Name: Carboxydibrachium pacificum JM
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 16791

Type strain:

Species: Carboxydibrachium pacificum

Strain Designation: JM

Culture col. no.: DSM 12653, ATCC BAA-271

Strain history: <- T. G. Sokolova, Russian Academy of Sciences, Inst. of Microbiology, Moscow, Russia; JM

NCBI tax ID(s): 109807 (subspecies)

SI-ID 49335

DSM 12653, ATCC BAA-271

Section

Carboxydibrachium pacificum JM is an anaerobe, spore-forming, thermophilic bacterium that was isolated from hydrothermal vent sample.

motile
spore-forming
anaerobe
thermophilic
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	*Bacillota*
	Class	*Clostridia*
	Order	*Thermoanaerobacterales*
	Family	*Thermoanaerobacteraceae*
	Genus	*Carboxydibrachium*
	Species	**Carboxydibrachium pacificum**
	Full Scientific Name (LPSN)	Carboxydibrachium pacificum corrig. Sokolova et al. 2001

	Synonym	Carboxydobrachium pacificum
	Synonym	Caldanaerobacter subterraneus subsp. pacificus

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	positive Confidence in %99.531

[Ref.: #69480]	Motility	yes Confidence in %93.223

Information on culture and growth conditions Culture and growth conditions

[Ref.: #4781]

Culture medium

CARCBOXYDOBRACHIUM PACIFICUM MEDIUM (DSMZ Medium 902)

[Ref.: #4781]

Culture medium growth

[Ref.: #4781]

Culture medium link

Medium recipe at MediaDive

[Ref.: #4781]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #4781]			growth	70 °C

[Ref.: #4781]	Temperature range	thermophilic
[Ref.: #69480]	Temperature range	thermophilic Confidence in %99.999

Information on physiology and metabolism Physiology and metabolism

[Ref.: #4781]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.589

[Ref.: #69480]

Ability of spore formation

yes Confidence in %98.05

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

[Ref.: #4781]	Sample type/isolated from	hydrothermal vent sample
[Ref.: #4781]	Geographic location (country and/or sea, region)	Pacific, Okinawa Trough
[Ref.: #4781]	Country	Japan
[Ref.: #4781]	Country ISO 3 Code	JPN
[Ref.: #4781]	Continent	Asia
[Ref.: #4781]	Geographic location	27.5500°/126.9330°
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Hydrothermal vent
#Condition	#Thermophilic (>45°C)	-

What are isolation sources categories?

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

[Ref.: #4781]

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.: #4781]	Carboxydibrachium pacificum DSM 12653 16S ribosomal RNA gene, partial sequence	AF174484	1486	ENA	391606 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Caldanaerobacter subterraneus subsp. pacificus DSM 12653	GCA_000156275	contig	GenBank	391606 tax ID	*
[Ref.: #66792]	Carboxydibrachium pacificum DSM 12653	391606.3	wgs	PATRIC	391606 tax ID	*
[Ref.: #66792]	Caldanaerobacter subterraneus pacificus JM, DSM 12653	647533123	draft	JGI IMG/M	391606 tax ID	*

[Ref.: #4781]

GC-content

33 mol%

thermal denaturation, midpoint method (Tm)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Carboxydibrachium pacificum DSM 12653 PATRIC: 391606.3
[Ref.: #69481]	spore-forming	no	69	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Carboxydibrachium pacificum DSM 12653 PATRIC: 391606.3
[Ref.: #69480]	gram-positive	no	80.414	no
[Ref.: #69480]	anaerobic	yes	99.111	yes
[Ref.: #69480]	halophile	no	97.905	no
[Ref.: #69480]	spore-forming	yes	67.585	no
[Ref.: #69480]	glucose-util	yes	86.611	no
[Ref.: #69480]	aerobic	no	97.89	yes
[Ref.: #69480]	motile	yes	80.337	no
[Ref.: #69480]	flagellated	no	86.553	no
[Ref.: #69480]	thermophile	yes	99.999	yes
[Ref.: #69480]	glucose-ferment	yes	52.588	no

Availability in culture collections External links

[Ref.: #4781]

Culture collection no.

DSM 12653, ATCC BAA-271

[Ref.: #85807]

SI-ID 49335

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Isolation from oil reservoirs of novel thermophilic anaerobes phylogenetically related to Thermoanaerobacter subterraneus: reassignment of T. subterraneus, Thermoanaerobacter yonseiensis, Thermoanaerobacter tengcongensis and Carboxydibrachium pacificum to Caldanaerobacter subterraneus gen. nov., sp. nov., comb. nov. as four novel subspecies.	Fardeau ML, Salinas MB, L'Haridon S, Jeanthon C, Verhe F, Cayol JL, Patel BKC, Garcia JL, Ollivier B	Int J Syst Evol Microbiol	10.1099/ijs.0.02711-0	2004	*

References

#4781

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 12653

#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 )

#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) .

#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 )

#85807

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-ID49335.1 )

* These data were automatically processed and therefore are not curated

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Carboxydibrachium pacificum DSM 12653

Carboxydibrachium pacificum DSM 12653

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