Name: Desulfolucanica intricata SR45
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 24301

Type strain:

Species: Desulfolucanica intricata

Strain Designation: SR45

Culture col. no.: DSM 26801, NBRC 109411

Strain history: <- M. Watanabe, Inst. Low Temperature Sci., Hokkaido Univ., Sapporo, Japan; SR45 <- M. Watanabe {2011}

NCBI tax ID(s): 1285191 (species)

SI-ID 404108

DSM 26801

Special Collections

Section

When using BacDive for research please cite our paper

Desulfolucanica intricata SR45 is an anaerobe, spore-forming, thermophilic bacterium that was isolated from freshwater lake sediment.

Gram-negative
motile
rod-shaped
spore-forming
anaerobe
thermophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Bacillota*
	Class	*Clostridia*
	Order	*Eubacteriales*
	Family	*Peptococcaceae*
	Genus	*Desulfolucanica*
	Species	**Desulfolucanica intricata**
	Full Scientific Name (LPSN)	Desulfolucanica intricata corrig. (Watanabe et al. 2013) Watanabe et al. 2021

	Synonym	Desulfotomaculum intricatum
	Synonym	Desulfofarcimen intricatum
	Synonym	Desulfolucianica intricata

Information on morphological and physiological properties Morphology

[Ref.: #31091]	Gram stain	negative

[Ref.: #31091]	Cell length	3.5 µm

[Ref.: #31091]	Cell width	1.25 µm

[Ref.: #31091]	Cell shape	rod-shaped

[Ref.: #31091]	Motility	yes

[Ref.: #20954]

Incubation period

2-3 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #20954]

Culture medium

DESULFOFARCIMEN MEDIUM (DSMZ Medium 124)

[Ref.: #20954]

Culture medium growth

[Ref.: #20954]

Culture medium link

Medium recipe at MediaDive

[Ref.: #20954]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #20954]	growth	45 °C
[Ref.: #31091]	growth	28-58 °C
[Ref.: #31091]	optimum	43.5 °C

	pH	Kind of pH		pH
[Ref.: #31091]			optimum	6.6
[Ref.: #31091]			growth	6.0-7.3

Information on physiology and metabolism Physiology and metabolism

[Ref.: #20954]	Oxygen tolerance	anaerobe
[Ref.: #125439]	Oxygen tolerance	anaerobe Confidence in %99.1

[Ref.: #31091]

Ability of spore formation

yes

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31091]		NaCl		growth	0-1.0	%

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31091]		acetate ChEBI	+	carbon source

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

[Ref.: #20954]	Sample type/isolated from	freshwater lake sediment
[Ref.: #20954]	Geographic location (country and/or sea, region)	Yamanshi Prefecture, Lake Mizugaki
[Ref.: #20954]	Country	Japan
[Ref.: #20954]	Country ISO 3 Code	JPN
[Ref.: #20954]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Lake (large)
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB778017 (>99% sequence identity) for Desulfofarcimen intricatum subclade from Microbeatlas

Aquatic Samples	35
Soil Samples	44
Animal Samples	7
Plant Samples	11
Total Samples	97

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

[Ref.: #20954]

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.: #20954]	Desulfofarcimen intricatum gene for 16S ribosomal RNA, partial sequence, clone: A	AB778017	1408	GenBank ENA	1285191 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Desulfolucanica intricata NBRC 109411	GCA_001592105	contig	GenBank ENA	1285191 tax ID	*
[Ref.: #66792]	Desulfotomaculum intricatum strain NBRC 109411	1285191.3	wgs	PATRIC	1285191 tax ID	*
[Ref.: #66792]	Desulfofarcimen intricatum NBRC 109411	2713896921	draft	JGI IMG/M	1285191 tax ID	*

[Ref.: #20954]	GC-content	41.1 mol%	high performance liquid chromatography (HPLC)
[Ref.: #31091]	GC-content	41.1 mol%

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Desulfotomaculum intricatum strain NBRC 109411 PATRIC: 1285191.3
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	62.337	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	yes	89.28	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	yes	80.334	no
[Ref.: #125438]	aerobic	aerobicⓘ	no	88.89	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	58.743	no
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	58.023	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Desulfolucanica intricata NBRC 109411 NCBI: GCA_001592105
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	anaerobe	99.1
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	positive	66.5
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	56.7
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	yes	72.9

Availability in culture collections External links

[Ref.: #20954]

Culture collection no.

DSM 26801, NBRC 109411

[Ref.: #88234]

SI-ID 404108

References

#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 )

#20954

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26801

#31091

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 #27420 (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 .

#88234

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-ID404108.1 )

#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 .

#27420

IJSEM 3574 2013 ( DOI 10.1099/ijs.0.051854-0 , PubMed 23584284 )

* These data were automatically processed and therefore are not curated

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Desulfotomaculum intricatum strain NBRC 109411

Desulfolucanica intricata NBRC 109411

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