Strain identifier
BacDive ID: 133006
Type strain:
Species: Lacinutrix iliipiscaria
Strain Designation: Th68
Strain history: <- X-H Zhang, Ocean Univ. of China
NCBI tax ID(s): 1230532 (species)
General
@ref: 24794
BacDive-ID: 133006
DSM-Number: 26284
keywords: genome sequence, 16S sequence, Bacteria, aerobe, chemoheterotroph, mesophilic, Gram-negative, motile, rod-shaped
description: Lacinutrix iliipiscaria Th68 is an aerobe, chemoheterotroph, mesophilic bacterium that was isolated from From intestine of cultured flounder `Paralichthys olivaceus`.
NCBI tax id
- NCBI tax id: 1230532
- Matching level: species
strain history
@ref | history |
---|---|
24794 | <- X.-H. Zhang, Ocean Univ. China, Dept. of Marine Biology, Qingdao, P. R. China; Th68 <- K. Tang |
67770 | X.-H. Zhang and Y. Zhang <-- K. Tang Th68. |
67771 | <- X-H Zhang, Ocean Univ. of China |
doi: 10.13145/bacdive133006.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Flavobacteriia
- order: Flavobacteriales
- family: Flavobacteriaceae
- genus: Lacinutrix
- species: Lacinutrix iliipiscaria
- full scientific name: Lacinutrix iliipiscaria (Shakeela et al. 2015) Nedashkovskaya et al. 2016
synonyms
- @ref: 20215
- synonym: Flavirhabdus iliipiscaria
@ref: 24794
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Flavobacteriaceae
genus: Lacinutrix
species: Lacinutrix iliipiscaria
full scientific name: Lacinutrix iliipiscaria (Shakeela et al. 2015) Nedashkovskaya et al. 2016
strain designation: Th68
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | flagellum arrangement | confidence |
---|---|---|---|---|---|---|---|
24984 | negative | 0.3-3.0 µm | 0.2-0.8 µm | rod-shaped | yes | ||
67771 | rod-shaped | yes | gliding | ||||
67771 | negative | ||||||
69480 | negative | 99.981 |
pigmentation
- @ref: 24984
- production: yes
- name: Flexirubin-type
Culture and growth conditions
culture medium
- @ref: 24794
- name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514
- composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
24794 | positive | growth | 28 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
67771 | positive | growth | 28 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
24984 | aerobe |
67771 | aerobe |
nutrition type
- @ref: 24984
- type: chemoheterotroph
spore formation
@ref | spore formation | confidence |
---|---|---|
24984 | no | |
69481 | no | 100 |
69480 | no | 99.996 |
observation
@ref | observation |
---|---|
67770 | quinones: MK-6 |
67771 | quinones: MK-6 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
24984 | 28816 | 2-deoxy-d-ribose | - | builds acid from |
24984 | 2509 | agar | - | hydrolysis |
24984 | 17057 | cellobiose | - | builds acid from |
24984 | 17029 | chitin | - | hydrolysis |
24984 | 16947 | citrate | - | carbon source |
24984 | 15824 | D-fructose | - | builds acid from |
24984 | 17716 | lactose | - | builds acid from |
24984 | 16899 | D-mannitol | - | builds acid from |
24984 | 16991 | dna | - | hydrolysis |
24984 | 24265 | gluconate | - | carbon source |
24984 | 17234 | glucose | - | builds acid from |
24984 | 17754 | glycerol | - | builds acid from |
24984 | 30849 | L-arabinose | - | builds acid from |
24984 | 62345 | L-rhamnose | - | builds acid from |
24984 | 17716 | lactose | - | carbon source |
24984 | 17306 | maltose | - | builds acid from |
24984 | 37684 | mannose | - | builds acid from |
24984 | 16634 | raffinose | - | builds acid from |
24984 | 30911 | sorbitol | - | carbon source |
24984 | 28017 | starch | - | hydrolysis |
24984 | 17992 | sucrose | - | builds acid from |
24984 | 53423 | tween 40 | - | hydrolysis |
24984 | 53426 | tween 80 | - | hydrolysis |
24984 | casein | + | hydrolysis | |
24984 | 17634 | D-glucose | + | carbon source |
24984 | 4853 | esculin | + | hydrolysis |
24984 | 5291 | gelatin | + | hydrolysis |
24984 | 30849 | L-arabinose | + | carbon source |
24984 | 17306 | maltose | + | carbon source |
24984 | 29864 | mannitol | + | carbon source |
24984 | 37684 | mannose | + | carbon source |
24984 | 17632 | nitrate | + | reduction |
24984 | 17992 | sucrose | + | carbon source |
24984 | 27897 | tryptophan | + | energy source |
24984 | 53424 | tween 20 | + | hydrolysis |
24984 | 16199 | urea | + | hydrolysis |
antibiotic resistance
@ref | ChEBI | metabolite | is antibiotic | is sensitive | is resistant |
---|---|---|---|---|---|
24984 | 17698 | chloramphenicol | yes | yes | |
24984 | 48923 | erythromycin | yes | yes | |
24984 | 6472 | lincomycin | yes | yes | |
24984 | 7731 | ofloxacin | yes | yes | |
24984 | 16869 | oleandomycin | yes | yes | |
24984 | 28001 | vancomycin | yes | yes | |
24984 | 6104 | kanamycin | yes | yes | |
24984 | 59062 | polymyxin | yes | yes | |
24984 | 28971 | ampicillin | yes | yes | |
24984 | 3393 | carbenicillin | yes | yes | |
24984 | 7507 | neomycin | yes | yes | |
24984 | 17076 | streptomycin | yes | yes | |
24984 | 18208 | penicillin g | yes | no | |
24984 | 50845 | doxycycline | yes | no | |
24984 | 100147 | nalidixic acid | yes | no | |
24984 | 474053 | cefazolin | yes | no | |
24984 | 17833 | gentamicin | yes | no | |
