Strain identifier
BacDive ID: 6221
Type strain:
Species: Henriciella marina
Strain Designation: IS4
Strain history: <- ZX Quan, KRIBB
NCBI tax ID(s): 1121949 (strain), 453851 (species)
General
@ref: 8199
BacDive-ID: 6221
DSM-Number: 19595
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative
description: Henriciella marina IS4 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from Sea water.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1121949 | strain |
453851 | species |
strain history
@ref | history |
---|---|
8199 | <- S. W. Roh, Korea Res. Inst. Biosci. & Biotechnol. (KRIBB), Taejon, South Korea; Iso4 |
67770 | S. W. Roh Iso4. |
67771 | <- ZX Quan, KRIBB |
doi: 10.13145/bacdive6221.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Caulobacterales
- family: Hyphomonadaceae
- genus: Henriciella
- species: Henriciella marina
- full scientific name: Henriciella marina Quan et al. 2009
@ref: 8199
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Caulobacterales
family: Hyphomonadaceae
genus: Henriciella
species: Henriciella marina
full scientific name: Henriciella marina Quan et al. 2009
strain designation: IS4
type strain: yes
Morphology
cell morphology
@ref | gram stain | confidence |
---|---|---|
67771 | negative | |
69480 | negative | 99.998 |
multimedia
@ref | multimedia content | caption | intellectual property rights |
---|---|---|---|
66793 | EM_DSM_19595_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_19595_2.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_19595_3.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_19595_4.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_19595_5.jpg | electron microscopic image | © HZI/Manfred Rohde |
Culture and growth conditions
culture medium
- @ref: 8199
- 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 |
---|---|---|---|---|
8199 | positive | growth | 28 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
67771 | positive | growth | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.999 |
observation
- @ref: 67770
- observation: quinones: Q-10
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent | geographic location |
---|---|---|---|---|---|
8199 | Sea water | Republic of Korea | KOR | Asia | |
67770 | Seawater | ||||
67771 | From sea water | Republic of Korea | KOR | Asia | Goseong, East Sea |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Marine
taxonmaps
- @ref: 69479
- File name: preview.99_7202.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_269;96_2377;97_2893;98_3605;99_7202&stattab=map
- Last taxonomy: Henriciella
- 16S sequence: EF660760
- Sequence Identity:
- Total samples: 1463
- soil counts: 30
- aquatic counts: 1366
- animal counts: 59
- plant counts: 8
Safety information
risk assessment
- @ref: 8199
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 8199
- description: Henriciella marina DSM 19595 strain Iso4 16S ribosomal RNA gene, partial sequence
- accession: EF660760
- length: 1391
- database: ena
- NCBI tax ID: 1121949
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Henriciella marina DSM 19595 | 1121949.8 | wgs | patric | 1121949 |
66792 | Henriciella marina DSM 19595 | 2519103046 | draft | img | 1121949 |
67770 | Henriciella marina DSM 19595 | GCA_000376805 | contig | ncbi | 1121949 |
GC content
- @ref: 67770
- GC-content: 56.2
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 88.944 | no |
flagellated | no | 70.663 | no |
gram-positive | no | 98.741 | yes |
anaerobic | no | 97.791 | yes |
halophile | no | 62.748 | no |
spore-forming | no | 96.373 | no |
thermophile | no | 98.512 | yes |
glucose-util | yes | 78.58 | no |
aerobic | yes | 92.059 | yes |
glucose-ferment | no | 94.881 | no |
External links
@ref: 8199
culture collection no.: DSM 19595, JCM 15116, KCTC 12513, ISO Iso4, ISO 4
straininfo link
- @ref: 75700
- straininfo: 399096
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 19412598 | Henriciella marina gen. nov., sp. nov., a novel member of the family Hyphomonadaceae isolated from the East Sea. | Quan ZX, Zeng DN, Xiao YP, Roh SW, Nam YD, Chang HW, Yoon JH, Oh HM, Bae JW | J Microbiol | 10.1007/s12275-008-0290-0 | 2009 | Alphaproteobacteria/*classification/genetics/*isolation & purification/metabolism, Bacterial Typing Techniques, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology | Metabolism |
Phylogeny | 28820101 | Henriciella pelagia sp. nov., isolated from seawater. | Wu YH, Cheng H, Huo YY, Jin XB, Wang CS, Xu XW | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002066 | 2017 | Alphaproteobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Pacific Ocean, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry | Transcriptome |
Phylogeny | 34296989 | Physiological and genomic features of Henriciella with the description of Henriciella mobilis sp. nov. | Ren WT, Cheng H, Wang CS, Xu XW, Zhou P, Wu YH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004889 | 2021 | Alphaproteobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
8199 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19595) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19595 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
75700 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID399096.1 | StrainInfo: A central database for resolving microbial strain identifiers |