Name: Parvibaculum lavamentivorans DS-1
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 13867

Type strain:

Species: Parvibaculum lavamentivorans

Strain Designation: DS-1

Culture col. no.: DSM 13023, KCTC 22775, NCIMB 13966

Strain history: <- DSM <- D. Schleheck and K. Denger, Univ. Konstanz

NCBI tax ID(s): 256618 (species)

SI-ID 49388

DSM 13023, NCIMB 13966

Special Collections

Section

Parvibaculum lavamentivorans DS-1 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from activated sludge of industrial sewage plant.

Gram-negative
rod-shaped
aerobe
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Parvibaculaceae*
	Genus	*Parvibaculum*
	Species	**Parvibaculum lavamentivorans**
	Full Scientific Name (LPSN)	Parvibaculum lavamentivorans Schleheck et al. 2004

Information on morphological and physiological properties Morphology

[Ref.: #30169]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %98.828

[Ref.: #30169]	Cell shape	rod-shaped

[Ref.: #30169]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #4875]

Culture medium

TWEEN 80-AGAR (DSMZ Medium 884)

[Ref.: #4875]

Culture medium growth

[Ref.: #4875]

Culture medium link

Medium recipe at MediaDive

[Ref.: #4875]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #4875]			growth	30 °C
[Ref.: #67771]			growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30169]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30169]	acetate ChEBI	+	carbon source
[Ref.: #30169]	ethanol ChEBI	+	carbon source
[Ref.: #30169]	pyruvate ChEBI	+	carbon source
[Ref.: #30169]	succinate ChEBI	+	carbon source
[Ref.: #30169]	tween 20 ChEBI	+	carbon source
[Ref.: #30169]	tween 80 ChEBI	+	carbon source

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #30169]		catalase	+	1.11.1.6
[Ref.: #30169]		cytochrome oxidase	+	1.9.3.1

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #4875]	Sample type/isolated from	activated sludge of industrial sewage plant
[Ref.: #4875]	Geographic location (country and/or sea, region)	Ludwigshafen
[Ref.: #4875]	Country	Germany
[Ref.: #4875]	Country ISO 3 Code	DEU
[Ref.: #4875]	Continent	Europe

[Ref.: #67771]	Sample type/isolated from	From activated sludge of industrial sewage plant
[Ref.: #67771]	Country	Germany
[Ref.: #67771]	Country ISO 3 Code	DEU
[Ref.: #67771]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered	#Industrial	-
#Engineered	#Waste	#Activated sludge
#Engineered	#Waste	#Water treatment plant

What are isolation sources categories?

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #4875]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #4875]	Parvibaculum lavamentivorans 16S ribosomal RNA gene, complete sequence	AY387398	1451	GenBank ENA	402881 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Parvibaculum lavamentivorans DS-1	GCA_000017565	complete	GenBank ENA	402881 tax ID	*
[Ref.: #66792]	Parvibaculum lavamentivorans DS-1	402881.8	complete	PATRIC	402881 tax ID	*
[Ref.: #66792]	Parvibaculum lavamentivorans DS-1	640753040	complete	JGI IMG/M	402881 tax ID	*

[Ref.: #4875]

GC-content

64 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Parvibaculum lavamentivorans DS-1 DS-1 NCBI: GCA_000017565.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	98.828	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	87.375	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	81.132	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	88.489	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	96.707	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	57.014	no

Availability in culture collections External links

[Ref.: #4875]

Culture collection no.

DSM 13023, KCTC 22775, NCIMB 13966

[Ref.: #83043]

SI-ID 49388

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Enzymology	Exploration and structure-based engineering of alkenal double bond reductases catalyzing the CalphaCbeta double bond reduction of coniferaldehyde.	Kamimura N, Watanabe S, Sugimoto K, Senda M, Araki T, Yu HY, Hishiyama S, Kajita S, Senda T, Masai E	N Biotechnol	10.1016/j.nbt.2022.01.007	2022	*
Metabolism	An enzymatic method for determination of azide and cyanide in aqueous phase.	Wan NW, Liu ZQ, Xue F, Zheng YG	J Biotechnol	10.1016/j.jbiotec.2015.09.001	2015	*
Metabolism	An efficient high-throughput screening assay for rapid directed evolution of halohydrin dehalogenase for preparation of beta-substituted alcohols.	Wan NW, Liu ZQ, Xue F, Huang K, Tang LJ, Zheng YG	Appl Microbiol Biotechnol	10.1007/s00253-015-6527-z	2015	*
Genetics	Complete genome sequence of Parvibaculum lavamentivorans type strain (DS-1(T)).	Schleheck D, Weiss M, Pitluck S, Bruce D, Land ML, Han S, Saunders E, Tapia R, Detter C, Brettin T, Han J, Woyke T, Goodwin L, Pennacchio L, Nolan M, Cook AM, Kjelleberg S, Thomas T	Stand Genomic Sci	10.4056/sigs.2215005	2011	*
Phylogeny	Parvibaculum hydrocarboniclasticum sp. nov., a mesophilic, alkane-oxidizing alphaproteobacterium isolated from a deep-sea hydrothermal vent on the East Pacific Rise.	Rosario-Passapera R, Keddis R, Wong R, Lutz RA, Starovoytov V, Vetriani C	Int J Syst Evol Microbiol	10.1099/ijs.0.039594-0	2012	*
Phylogeny	Parvibaculum indicum sp. nov., isolated from deep-sea water.	Lai Q, Wang L, Liu Y, Yuan J, Sun F, Shao Z	Int J Syst Evol Microbiol	10.1099/ijs.0.021899-0	2010	*
Metabolism	Parvibaculum lavamentivorans DS-1T degrades centrally substituted congeners of commercial linear alkylbenzenesulfonate to sulfophenyl carboxylates and sulfophenyl dicarboxylates.	Schleheck D, Knepper TP, Eichhorn P, Cook AM	Appl Environ Microbiol	10.1128/AEM.00632-07	2007	*
Metabolism	Omega-oxygenation of the alkyl sidechain of linear alkylbenzenesulfonate (LAS) surfactant in Parvibaculum lavamentivorans(T).	Schleheck D, Cook AM	Arch Microbiol	10.1007/s00203-005-0002-7	2005	*
Phylogeny	Parvibaculum lavamentivorans gen. nov., sp. nov., a novel heterotroph that initiates catabolism of linear alkylbenzenesulfonate.	Schleheck D, Tindall BJ, Rossello-Mora R, Cook AM	Int J Syst Evol Microbiol	10.1099/ijs.0.03020-0	2004	*
Metabolism	Mineralization of individual congeners of linear alkylbenzenesulfonate by defined pairs of heterotrophic bacteria.	Schleheck D, Knepper TP, Fischer K, Cook AM	Appl Environ Microbiol	10.1128/AEM.70.7.4053-4063.2004	2004	*

References

#4875

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 13023

#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 )

#30169

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26518 (see below)

#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) .

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#83043

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID49388.1 )

#26518

IJSEM 1489 2004 ( DOI 10.1099/ijs.0.03020-0 , PubMed 15388700 )

* These data were automatically processed and therefore are not curated

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Parvibaculum lavamentivorans DS-1 DS-1

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