Archive BacDiveID:10.13145/bacdive18014.20230509.8.1

Strain identifier

BacDive ID: 18014

Type strain:

Species: Thermosediminibacter litoriperuensis

Strain Designation: JW/YJL-1230-7/2

Strain history: <- J. Wiegel, Univ. of Georgia, Athens, USA <- Y.-J. Lee; JW/YJL-1230-7/2 {2003}

NCBI tax ID(s): 1123379 (strain), 291989 (species)

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

General

@ref: 6548

BacDive-ID: 18014

DSM-Number: 16647

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, thermophilic, motile

description: Thermosediminibacter litoriperuensis JW/YJL-1230-7/2 is an anaerobe, spore-forming, thermophilic bacterium that was isolated from core sample of deep sea sediment.

NCBI tax id

NCBI tax id	Matching level
1123379	strain
291989	species

strain history

@ref: 6548
history: <- J. Wiegel, Univ. of Georgia, Athens, USA <- Y.-J. Lee; JW/YJL-1230-7/2 {2003}

doi: 10.13145/bacdive18014.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/bacillota
domain: Bacteria
phylum: Bacillota
class: Clostridia
order: Thermosediminibacterales
family: Thermosediminibacteraceae
genus: Thermosediminibacter
species: Thermosediminibacter litoriperuensis
full scientific name: Thermosediminibacter litoriperuensis Lee et al. 2006

@ref: 6548

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Thermoanaerobacterales

family: Thermosediminibacteraceae

genus: Thermosediminibacter

species: Thermosediminibacter litoriperuensis

full scientific name: Thermosediminibacter litoriperuensis Lee et al. 2006

strain designation: JW/YJL-1230-7/2

type strain: yes

Morphology

cell morphology

@ref	motility	confidence	gram stain
69480	yes	91.041
69480		96.167	positive

Culture and growth conditions

culture medium

@ref: 6548
name: THERMOTOGA ELFII MEDIUM (DSMZ Medium 664)
growth: yes
link: https://mediadive.dsmz.de/medium/664
composition: Name: PSEUDOTHERMOTOGA ELFII MEDIUM (DSMZ Medium 664) Composition: Na2S2O3 x 5 H2O 4.9505 g/l Trypticase peptone 4.9505 g/l Yeast extract 4.9505 g/l D-Glucose 3.9604 g/l Na2CO3 1.48515 g/l NH4Cl 0.990099 g/l L-Cysteine HCl x H2O 0.49505 g/l Na2S x 9 H2O 0.49505 g/l Na-acetate 0.49505 g/l K2HPO4 0.29703 g/l KH2PO4 0.29703 g/l MgCl2 x 6 H2O 0.19802 g/l KCl 0.0990099 g/l MgSO4 x 7 H2O 0.029703 g/l Nitrilotriacetic acid 0.0148515 g/l NaCl 0.00990099 g/l MnSO4 x H2O 0.00495049 g/l ZnSO4 x 7 H2O 0.00178218 g/l CoSO4 x 7 H2O 0.00178218 g/l FeSO4 x 7 H2O 0.000990099 g/l CaCl2 x 2 H2O 0.000990099 g/l Sodium resazurin 0.00049505 g/l NiCl2 x 6 H2O 0.00029703 g/l AlK(SO4)2 x 12 H2O 0.00019802 g/l Na2MoO4 x 2 H2O 9.90099e-05 g/l H3BO3 9.90099e-05 g/l CuSO4 x 5 H2O 9.90099e-05 g/l Na2WO4 x 2 H2O 3.9604e-06 g/l Na2SeO3 x 5 H2O 2.9703e-06 g/l Distilled water

culture temp

@ref	growth	type	temperature	range	confidence
6548	positive	growth	64	thermophilic
69480				thermophilic	100

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
6548	anaerobe
69480	anaerobe	100

spore formation

@ref: 69480
spore formation: yes
confidence: 98.047

Isolation, sampling and environmental information

isolation

@ref: 6548
sample type: core sample of deep sea sediment
geographic location: Peru Margin
country: Peru
origin.country: PER
continent: Middle and South America

isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Terrestrial	#Core sample
#Environmental	#Terrestrial	#Sediment

Safety information

risk assessment

@ref: 6548
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 6548
description: Thermosediminibacter litoriperuensis strain JW/YJL-1230-2 16S ribosomal RNA gene, partial sequence
accession: AY703479
length: 1402
database: ena
NCBI tax ID: 291989

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Thermosediminibacter litoriperuensis DSM 16647	GCA_008124715	scaffold	ncbi	291989
66792	Thermosediminibacter litoriperuensis strain DSM 16647	291989.3	wgs	patric	291989
66792	Thermosediminibacter litoriperuensis DSM 16647	2599185220	draft	img	291989

GC content

@ref: 6548
GC-content: 50
method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	yes	61	no
motile	yes	89.57	no
flagellated	no	89.849	no
gram-positive	no	71.908	no
anaerobic	yes	99.2	no
aerobic	no	98.578	yes
halophile	no	85.042	no
spore-forming	yes	52.437	no
glucose-util	yes	89.056	no
thermophile	yes	100	no
glucose-ferment	yes	56.735	no

External links

@ref: 6548

culture collection no.: DSM 16647, ATCC BAA 1035

straininfo link

@ref: 87001
straininfo: 201404

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	15965715	Thermosediminibacter oceani gen. nov., sp. nov. and Thermosediminibacter litoriperuensis sp. nov., new anaerobic thermophilic bacteria isolated from Peru Margin.	Lee YJ, Wagner ID, Brice ME, Kevbrin VV, Mills GL, Romanek CS, Wiegel J	Extremophiles	10.1007/s00792-005-0453-4	2005	Anaerobiosis, DNA, Bacterial/genetics, Electron Transport, Fatty Acids/analysis/chemistry, Microscopy, Electron, Peru, Phospholipids/chemistry/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Substrate Specificity, Thermoanaerobacter/classification/cytology/genetics/isolation & purification	Metabolism
Phylogeny	19305944	Thermovorax subterraneus, gen. nov., sp. nov., a thermophilic hydrogen-producing bacterium isolated from geothermally active underground mine.	Makinen AE, Kaksonen AH, Puhakka JA	Extremophiles	10.1007/s00792-009-0235-5	2009	Bacteria/classification/genetics/isolation & purification/metabolism, Base Sequence, DNA Primers, Genes, Bacterial, Hydrogen/metabolism, *Mining, Phylogeny, RNA, Ribosomal, 16S/genetics, Spectrophotometry, Ultraviolet	Metabolism
Phylogeny	19625440	Caldanaerovirga acetigignens gen. nov., sp. nov., an anaerobic xylanolytic, alkalithermophilic bacterium isolated from Trego Hot Spring, Nevada, USA.	Wagner ID, Ahmed S, Zhao W, Zhang CL, Romanek CS, Rohde M, Wiegel J	Int J Syst Evol Microbiol	10.1099/ijs.0.005207-0	2009	Alkalies/metabolism, Anaerobiosis, Bacteria/chemistry/genetics/isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Hot Springs/microbiology, Hot Temperature, Molecular Sequence Data, Nevada, Phylogeny, RNA, Ribosomal, 16S/genetics, Xylose/*metabolism	Metabolism

Reference

@id	authors	catalogue	doi/url	title
6548	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16647)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-16647
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	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		https://diaspora-project.de/progress.html#genomes	Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
87001	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID201404.1	StrainInfo: A central database for resolving microbial strain identifiers