25189D. C. Z. Lu, J. X.,Wang, F. Q.,Xie, Z. H.,Du, Z. J.Labilibacter aurantiacus gen. nov., sp. nov., isolated from sea squirt (Styela clava) and reclassification of Saccharicrinis marinus as Labilibacter marinus comb. nov10.1099/ijsem.0.001649IJSEM 67: 441-446 201727902253
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
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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/