Archive BacDiveID:10.13145/bacdive22908.20230509.8.1

Strain identifier

BacDive ID: 22908

Type strain:

Species: Agarivorans gilvus

Strain Designation: WH0801

Strain history: <- NRRL <- Z.-J. Du, State Key Lab. Microbial Technology, Shandong University

NCBI tax ID(s): 680279 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 19113

BacDive-ID: 22908

DSM-Number: 26780

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, motile, rod-shaped

description: Agarivorans gilvus WH0801 is an aerobe, Gram-negative, motile bacterium that was isolated from surface of seaweed.

NCBI tax id

NCBI tax id: 680279
Matching level: species

strain history

@ref: 19113
history: <- NRRL <- Z.-J. Du, State Key Lab. Microbial Technology, Shandong University

doi: 10.13145/bacdive22908.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Gammaproteobacteria
order: Alteromonadales
family: Alteromonadaceae
genus: Agarivorans
species: Agarivorans gilvus
full scientific name: Agarivorans gilvus Du et al. 2011

@ref: 19113

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Alteromonadaceae

genus: Agarivorans

species: Agarivorans gilvus

full scientific name: Agarivorans gilvus Du et al. 2011

strain designation: WH0801

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell shape	motility	confidence
29739	negative	rod-shaped	yes
69480			yes	98.004
69480	negative			99.992

pigmentation

@ref: 29739
production: yes

multimedia

@ref: 19113
multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_26780.jpg
intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@ref: 19113
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
29739	positive	growth	10-45
29739	positive	optimum	28-32	mesophilic

culture pH

@ref	ability	type	pH	PH range
29739	positive	growth	6.5-9.5	alkaliphile
29739	positive	optimum	8.4-8.6

Physiology and metabolism

oxygen tolerance

@ref: 29739
oxygen tolerance: aerobe

spore formation

@ref	spore formation	confidence
29739	no
69481	no	100
69480	no	99.985

halophily

@ref: 29739
salt: NaCl
growth: positive
tested relation: growth
concentration: 3 %

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
29739	22599	arabinose	+	carbon source
29739	28260	galactose	+	carbon source
29739	28087	glycogen	+	carbon source
29739	17716	lactose	+	carbon source
29739	37684	mannose	+	carbon source
29739	17814	salicin	+	carbon source
29739	18222	xylose	+	carbon source
29739	4853	esculin	+	hydrolysis

enzymes

@ref	value	activity	ec
29739	alkaline phosphatase	+	3.1.3.1
29739	catalase	+	1.11.1.6
29739	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

isolation

@ref: 19113
sample type: surface of seaweed
geographic location: shallow coastal region, Weihai
country: China
origin.country: CHN
continent: Asia

isolation source categories

Cat1	Cat2	Cat3
#Host	#Algae
#Host	#Plants	#Aquatic plant
#Host Body-Site	#Plant	#Leaf (Phyllosphere)

taxonmaps

@ref: 69479
File name: preview.99_2956.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_361;96_1556;97_1856;98_2281;99_2956&stattab=map
Last taxonomy: Agarivorans gilvus subclade
16S sequence: GQ200591
Sequence Identity:
Total samples: 180
soil counts: 3
aquatic counts: 154
animal counts: 20
plant counts: 3

Safety information

risk assessment

@ref: 19113
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 19113
description: Agarivorans gilvus strain WH0801 16S ribosomal RNA gene, partial sequence
accession: GQ200591
length: 1455
database: ena
NCBI tax ID: 680279

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Agarivorans gilvus CGMCC 1.10131	GCA_014636215	contig	ncbi	680279
66792	Agarivorans gilvus WH0801	GCA_001420915	complete	ncbi	680279
66792	Agarivorans gilvus strain CGMCC 1.10131	680279.10	wgs	patric	680279

GC content

@ref: 29739
GC-content: 48.5

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	100	no
flagellated	yes	89.948	no
gram-positive	no	98.641	yes
anaerobic	no	95.313	yes
aerobic	yes	80.24	yes
halophile	yes	78.784	no
spore-forming	no	95.829	no
thermophile	no	99.375	yes
glucose-util	yes	87	no
motile	yes	90.853	yes
glucose-ferment	yes	79.736	no

