Cite this strain

Advenella mimigardefordensis (DSM 17166, LMG 22922, DPN7)

Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 384

Type strain

Strain Designation DPN7

Culture col. no. DSM 17166 LMG 22922 DPN7

NCBI tax ID(s) 302406

Special Collections DSMZ Literature strains

Links

Name and taxonomic classification

Advenella mimigardefordensis DPN7 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from matured compost after the sieving process from the compost plant Coerde.

Gram-negative motile ovoid-shaped aerobe mesophilic genome sequence 16S sequence Bacteria

SI-ID 133642

LMG22922, DSM 17166

Last LPSN update 2024-12-09 10:43:09

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Alcaligenaceae

Genus Advenella

Species Advenella mimigardefordensis

Full scientific name Advenella mimigardefordensis (Wübbeler et al. 2006) Gibello et al. 2009

Synonyms (1)

Tetrathiobacter mimigardefordensis

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape
31724	negative	1.5-2 µm	1.5 µm	ovoid-shaped
125438	negative
125439	negative

Pigmentation

31724

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
6801	NUTRIENT AGAR (DSMZ Medium 1)		Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
6801	positive	growth	28	mesophilic
31724	positive	growth	15-40
31724	positive	optimum	30-37	mesophilic

Physiology and metabolism

Observation

31724

Observationaggregates in chains

Spore formation

31724

Spore formationno

Enzymes

@ref	Value	Activity	Ec
31724	catalase	+	1.11.1.6
31724	cytochrome oxidase	+	1.9.3.1

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31724	17128 ChEBI	adipate	+	carbon source
31724	22599 ChEBI	arabinose	+	carbon source
31724	16947 ChEBI	citrate	+	carbon source
31724	25115 ChEBI	malate	+	carbon source

Oxygen tolerance

@ref	Oxygen tolerance
31724	aerobe
125439	aerobe

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Biodegradation	#Composting

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
6801	matured compost after the sieving process from the compost plant Coerde	Münster	Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence AY880023 (>99% sequence identity) for Advenella mimigardefordensis from Microbeatlas

Aquatic Samples	111
Soil Samples	227
Animal Samples	194
Plant Samples	108
Total Samples	640

Safety information

Risk assessment

@ref	Biosafety level	Biosafety level comment
6801	1	Risk group (German classification) According to TRBA 466

Sequence information

GC content

6801

GC-content (mol%)55.1

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6801	Advenella mimigardefordensis DPN7 16S ribosomal RNA gene, partial sequence	AY880023	1502		1247726

Genome sequences

@ref	Description	Accession	Assembly level	Database	NCBI tax ID
66792	Advenella mimigardefordensis DPN7	GCA_000521505	complete		1247726
66792	Advenella mimigardefordensis DPN7	1247726.3	complete	PATRIC	1247726
66792	Advenella mimigardefordensis DPN7	1247726.11	plasmid	PATRIC	1247726
66792	Advenella mimigardefordensis DPN7	2548877156	complete	JGI IMG/M	1247726

Genome-based predictions

Predictions

Predictions from Diaspora project based on:
Advenella mimigardefordensis DPN7
PATRIC: 1247726.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	96.40	no
125439	gram_stain	BacteriaNetⓘ	negative	95.40	no
125439	motility	BacteriaNetⓘ	yes	81.50	no
125439	spore_formation	BacteriaNetⓘ	no	84.00	no

Predictions from Diaspora project based on:
Advenella mimigardefordensis DPN7 DPN7
NCBI: GCA_000521505.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.22	yes
125438	anaerobic	anaerobicⓘ	no	99.13	yes
125438	aerobic	aerobicⓘ	yes	89.59	yes
125438	spore-forming	spore-formingⓘ	no	85.51	yes
125438	thermophilic	thermophileⓘ	no	99.00	no
125438	flagellated	motile2+ⓘ	yes	51.20	no

External links

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Reclassification of the members of the genus Tetrathiobacter Ghosh et al. 2005 to the genus Advenella Coenye et al. 2005.	Gibello A, Vela AI, Martin M, Barra-Caracciolo A, Grenni P, Fernandez-Garayzabal JF	Int J Syst Evol Microbiol	10.1099/ijs.0.007443-0	2009
Metabolism	Novel pathway for catabolism of the organic sulfur compound 3,3'-dithiodipropionic acid via 3-mercaptopropionic acid and 3-Sulfinopropionic acid to propionyl-coenzyme A by the aerobic bacterium Tetrathiobacter mimigardefordensis strain DPN7.	Wubbeler JH, Bruland N, Kretschmer K, Steinbuchel A	Appl Environ Microbiol	10.1128/AEM.00422-08	2008
Phylogeny	Advenella alkanexedens sp. nov., an alkane-degrading bacterium isolated from biogas slurry samples.	Wang H, Zhou S, Wang Y, Kong D, Guo X, Zhu J, Dong W, Ruan Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.000811	2015
Phylogeny	Description of Pelistega indica sp. nov., isolated from human gut.	Prakash O, Munot H, Nimonkar Y, Sharma M, Kumbhare S, Shouche YS	Int J Syst Evol Microbiol	10.1099/ijs.0.059782-0	2014
Phylogeny	Tetrathiobacter mimigardefordensis sp. nov., isolated from compost, a betaproteobacterium capable of utilizing the organic disulfide 3,3'-dithiodipropionic acid.	Wubbeler JH, Lutke-Eversloh T, Van Trappen S, Vandamme P, Steinbuchel A	Int J Syst Evol Microbiol	10.1099/ijs.0.64126-0	2006

Straininfo Link

@ref	Straininfo	Culture collections
70064	133642	LMG22922, DSM 17166

Culture collection no.

Culture collection no.
DSM 17166
LMG 22922
DPN7

References

#6801	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17166
#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 )
#31724	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 #28000 (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) .
#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 .
#70064	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-ID133642.1 )
#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 .

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Advenella mimigardefordensis (DSM 17166, LMG 22922, DPN7)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Observation

Spore formation

Enzymes

Metabolite utilization

Oxygen tolerance

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Safety information

Risk assessment

Sequence information

GC content

16S sequences

Genome sequences

Genome-based predictions

Predictions

External links

Literature

Straininfo Link

Culture collection no.

References

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