Spiribacter vilamensis (DSM 21056, JCM 16388, NCIMB 14596)

Name: Spiribacter vilamensis (DSM 21056, JCM 16388, NCIMB 14596)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132270

Type strain

Strain Designation SV525

Culture col. no. DSM 21056 JCM 16388 NCIMB 14596 SV525

NCBI tax ID(s) 531306

Special Collections DSMZ JCM

Links

Spiribacter vilamensis SV525 is a mesophilic prokaryote that was isolated from sediment from a hypersaline lagoon.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 405587

JCM 16388,NCIMB 14596,DSM 21056

@ref 20215

Last LPSN update 2025-12-16 10:01:28

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Chromatiales

Family Ectothiorhodospiraceae

Genus Spiribacter

Species Spiribacter vilamensis

Full scientific name Spiribacter vilamensis (Menes et al. 2016) León et al. 2020

Synonyms (1)

Halopeptonella vilamensis

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	99.2
125438	negative	97.5

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
24059	MEDIUM 514 PLUS ADDITIONAL SALT (DSMZ Medium 514b)		Medium recipe at MediaDive	Name: MEDIUM 514 plus additional salt (DSMZ Medium 514b; with strain-specific modifications) Composition: NaCl 60.0 g/l Agar 17.5 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 (°C)	Range
24059	positive	growth	28	mesophilic
67770	positive	growth	30	mesophilic

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		98.8
125438		92.852

Observation

67770

Observationquinones: Q-8

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Sediment
#Condition	#Saline	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
24059	sediment from a hypersaline lagoon	Jujuy, Laguna Vilama (22° 35' S 66° 55' W at 4600 m above sea level)	Argentina	ARG	Middle and South America	-22.5833	-66.9168 -22.5833/-66.9168
67770	Sediment from a hypersaline lake located at 4,600 m above sea level	Laguna Vilama	Argentina	ARG	Middle and South America

Taxonmaps

69479

Global distribution of 16S sequence EU557314 (>99% sequence identity) for Spiribacter from Microbeatlas

Aquatic Samples	14
Soil Samples	3
Animal Samples
Plant Samples
Total Samples	17

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
24059	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM421741v1 assembly for Spiribacter vilamensis DSM 21056	contig	GCA_004217415	531306.3	2802429687	531306	73.42
66792	ASM762516v1 assembly for Spiribacter vilamensis DSM 21056	scaffold	GCA_007625165	531306.4	8065696380	531306	73.02

Genome browser: GCA_004217415

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24059	Spiribacter vilamensis strain SV525 16S ribosomal RNA gene, partial sequence	EU557314	1437		531306

GC content

@ref	GC-content (mol%)	Method
24059	60.4	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Spiribacter vilamensis DSM 21056
NCBI: GCA_007625165

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.80	no
125439	motility	BacteriaNetⓘ	yes	81.30	no
125439	gram_stain	BacteriaNetⓘ	negative	99.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	81.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Halopeptonella vilamensis DSM 21056
NCBI: GCA_007625165.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.50	no
125438	anaerobic	anaerobicⓘ	no	85.38	no
125438	aerobic	aerobicⓘ	yes	60.56	no
125438	spore-forming	spore-formingⓘ	no	92.85	no
125438	thermophilic	thermophileⓘ	no	92.68	yes
125438	flagellated	motile2+ⓘ	no	73.63	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Metagenomic analysis of soybean endosphere microbiome to reveal signatures of microbes for health and disease.	Chouhan U, Gamad U, Choudhari JK.	J Genet Eng Biotechnol	10.1186/s43141-023-00535-4	2023
Phylogeny	Spiribacter aquaticus Leon et al. 2017 is a later heterotypic synonym of Spiribacter roseus Leon et al. 2016. Reclassification of Halopeptonella vilamensis Menes et al. 2016 as Spiribacter vilamensis comb. nov.	Leon MJ, Galisteo C, Ventosa A, Sanchez-Porro C	Int J Syst Evol Microbiol	10.1099/ijsem.0.004113	2020
Phylogeny	Halopeptonella vilamensis gen. nov, sp. nov., a halophilic strictly aerobic bacterium of the family Ectothiorhodospiraceae.	Menes RJ, Viera CE, Farias ME, Seufferheld MJ	Extremophiles	10.1007/s00792-015-0793-7	2016

References

#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. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#24059	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21056
#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) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Spiribacter vilamensis (DSM 21056, JCM 16388, NCIMB 14596)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Spore formation

Observation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_004217415

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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