Strain identifier
BacDive ID: 5380
Type strain:
Species: Erythrobacter longus
Strain history: CIP <- 1994, M. Gauthier, INSERM, Nice, France <- ATCC <- T. Shiba: strain OCh 101
NCBI tax ID(s): 1044 (species)
General
@ref: 2940
BacDive-ID: 5380
DSM-Number: 6997
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Erythrobacter longus DSM 6997 is a mesophilic, Gram-negative bacterium that was isolated from seaweed, Enteromorpha linza.
NCBI tax id
- NCBI tax id: 1044
- Matching level: species
strain history
@ref | history |
---|---|
2940 | <- T. Shiba, Otsuchi Marine Res. Center, Univ. Tokyo, OCh 101 |
67770 | T. Shiba OCh101. |
120654 | CIP <- 1994, M. Gauthier, INSERM, Nice, France <- ATCC <- T. Shiba: strain OCh 101 |
doi: 10.13145/bacdive5380.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Sphingomonadales
- family: Erythrobacteraceae
- genus: Erythrobacter
- species: Erythrobacter longus
- full scientific name: Erythrobacter longus Shiba and Simidu 1982
@ref: 2940
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Sphingomonadales
family: Erythrobacteraceae
genus: Erythrobacter
species: Erythrobacter longus
full scientific name: Erythrobacter longus Shiba and Simidu 1982
type strain: yes
Morphology
cell morphology
@ref | gram stain | confidence | cell shape | motility |
---|---|---|---|---|
69480 | negative | 99.981 | ||
120654 | negative | rod-shaped | yes |
colony morphology
- @ref: 120654
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
2940 | BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) | yes | https://mediadive.dsmz.de/medium/514 | 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 |
37982 | Marine agar (MA) | yes | Distilled water make up to (1000.000 ml);Marine agar (55.100 g) | |
120654 | CIP Medium 13 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
2940 | positive | growth | 28 | mesophilic |
37982 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 26 | mesophilic |
120654 | positive | growth | 15-30 | |
120654 | no | growth | 5 | psychrophilic |
120654 | no | growth | 37 | mesophilic |
120654 | no | growth | 41 | thermophilic |
120654 | no | growth | 45 | thermophilic |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.996 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
120654 | NaCl | no | growth | 0 % |
120654 | NaCl | no | growth | 2 % |
120654 | NaCl | no | growth | 4 % |
120654 | NaCl | no | growth | 6 % |
120654 | NaCl | no | growth | 8 % |
120654 | NaCl | no | growth | 10 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
120654 | 16947 | citrate | - | carbon source |
120654 | 4853 | esculin | - | hydrolysis |
120654 | 606565 | hippurate | + | hydrolysis |
120654 | 17632 | nitrate | + | reduction |
120654 | 16301 | nitrite | - | reduction |
120654 | 15792 | malonate | - | assimilation |
metabolite production
- @ref: 120654
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
120654 | 15688 | acetoin | - | |
120654 | 17234 | glucose | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | - | 3.1.3.2 |
68382 | alpha-chymotrypsin | + | 3.4.21.1 |
68382 | trypsin | + | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | + | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
120654 | oxidase | + | |
120654 | beta-galactosidase | + | 3.2.1.23 |
120654 | alcohol dehydrogenase | - | 1.1.1.1 |
120654 | gelatinase | +/- | |
120654 | amylase | - | |
120654 | caseinase | - | 3.4.21.50 |
120654 | catalase | + | 1.11.1.6 |
120654 | tween esterase | + | |
120654 | gamma-glutamyltransferase | + | 2.3.2.2 |
120654 | lecithinase | - | |
120654 | lipase | - | |
120654 | lysine decarboxylase | - | 4.1.1.18 |
120654 | ornithine decarboxylase | - | 4.1.1.17 |
120654 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
120654 | protease | - | |
120654 | tryptophan deaminase | - | |
120654 | urease | - | 3.5.1.5 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120654 | - | + | + | + | - | + | + | - | + | + | - | + | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | country | origin.country | continent |
---|---|---|---|---|---|
2940 | seaweed, Enteromorpha linza | Enteromorpha linza | |||
67770 | Seaweed (Enteromorpha linza) | Enteromorpha linza | |||
120654 | Seaweed | Japan | JPN | Asia |
isolation source categories
- Cat1: #Host
- Cat2: #Plants
- Cat3: #Aquatic plant
taxonmaps
- @ref: 69479