24984 | 3534 | cephalexin | yes | no | |
24984 | 27902 | tetracycline | yes | yes | |
24984 | 28077 | rifampicin | yes | yes | |
24984 | 7809 | oxacillin | yes | no |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
24984 | 15688 | acetoin | no |
24984 | 16136 | hydrogen sulfide | no |
24984 | 35581 | indole | yes |
metabolite tests
@ref | Chebi-ID | metabolite | indole test | citrate test |
---|---|---|---|---|
24984 | 35581 | indole | + | |
24984 | 16947 | citrate | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
24984 | acid phosphatase | - | 3.1.3.2 |
24984 | alkaline phosphatase | + | 3.1.3.1 |
24984 | alpha-chymotrypsin | - | 3.4.21.1 |
24984 | alpha-galactosidase | - | 3.2.1.22 |
24984 | alpha-glucosidase | - | 3.2.1.20 |
24984 | beta-galactosidase | - | 3.2.1.23 |
24984 | beta-glucosidase | - | 3.2.1.21 |
24984 | catalase | + | 1.11.1.6 |
24984 | cystine arylamidase | - | 3.4.11.3 |
24984 | cytochrome oxidase | + | 1.9.3.1 |
24984 | esterase (C 4) | - | |
24984 | esterase Lipase (C 8) | - | |
24984 | leucine arylamidase | - | 3.4.11.1 |
24984 | lipase (C 14) | - | |
24984 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
24984 | naphthol-AS-BI-phosphohydrolase | - | |
24984 | trypsin | + | 3.4.21.4 |
24984 | tryptophan deaminase | + | 4.1.99.1 |
24984 | valine arylamidase | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | host species |
---|---|---|---|---|---|---|
67771 | From intestine of cultured flounder `Paralichthys olivaceus` | Shandong Province | China | CHN | Asia | |
24794 | intestine of flounder Paralichthys olivaceus | Shandong Province | China | CHN | Asia | Paralichthys olivaceus |
67770 | Intestine of cultured flounder (Paralichthys olivaceus) collected from a fish farm in Shandong Province | China | CHN | Asia | Paralichthys olivaceus |
isolation source categories
Cat1 | Cat2 |
---|---|
#Host | #Fishes |
#Host Body-Site | #Gastrointestinal tract |
taxonmaps
- @ref: 69479
- File name: preview.99_93211.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_107;96_14427;97_42169;98_64116;99_93211&stattab=map
- Last taxonomy: Lacinutrix iliipiscaria subclade
- 16S sequence: JX412960
- Sequence Identity:
- Total samples: 99
- soil counts: 13
- aquatic counts: 76
- animal counts: 9
- plant counts: 1
Safety information
risk assessment
- @ref: 24794
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 24794
- description: Flavirhabdus iliipiscaria strain Th68 16S ribosomal RNA gene, partial sequence
- accession: JX412960
- length: 1486
- database: ena
- NCBI tax ID: 1230532
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Lacinutrix iliipiscaria strain DSM 26284 | 1230532.3 | wgs | patric | 1230532 |
66792 | Lacinutrix iliipiscaria DSM 26284 | 2861378864 | draft | img | 1230532 |
GC content
@ref | GC-content | method |
---|---|---|
24984 | 32.5 | thermal denaturation, midpoint method (Tm) |
24794 | 33.0 | high performance liquid chromatography (HPLC) |
67770 | 33 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 87.329 | yes |
gram-positive | no | 98.111 | yes |
anaerobic | no | 99.466 | no |
aerobic | yes | 91.842 | yes |
halophile | no | 69.869 | no |
spore-forming | no | 96.863 | yes |
thermophile | no | 98.698 | yes |
glucose-util | yes | 87.359 | yes |
flagellated | no | 96.432 | no |
glucose-ferment | no | 90.951 | no |
External links
@ref: 24794
culture collection no.: DSM 26284, JCM 18637, KCTC 32141
straininfo link
- @ref: 91281
- straininfo: 406769
literature
- topic: Phylogeny
- Pubmed-ID: 25667395
- title: Flavirhabdus iliipiscaria gen. nov., sp. nov., isolated from intestine of flounder (Paralichthys olivaceus) and emended descriptions of the genera Flavivirga, Algibacter, Bizionia and Formosa.
- authors: Shakeela Q, Shehzad A, Zhang Y, Tang K, Zhang XH
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.000110
- year: 2015
- mesh: Animals, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Flounder/*microbiology, Intestines/*microbiology, Molecular Sequence Data, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
- topic2: Genetics
Reference
@id | authors | title | doi/url | catalogue | journal | pubmed |
---|---|---|---|---|---|---|
20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | |||
24794 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-26284 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26284) | |||
24984 | O. I. K. Nedashkovskaya, Song-Gun,Zhukova, Natalia V.,Lee, Jung-Sook,Mikhailov, Valery V. | Lacinutrix cladophorae sp. nov., a flavobacterium isolated from the green alga Cladophora stimpsonii, transfer of Flavirhabdus iliipiscaria Shakeela et al. 2015 to the genus Lacinutrix as Lacinutrix iliipiscaria comb. nov. and emended description of the genus Lacinutrix | 10.1099/ijsem.0.001353 | IJSEM 66: 4339-4346 2016 | 27473360 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
69479 | João 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 beta | https://microbeatlas.org/ | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
91281 | Reimer, 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 identifiers | 10.60712/SI-ID406769.1 |