Name: Desulfatirhabdium butyrativorans HB1
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 3996

Type strain:

Species: Desulfatirhabdium butyrativorans

Strain Designation: HB1

Culture col. no.: DSM 18734, JCM 14470

Strain history: M. Balk HB1.

NCBI tax ID(s): 1121394 (strain), 340467 (species)

SI-ID 323960

DSM 18734, JCM 14470

Special Collections

Section

Desulfatirhabdium butyrativorans HB1 is an anaerobe, Gram-negative, rod-shaped bacterium that was isolated from upflow anaerobic sludge blanket reactor.

Gram-negative
rod-shaped
anaerobe
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	*Deltaproteobacteria*
	Order	*Desulfobacterales*
	Family	*Desulfobacteraceae*
	Genus	*Desulfatirhabdium*
	Species	**Desulfatirhabdium butyrativorans**
	Full Scientific Name (LPSN)	Desulfatirhabdium butyrativorans Balk et al. 2008

Information on morphological and physiological properties Morphology

[Ref.: #32373]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %95.629

[Ref.: #32373]	Cell length	3.05 µm

[Ref.: #32373]	Cell width	1.15 µm

[Ref.: #32373]	Cell shape	rod-shaped

[Ref.: #7679]

Incubation period

>14 days

[Ref.: #32373]

Pigment production

yes

Multimedia content

[Ref.: #66793]

Caption:

electron microscopic image

[Ref.: #66793]

Intellectual property rights:

[Ref.: #66793]

Caption:

electron microscopic image

[Ref.: #66793]

Intellectual property rights:

[Ref.: #66793]

Caption:

electron microscopic image

[Ref.: #66793]

Intellectual property rights:

[Ref.: #66793]

Caption:

electron microscopic image

[Ref.: #66793]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7679]

Culture medium

DESULFATIRHABDIUM MEDIUM (DSMZ Medium 1086)

[Ref.: #7679]

Culture medium growth

[Ref.: #7679]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7679]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7679]	growth	28 °C
[Ref.: #32373]	growth	15-37 °C
[Ref.: #32373]	optimum	29 °C
[Ref.: #67770]	growth	30 °C

	pH	Kind of pH		pH
[Ref.: #32373]			optimum	7
[Ref.: #32373]			growth	6.5-8

Information on physiology and metabolism Physiology and metabolism

[Ref.: #7679]	Oxygen tolerance	anaerobe
[Ref.: #32373]	Oxygen tolerance	anaerobe

[Ref.: #32373]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32373]	2,3-butanediol ChEBI	+	carbon source
[Ref.: #32373]	4-hydroxybenzoate ChEBI	+	carbon source
[Ref.: #32373]	acetate ChEBI	+	carbon source
[Ref.: #32373]	ethanol ChEBI	+	carbon source
[Ref.: #32373]	formate ChEBI	+	carbon source
[Ref.: #32373]	propionate ChEBI	+	carbon source
[Ref.: #32373]	pyruvate ChEBI	+	carbon source
[Ref.: #32373]	succinate ChEBI	+	carbon source

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

[Ref.: #7679]	Sample type/isolated from	upflow anaerobic sludge blanket (UASB) reactor
[Ref.: #7679]	Country	Netherlands
[Ref.: #7679]	Country ISO 3 Code	NLD
[Ref.: #7679]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Upflow anaerobic sludge blanket (UASB) reactor treating paper-mill wastewater
[Ref.: #67770]	Country	Netherlands
[Ref.: #67770]	Country ISO 3 Code	NLD
[Ref.: #67770]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered	#Biodegradation	#Anaerobic digestor
#Condition	#Anoxic (anaerobic)	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence DQ146482 (>99% sequence identity) for Desulfatirhabdium butyrativorans subclade from Microbeatlas

Aquatic Samples	1057
Soil Samples	132
Animal Samples	19
Plant Samples	9
Total Samples	1217

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

[Ref.: #7679]

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.: #7679]	Desulfatirhabdium butyrativorans strain HB1 16S ribosomal RNA gene, partial sequence	DQ146482	1535	GenBank ENA	340467 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Desulfatirhabdium butyrativorans DSM 18734	GCA_000429925	scaffold	GenBank ENA	1121394 tax ID
[Ref.: #66792]	Desulfatirhabdium butyrativorans DSM 18734	1121394.3	wgs	PATRIC	1121394 tax ID	*
[Ref.: #66792]	Desulfatirhabdium butyrativorans DSM 18734	2524023145	draft	JGI IMG/M	1121394 tax ID	*

[Ref.: #7679]	GC-content	55.1 mol%	high performance liquid chromatography (HPLC)
[Ref.: #32373]	GC-content	55.1 mol%

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Desulfatirhabdium butyrativorans DSM 18734 DSM 18734 NCBI: GCA_000429925.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Desulfatirhabdium butyrativorans DSM 18734 PATRIC: 1121394.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	95.629	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	yes	81.844	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	83.998	yes
[Ref.: #69480]	aerobic	aerobicⓘ	no	86.851	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	76.416	no
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	71.465	no

Availability in culture collections External links

[Ref.: #7679]

Culture collection no.

DSM 18734, JCM 14470

[Ref.: #73501]

SI-ID 323960

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Desulfatirhabdium butyrativorans gen. nov., sp. nov., a butyrate-oxidizing, sulfate-reducing bacterium isolated from an anaerobic bioreactor.	Balk M, Altinbas M, Rijpstra WI, Sinninghe Damste JS, Stams AJ	Int J Syst Evol Microbiol	10.1099/ijs.0.65396-0	2008	*

References

#7679

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18734

#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 )

#32373

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 #28601 (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) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#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 .

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#73501

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-ID323960.1 )

#28601

IJSEM 110 2008 ( DOI 10.1099/ijs.0.65396-0 , PubMed 18175693 )

* These data were automatically processed and therefore are not curated

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Desulfatirhabdium butyrativorans DSM 18734 DSM 18734

Desulfatirhabdium butyrativorans DSM 18734

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