- File name: preview.99_3645.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_251;97_274;98_2787;99_3645&stattab=map
- Last taxonomy: Erythrobacter longus
- 16S sequence: L01786
- Sequence Identity:
- Total samples: 151
- soil counts: 1
- aquatic counts: 136
- animal counts: 13
- plant counts: 1
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
2940 | 1 | Risk group (German classification) |
120654 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Erythrobacter longus (ATCC 33941) 16S ribosomal RNA (partial) | M55493 | 261 | ena | 1044 |
20218 | Erythrobacter longus 16S ribosomal RNA | M59062 | 1488 | ena | 1044 |
20218 | Erythrobacter longus 16S rRNA, partial sequence | D12699 | 1314 | ena | 1044 |
20218 | Erythrobacter longus 16S ribosomal RNA | L01786 | 1403 | ena | 1044 |
20218 | Erythrobacter longus strain OCh101 16S ribosomal RNA gene, partial sequence | M96744 | 1412 | ena | 1044 |
2940 | Erythrobacter longus strain DSM 6997 16S ribosomal RNA gene, partial sequence | AF465835 | 1414 | ena | 1044 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Erythrobacter longus strain DSM 6997 | 1044.3 | wgs | patric | 1044 |
66792 | Erythrobacter longus DSM 6997 | 2585427956 | draft | img | 1044 |
67770 | Erythrobacter longus DSM 6997 | GCA_000715015 | contig | ncbi | 1044 |
GC content
@ref | GC-content | method |
---|---|---|
67770 | 60.7 | thermal denaturation, midpoint method (Tm) |
67770 | 57.4 | genome sequence analysis |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 65.593 | no |
flagellated | no | 82.41 | no |
gram-positive | no | 97.704 | no |
anaerobic | no | 99.354 | no |
aerobic | yes | 93.434 | no |
halophile | no | 77.663 | no |
spore-forming | no | 95.012 | no |
thermophile | no | 93.024 | yes |
glucose-util | yes | 82.99 | no |
glucose-ferment | no | 93.036 | no |
External links
@ref: 2940
culture collection no.: DSM 6997, ATCC 33941, IAM 14242, IFO 14126, JCM 6170, NBRC 14126, OCh 101, CECT 5010, CGMCC 1.8459, CIP 104268, KCTC 2829, LMG 3982, LMG 5510, NCIMB 2174
straininfo link
- @ref: 74870
- straininfo: 11116
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Enzymology | 22033765 | Photosynthetic characteristics of marine aerobic anoxygenic phototrophic bacteria Roseobacter and Erythrobacter strains. | Sato-Takabe Y, Hamasaki K, Suzuki K | Arch Microbiol | 10.1007/s00203-011-0761-2 | 2011 | Bacteria, Aerobic/chemistry/growth & development/isolation & purification, Bacteriochlorophyll A/analysis, *Photosynthesis, Photosynthetic Reaction Center Complex Proteins/analysis, Roseobacter/*chemistry/growth & development/isolation & purification, Sphingomonadaceae/*chemistry/growth & development | Phylogeny |
Phylogeny | 22843716 | Erythrobacter jejuensis sp. nov., isolated from seawater. | Yoon BJ, Lee DH, Oh DC | Int J Syst Evol Microbiol | 10.1099/ijs.0.038349-0 | 2012 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/analysis, Water Microbiology | Genetics |
Genetics | 25059862 | Draft Genome Sequences of Two Marine Phototrophic Bacteria, Erythrobacter longus Strain DSM 6997 and Erythrobacter litoralis Strain DSM 8509. | Wang Y, Zhang R, Zheng Q, Jiao N | Genome Announc | 10.1128/genomeA.00677-14 | 2014 | ||
Phylogeny | 34997854 | Erythrobacter rubeus sp. nov., a carotenoid-producing alphaproteobacterium isolated from coastal seawater. | Yoon J, Lee EY, Nam SJ | Arch Microbiol | 10.1007/s00203-021-02736-2 | 2022 | Bacterial Typing Techniques, Carotenoids, DNA, Bacterial/genetics, Fatty Acids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater, Sequence Analysis, DNA, *Sphingomonadaceae/genetics | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
2940 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6997) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-6997 | |||
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 | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
37982 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/16158 | ||||
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) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68382 | Automatically annotated from API zym | |||||
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 | |||
74870 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID11116.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
120654 | Curators of the CIP | Collection of Institut Pasteur (CIP 104268) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104268 |