Archive BacDiveID:10.13145/bacdive18110.20230509.8.1

Strain identifier

BacDive ID: 18110

Type strain:

Species: Exiguobacterium aestuarii

Strain Designation: TF-16

Strain history: <- IG Kim, KRIBB

NCBI tax ID(s): 273527 (species)

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

General

@ref: 6354

BacDive-ID: 18110

DSM-Number: 16306

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

description: Exiguobacterium aestuarii TF-16 is an aerobe, mesophilic, motile bacterium that was isolated from tidal flat.

NCBI tax id

NCBI tax id: 273527
Matching level: species

strain history

@ref	history
6354	<- J.-H. Yoon; TF-16
67771	<- IG Kim, KRIBB

doi: 10.13145/bacdive18110.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/bacillota
domain: Bacteria
phylum: Bacillota
class: Bacilli
order: Caryophanales
family: Bacillaceae
genus: Exiguobacterium
species: Exiguobacterium aestuarii
full scientific name: Exiguobacterium aestuarii Kim et al. 2005

@ref: 6354

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacilli, not assigned to family

genus: Exiguobacterium

species: Exiguobacterium aestuarii

full scientific name: Exiguobacterium aestuarii Kim et al. 2005

strain designation: TF-16

type strain: yes

Morphology

cell morphology

@ref	cell shape	motility	flagellum arrangement	gram stain
67771	rod-shaped	yes	peritrichous
67771	coccus-shaped
67771				variable

Culture and growth conditions

culture medium

@ref: 6354
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
6354	positive	growth	28	mesophilic
60657	positive	growth	30	mesophilic
67771	positive	growth	30-37	mesophilic

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance
60657	aerobe
67771	facultative anaerobe

murein

@ref: 6354
murein short key: A11.01
type: A3alpha L-Lys-Gly

observation

@ref: 67771
observation: quinones: MK-7

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
6354	tidal flat	Yellow Sea, Daepo Beach	Republic of Korea	KOR	Asia
60657	Tidal flat	Yellow Sea,Daepo Beach	Republic of Korea	KOR	Asia
67771	From tidal flat; Daepo Beach	Yellow Sea, near Mokpo City	Republic of Korea	KOR	Asia

isolation source categories

Cat1: #Environmental
Cat2: #Terrestrial
Cat3: #Tidal flat

taxonmaps

@ref: 69479
File name: preview.99_2494.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_130;96_715;97_837;98_973;99_2494&stattab=map
Last taxonomy: Exiguobacterium
16S sequence: AY594264
Sequence Identity:
Total samples: 1790
soil counts: 61
aquatic counts: 453
animal counts: 1235
plant counts: 41

Safety information

risk assessment

@ref: 6354
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 6354
description: Exiguobacterium aestuarii strain TF-16 16S ribosomal RNA gene, partial sequence
accession: AY594264
length: 1517
database: ena
NCBI tax ID: 273527

Genome sequences

@ref: 66792
description: Exiguobacterium aestuarii TF_16
accession: GCA_025234735
assembly level: contig
database: ncbi
NCBI tax ID: 273527

GC content

@ref: 6354
GC-content: 48.6

Genome-based predictions

predictions

trait	prediction	confidence	training_data
motile	yes	91.304	yes
flagellated	yes	75.924	no
gram-positive	yes	86.648	yes
anaerobic	no	99.002	yes
aerobic	yes	61.894	no
halophile	yes	78.342	no
spore-forming	no	73.264	no
glucose-ferment	no	79.7	no
thermophile	no	99.743	yes
glucose-util	yes	91.361	no

External links

@ref: 6354

culture collection no.: DSM 16306, KCTC 19035, CCUG 55590, CIP 108732, DSM 10306

straininfo link

@ref: 87098
straininfo: 48804

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	15774680	Exiguobacterium aestuarii sp. nov. and Exiguobacterium marinum sp. nov., isolated from a tidal flat of the Yellow Sea in Korea.	Kim IG, Lee MH, Jung SY, Song JJ, Oh TK, Yoon JH	Int J Syst Evol Microbiol	10.1099/ijs.0.63308-0	2005	Bacillaceae/chemistry/classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Geologic Sediments/microbiology, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA	Genetics
Phylogeny	17267965	Exiguobacterium profundum sp. nov., a moderately thermophilic, lactic acid-producing bacterium isolated from a deep-sea hydrothermal vent.	Crapart S, Fardeau ML, Cayol JL, Thomas P, Sery C, Ollivier B, Combet-Blanc Y	Int J Syst Evol Microbiol	10.1099/ijs.0.64639-0	2007	Anaerobiosis, Bacillaceae/classification/cytology/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Carbohydrate Metabolism, Catalase/analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Genes, rRNA, Hot Springs/microbiology, Hydrogen-Ion Concentration, Lactic Acid/metabolism, Molecular Sequence Data, Nitrates/metabolism, Nitrites/metabolism, Oxidation-Reduction, Oxidoreductases/analysis, Pacific Ocean, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sodium Chloride, Spores, Bacterial, Temperature	Metabolism
Phylogeny	23229437	Exiguobacterium himgiriensis sp. nov. a novel member of the genus Exiguobacterium, isolated from the Indian Himalayas.	Singh NK, Raichand R, Kaur I, Kaur C, Pareek S, Mayilraj S	Antonie Van Leeuwenhoek	10.1007/s10482-012-9861-5	2012	Bacillales/classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, India, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Pigments, Biological/metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology	Genetics

Reference

@id	authors	catalogue	doi/url	title
6354	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16306)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-16306
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
60657	Curators of the CCUG	Culture Collection University of Gothenburg (CCUG) (CCUG 55590)	https://www.ccug.se/strain?id=55590
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)
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
87098	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID48804.1	StrainInfo: A central database for resolving microbial strain identifiers