External links

@ref: 19113

culture collection no.: DSM 26780, CGMCC 1.10131, NRRL B-59247

straininfo link

@ref: 87156
straininfo: 398825

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	20363930	Agarivorans gilvus sp. nov. isolated from seaweed.	Du ZJ, Lv GQ, Rooney AP, Miao TT, Xu QQ, Chen GJ	Int J Syst Evol Microbiol	10.1099/ijs.0.019810-0	2010	Alteromonadaceae/classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Glycoside Hydrolases/metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Seaweed/*microbiology, Sequence Analysis, DNA	Genetics
Enzymology	24395600	Gene cloning, expression and characterisation of a new beta-agarase, AgWH50C, producing neoagarobiose from Agarivorans gilvus WH0801.	Liu N, Mao X, Yang M, Mu B, Wei D	World J Microbiol Biotechnol	10.1007/s11274-013-1591-y	2014	Alteromonadaceae/chemistry/enzymology/genetics, Amino Acid Sequence, Bacterial Proteins/chemistry/genetics/metabolism, Cloning, Molecular, Disaccharides/metabolism, Enzyme Stability, Gene Expression, Glycoside Hydrolases/*chemistry/genetics/metabolism, Hydrogen-Ion Concentration, Kinetics, Molecular Sequence Data, Sequence Alignment	Metabolism
Enzymology	24642364	Cloning and characterisation of a novel neoagarotetraose-forming-beta-agarase, AgWH50A from Agarivorans gilvus WH0801.	Liu N, Mao X, Du Z, Mu B, Wei D	Carbohydr Res	10.1016/j.carres.2014.02.019	2014	Alteromonadaceae/chemistry/enzymology, Amino Acid Sequence, Bacterial Proteins/chemistry/genetics, Cloning, Molecular, Escherichia coli/enzymology/genetics, Galactosides/chemistry, Glycoside Hydrolases/chemistry/genetics, Hydrogen-Ion Concentration, Hydrolysis, Kinetics, Molecular Sequence Data, Molecular Weight, Oligosaccharides/chemistry, Open Reading Frames, Phylogeny, Protein Sorting Signals, Recombinant Proteins/chemistry/genetics, Sepharose/chemistry	Genetics
Enzymology	25676340	Molecular cloning and expression of a new alpha-neoagarobiose hydrolase from Agarivorans gilvus WH0801 and enzymatic production of 3,6-anhydro-l-galactose.	Liu N, Yang M, Mao X, Mu B, Wei D	Biotechnol Appl Biochem	10.1002/bab.1363	2015	Alteromonadaceae/enzymology, Cloning, Molecular, Galactose/analogs & derivatives/biosynthesis/chemistry/isolation & purification, Glycoside Hydrolases/genetics/*metabolism	Biotechnology
Genetics	26689482	Complete genome sequence of Agarivorans gilvus WH0801(T), an agarase-producing bacterium isolated from seaweed.	Zhang P, Rui J, Du Z, Xue C, Li X, Mao X	J Biotechnol	10.1016/j.jbiotec.2015.12.007	2015	Agar/metabolism, Alteromonadaceae/genetics/isolation & purification/metabolism, Base Composition, Genome Size, Genome, Bacterial, Glycoside Hydrolases/genetics/metabolism, Seaweed/*microbiology	Metabolism
Enzymology	28817933	Biochemical Characterization and Substrate Degradation Mode of a Novel Exotype beta-Agarase from Agarivorans gilvus WH0801.	Liang Y, Ma X, Zhang L, Li F, Liu Z, Mao X	J Agric Food Chem	10.1021/acs.jafc.7b01533	2017	Alteromonadaceae/chemistry/enzymology/genetics, Bacterial Proteins/chemistry/genetics/metabolism, Enzyme Stability, Glycoside Hydrolases/chemistry/genetics/metabolism, Kinetics, Protein Domains, Sepharose/chemistry/metabolism, Substrate Specificity	Metabolism
Metabolism	29682702	A novel agaro-oligosaccharide-lytic beta-galactosidase from Agarivorans gilvus WH0801.	Yang X, Liu Z, Jiang C, Sun J, Xue C, Mao X	Appl Microbiol Biotechnol	10.1007/s00253-018-8999-0	2018	Alteromonadaceae/enzymology, Galactose/metabolism, Glycoside Hydrolases, Industrial Microbiology, Oligosaccharides/metabolism, Rhodophyta/metabolism, beta-Galactosidase/metabolism	Enzymology
Metabolism	30523371	Structure-based design of agarase AgWH50C from Agarivorans gilvus WH0801 to enhance thermostability.	Zhang P, Zhang J, Zhang L, Sun J, Li Y, Wu L, Zhou J, Xue C, Mao X	Appl Microbiol Biotechnol	10.1007/s00253-018-9540-1	2018	Alteromonadaceae/enzymology/genetics/metabolism, Bacterial Proteins/metabolism, Crystallography, X-Ray, Disaccharides/biosynthesis, Glycoside Hydrolases/genetics/metabolism, Hot Temperature, Mutagenesis, Mutation/genetics, Protein Structure, Secondary	Stress
Metabolism	30788710	Molecular Cloning and Characterization of a Novel Cold-Adapted Alkaline 1,3-alpha-3,6-Anhydro-L-galactosidase, Ahg558, from Gayadomonas joobiniege G7.	Asghar S, Lee CR, Chi WJ, Kang DK, Hong SK	Appl Biochem Biotechnol	10.1007/s12010-019-02963-w	2019	Chromatography, Thin Layer, Cloning, Molecular, Disaccharides/metabolism, Galactosidases/*metabolism, Galactosides/metabolism, Hydrogen-Ion Concentration, Mass Spectrometry, Oligosaccharides/metabolism	Enzymology

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed
19113	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26780)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-26780
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
29739	Barberan A, Caceres Velazquez H, Jones S, Fierer N.		10.1128/mSphere.00237-17	Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information	26121	28776041
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)
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
87156	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID398825.1	StrainInfo: A central database for resolving microbial strain identifiers