Archive BacDiveID:10.13145/bacdive24301.20230509.8.1

Strain identifier

BacDive ID: 24301

Type strain:

Species: Desulfolucanica intricata

Strain Designation: SR45

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

NCBI tax ID(s): 1285191 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 20954

BacDive-ID: 24301

DSM-Number: 26801

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

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

NCBI tax id

NCBI tax id: 1285191
Matching level: species

strain history

@ref: 20954
history: <- M. Watanabe, Inst. Low Temperature Sci., Hokkaido Univ., Sapporo, Japan; SR45 <- M. Watanabe {2011}

doi: 10.13145/bacdive24301.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/bacillota
domain: Bacteria
phylum: Bacillota
class: Clostridia
order: Eubacteriales
family: Peptococcaceae
genus: Desulfolucanica
species: Desulfolucanica intricata
full scientific name: Desulfolucanica intricata corrig. (Watanabe et al. 2013) Watanabe et al. 2021
synonyms
@ref synonym
20215 Desulfolucianica intricata
20215 Desulfotomaculum intricatum
20215 Desulfofarcimen intricatum

@ref	synonym
20215	Desulfolucianica intricata
20215	Desulfotomaculum intricatum
20215	Desulfofarcimen intricatum

@ref: 20954

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Peptococcaceae

genus: Desulfofarcimen

species: Desulfofarcimen intricatum

full scientific name: Desulfofarcimen intricatum (Watanabe et al. 2013) Watanabe et al. 2018

strain designation: SR45

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell length	cell width	cell shape	motility	confidence
31091	negative	3.5 µm	1.25 µm	rod-shaped	yes
69480	positive					100

colony morphology

@ref: 20954
incubation period: 2-3 days

Culture and growth conditions

culture medium

@ref: 20954
name: DESULFOFARCIMEN MEDIUM (DSMZ Medium 124)
growth: yes
link: https://mediadive.dsmz.de/medium/124
composition: Name: DESULFOFARCIMEN MEDIUM (DSMZ Medium 124) Composition: NaHCO3 4.48654 g/l Na2SO4 2.83151 g/l Na-acetate 1.39581 g/l Na-butyrate 1.39581 g/l NaCl 1.1665 g/l Yeast extract 0.997009 g/l MgCl2 x 6 H2O 0.398804 g/l Na2S x 9 H2O 0.398804 g/l KCl 0.299103 g/l NH4Cl 0.269192 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149551 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l NaOH 0.000498504 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l MnCl2 x 4 H2O 9.97009e-05 g/l Pyridoxine hydrochloride 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l Thiamine HCl 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Folic acid 1.99402e-05 g/l Biotin 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water

culture temp

@ref	growth	type	temperature	range	confidence
20954	positive	growth	45	thermophilic
31091	positive	growth	28-58
31091	positive	optimum	43.5	thermophilic
69480				thermophilic	99.64

culture pH

@ref	ability	type	pH
31091	positive	growth	6.0-7.3
31091	positive	optimum	6.6

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
20954	anaerobe
69480	anaerobe	99.998

spore formation

@ref	spore formation	confidence
31091	yes
69481	yes	100
69480	yes	100

halophily

@ref: 31091
salt: NaCl
growth: positive
tested relation: growth
concentration: 0-1.0 %

metabolite utilization

@ref: 31091
Chebi-ID: 30089
metabolite: acetate
utilization activity: +
kind of utilization tested: carbon source

Isolation, sampling and environmental information

isolation

@ref: 20954
sample type: freshwater lake sediment
geographic location: Yamanshi Prefecture, Lake Mizugaki
country: Japan
origin.country: JPN
continent: Asia

isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Lake (large)
#Environmental	#Aquatic	#Sediment

taxonmaps

@ref: 69479
File name: preview.99_147524.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_287;96_47225;97_60650;98_80610;99_147524&stattab=map
Last taxonomy: Desulfofarcimen intricatum subclade
16S sequence: AB778017
Sequence Identity:
Total samples: 97
soil counts: 44
aquatic counts: 35
animal counts: 7
plant counts: 11

Safety information

risk assessment

@ref: 20954
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 20954
description: Desulfotomaculum intricatum gene for 16S ribosomal RNA, partial sequence, clone: A
accession: AB778017
length: 1408
database: ena
NCBI tax ID: 1285191

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Desulfolucanica intricata NBRC 109411	GCA_001592105	contig	ncbi	1285191
66792	Desulfotomaculum intricatum strain NBRC 109411	1285191.3	wgs	patric	1285191
66792	Desulfofarcimen intricatum NBRC 109411	2713896921	draft	img	1285191

GC content

@ref	GC-content	method
20954	41.1	high performance liquid chromatography (HPLC)
31091	41.1

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	yes	100	no
motile	yes	80.326	no
gram-positive	no	89.089	yes
anaerobic	yes	99.274	yes
aerobic	no	96.155	no
halophile	no	94.032	yes
spore-forming	yes	95.809	yes
thermophile	yes	84.446	yes
glucose-util	yes	76.332	no
flagellated	no	90.418	no
glucose-ferment	no	87.328	no

External links

@ref: 20954

culture collection no.: DSM 26801, NBRC 109411

straininfo link

@ref: 88234
straininfo: 404108

Reference

@id	authors	title	doi/url	catalogue	ID_cross_reference	pubmed
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	10.1099/ijsem.0.004332
20954	Curators of the DSMZ		https://www.dsmz.de/collection/catalogue/details/culture/DSM-26801	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26801)
31091	Barberan A, Caceres Velazquez H, Jones S, Fierer N.	Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information	10.1128/mSphere.00237-17		27420	28776041
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)	https://diaspora-project.de/progress.html#genomes
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	https://microbeatlas.org/
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)	https://diaspora-project.de/progress.html#genomes
69481	Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch	Predictions based on the model GenomeNet Sporulation v. 1	10.21203/rs.3.rs-2527258/v1
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	10.60712/SI-ID404108.1

General

NCBI tax id

strain history

Name and taxonomic classification

LPSN

synonyms

Morphology

cell morphology

colony morphology

Culture and growth conditions

culture medium

culture temp

culture pH

Physiology and metabolism

oxygen tolerance

spore formation

halophily

metabolite utilization

Isolation, sampling and environmental information

isolation

isolation source categories

taxonmaps

Safety information

risk assessment

Sequence information

16S sequences

Genome sequences

GC content

Genome-based predictions

predictions

External links

straininfo link

Reference