Archive BacDiveID:10.13145/bacdive1647.20230509.8.1

Strain identifier

BacDive ID: 1647

Type strain:

Species: Bdellovibrio bacteriovorus

Strain Designation: Bd. 100, HD 100

Strain history: <- ICPB <- H. Stolp, HD 100

NCBI tax ID(s): 264462 (strain), 959 (species)

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

General

@ref: 12720

BacDive-ID: 1647

DSM-Number: 50701

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative

description: Bdellovibrio bacteriovorus Bd. 100 is a mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

NCBI tax id	Matching level
959	species
264462	strain

strain history

@ref: 12720
history: <- ICPB <- H. Stolp, HD 100

doi: 10.13145/bacdive1647.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Oligoflexia
order: Bdellovibrionales
family: Pseudobdellovibrionaceae
genus: Bdellovibrio
species: Bdellovibrio bacteriovorus
full scientific name: Bdellovibrio bacteriovorus Stolp and Starr 1963 (Approved Lists 1980)

@ref: 12720

domain: Bacteria

phylum: Proteobacteria

class: Oligoflexia

order: Bdellovibrionales

family: Bdellovibrionaceae

genus: Bdellovibrio

species: Bdellovibrio bacteriovorus

full scientific name: Bdellovibrio bacteriovorus Stolp and Starr 1963

strain designation: Bd. 100, HD 100

type strain: yes

Morphology

cell morphology

@ref: 69480
gram stain: negative
confidence: 100

Culture and growth conditions

culture medium

@ref	name	growth	link	composition
12720	PEREDIBACTER (DN) MEDIUM (DSMZ Medium 1012)	yes	https://mediadive.dsmz.de/medium/1012	Name: PEREDIBACTER (DN) MEDIUM (DSMZ Medium 1012) Composition: Nutrient broth 0.8 g/l MgCl2 x 6 H2O 0.6 g/l Casamino acids 0.5 g/l CaCl2 x 2 H2O 0.3 g/l Yeast extract 0.1 g/l Distilled water
12720	BDELLOVIBRIO MEDIUM (DSMZ Medium 257)	yes	https://mediadive.dsmz.de/medium/257	Name: BDELLOVIBRIO (YP) MEDIUM (DSMZ Medium 257) Composition: Yeast extract 3.0 g/l Peptone 0.6 g/l Tris-HCl buffer

culture temp

@ref: 12720
growth: positive
type: growth
temperature: 30
range: mesophilic

Physiology and metabolism

spore formation

@ref	spore formation	confidence
69481	no	100
69480	no	99.999

Isolation, sampling and environmental information

isolation

@ref: 12720
sample type: soil
country: USA
origin.country: USA
continent: North America

isolation source categories

Cat1: #Environmental
Cat2: #Terrestrial
Cat3: #Soil

taxonmaps

@ref: 69479
File name: preview.99_5567.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_271;96_2688;97_3301;98_4155;99_5567&stattab=map
Last taxonomy: Bdellovibrio bacteriovorus subclade
16S sequence: AJ292759
Sequence Identity:
Total samples: 2189
soil counts: 402
aquatic counts: 1150
animal counts: 411
plant counts: 226

Safety information

risk assessment

@ref: 12720
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref	description	accession	length	database	NCBI tax ID
20218	Bdellovibrio bacteriovorus 16S rRNA gene, partial cds	M61241	716	ena	959
12720	Bdellovibrio bacteriovorus partial 16S rRNA gene, strain HD 100, DSM 50701	AJ292759	1334	ena	264462

Genome sequences

@ref: 66792
description: Bdellovibrio bacteriovorus HD100
accession: 264462.9
assembly level: complete
database: patric
NCBI tax ID: 264462

GC content

@ref: 12720
GC-content: 50
method: sequence analysis

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	100	no
motile	yes	84.135	no
gram-positive	no	98.501	no
anaerobic	no	94.134	no
aerobic	yes	69.647	no
halophile	no	81.985	no
spore-forming	no	89.868	no
glucose-util	yes	68.685	no
flagellated	no	64.725	no
thermophile	no	97.708	yes
glucose-ferment	no	88.839	no

External links

@ref: 12720

culture collection no.: DSM 50701, ATCC 15356, ICPB 3268, NCIMB 9529

straininfo link

@ref: 71294
straininfo: 36348

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Genetics	15090518	Bdellovibrio bacteriovorus strains produce a novel major outer membrane protein during predacious growth in the periplasm of prey bacteria.	Beck S, Schwudke D, Strauch E, Appel B, Linscheid M	J Bacteriol	10.1128/JB.186.9.2766-2773.2004	2004	Amino Acid Sequence, Bacterial Outer Membrane Proteins/biosynthesis/chemistry, Bdellovibrio/growth & development/metabolism, Mass Spectrometry, Molecular Sequence Data, Periplasm/*microbiology, Protein Structure, Secondary	Metabolism
Proteome	21984111	Bacterial predators possess unique membrane lipid structures.	Muller FD, Beck S, Strauch E, Linscheid MW	Lipids	10.1007/s11745-011-3614-5	2011	Antibiosis/physiology, Bdellovibrio/chemistry, Cell Wall/chemistry, Chromatography, High Pressure Liquid, Chromatography, Thin Layer, Deltaproteobacteria/chemistry, Glutamates/metabolism, Glycerophospholipids/analysis, Membrane Lipids/analysis, Phosphatidylethanolamines/analysis, Sphingolipids/analysis, Tandem Mass Spectrometry, Threonine/analogs & derivatives/analysis	Metabolism
	23916156	Assessing the effects of bacterial predation on membrane biofouling.	Kim EH, Dwidar M, Mitchell RJ, Kwon YN	Water Res	10.1016/j.watres.2013.07.023	2013	Bdellovibrio/physiology, Biofouling, Escherichia coli/physiology, Filtration, Membranes, Artificial, Temperature
	24272279	Shedding light on microbial predator-prey population dynamics using a quantitative bioluminescence assay.	Im H, Kim D, Ghim CM, Mitchell RJ	Microb Ecol	10.1007/s00248-013-0323-z	2013	Bdellovibrio/physiology, Escherichia coli/genetics, Fluorescence, Food Chain, Genes, Reporter, Luciferases/genetics, Luminescent Measurements, Microscopy, Fluorescence, Plasmids/genetics, Population Dynamics, Transformation, Bacterial

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
12720	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 50701)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-50701
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
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
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
71294	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID36348.1	StrainInfo: A central database for resolving microbial strain identifiers