Archive BacDiveID:10.13145/bacdive18013.20230509.8.1

Strain identifier

BacDive ID: 18013

Type strain:

Species: Thermosediminibacter oceani

Strain Designation: JW/IW-1228P

Strain history: <- J. Wiegel, Univ. Georgia <- Y.-J. Lee; JW/IW-1228P {2003}

NCBI tax ID(s): 555079 (strain), 291990 (species)

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

General

@ref: 6547

BacDive-ID: 18013

DSM-Number: 16646

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, thermophilic

description: Thermosediminibacter oceani JW/IW-1228P is an anaerobe, thermophilic bacterium that was isolated from core sample of deep sea sediment.

NCBI tax id

NCBI tax id	Matching level
291990	species
555079	strain

strain history

@ref: 6547
history: <- J. Wiegel, Univ. Georgia <- Y.-J. Lee; JW/IW-1228P {2003}

doi: 10.13145/bacdive18013.20230509.8.1

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 oceani
full scientific name: Thermosediminibacter oceani Lee et al. 2006

@ref: 6547

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Thermoanaerobacterales

family: Thermosediminibacteraceae

genus: Thermosediminibacter

species: Thermosediminibacter oceani

full scientific name: Thermosediminibacter oceani Lee et al. 2006

strain designation: JW/IW-1228P

type strain: yes

Morphology

multimedia

@ref: 66793
multimedia content: EM_DSM_16646_1.jpg
caption: electron microscopic image
intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@ref: 6547
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: 6547
growth: positive
type: growth
temperature: 68
range: thermophilic

Physiology and metabolism

oxygen tolerance

@ref: 6547
oxygen tolerance: anaerobe

Isolation, sampling and environmental information

isolation

@ref: 6547
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

taxonmaps

@ref: 69479
File name: preview.99_5017.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_499;96_2453;97_2994;98_3751;99_5017&stattab=map
Last taxonomy: Thermosediminibacter oceani subclade
16S sequence: AY703478
Sequence Identity:
Total samples: 700
soil counts: 113
aquatic counts: 198
animal counts: 379
plant counts: 10

Safety information

risk assessment

@ref: 6547
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 6547
description: Thermosediminibacter oceani 16S ribosomal RNA gene, partial sequence
accession: AY703478
length: 1386
database: ena
NCBI tax ID: 291990

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Thermosediminibacter oceani DSM 16646	GCA_000144645	complete	ncbi	555079
66792	Thermosediminibacter oceani DSM 16646	555079.3	complete	patric	555079
66792	Thermosediminibacter oceani JW/IW-1228P, DSM 16646	648028061	complete	img	555079

GC content

@ref: 6547
GC-content: 50
method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
motile	yes	86.173	no
flagellated	no	91.428	no
gram-positive	no	70.547	no
anaerobic	yes	98.984	no
aerobic	no	97.945	yes
halophile	no	88.072	no
spore-forming	yes	57.834	no
thermophile	yes	100	yes
glucose-util	yes	88.281	no
glucose-ferment	yes	54.476	no

External links

@ref: 6547

culture collection no.: DSM 16646, ATCC BAA 1034

straininfo link

@ref: 87000
straininfo: 291138

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
Genetics	21304740	Complete genome sequence of Thermosediminibacter oceani type strain (JW/IW-1228P).	Pitluck S, Yasawong M, Munk C, Nolan M, Lapidus A, Lucas S, Glavina Del Rio T, Tice H, Cheng JF, Bruce D, Detter C, Tapia R, Han C, Goodwin L, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Spring S, Sikorski J, Goker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP	Stand Genomic Sci	10.4056/sigs.1133078	2010

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
6547	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16646)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-16646
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)
66793	Mukherjee et al.		10.1038/nbt.3886	GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life	35: 676-683 2017	28604660
66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg		10.1093/nar/gkaa1025	BRENDA, the ELIXIR core data resource in 2021: new developments and updates	Nucleic Acids Res. 49: D498-D508 2020	33211880
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.		https://microbeatlas.org/	MicrobeAtlas 1.0 beta
87000	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID291138.1	StrainInfo: A central database for resolving microbial strain identifiers