Archive BacDiveID:10.13145/bacdive17084.20230509.8.1

Strain identifier

BacDive ID: 17084

Type strain:

Species: Thiothrix lacustris

Strain Designation: BL

Strain history: <- G. A. Dubinina, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; BL <- M. Grabovich et al., Dept. Biology, Univ. Voronezh, Russia

NCBI tax ID(s): 1123401 (strain), 525917 (species)

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

General

@ref: 15526

BacDive-ID: 17084

DSM-Number: 21227

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped

description: Thiothrix lacustris BL is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from shallow site of a low-temperature carstic lake.

NCBI tax id

NCBI tax id	Matching level
525917	species
1123401	strain

strain history

@ref: 15526
history: <- G. A. Dubinina, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; BL <- M. Grabovich et al., Dept. Biology, Univ. Voronezh, Russia

doi: 10.13145/bacdive17084.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Gammaproteobacteria
order: Beggiatoales
family: Leucotrichaceae
genus: Thiothrix
species: Thiothrix lacustris
full scientific name: Thiothrix lacustris Chernousova et al. 2009

@ref: 15526

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Thiotrichales

family: Thiotrichaceae

genus: Thiothrix

species: Thiothrix lacustris

full scientific name: Thiothrix lacustris Chernousova et al. 2009

strain designation: BL

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell length	cell width	cell shape	motility	confidence
29249	negative	5.35 µm	1.6 µm	rod-shaped	no
69480	negative					99.999

Culture and growth conditions

culture medium

@ref: 15526
name: THIOTHRIX MEDIUM (DSMZ Medium 573)
growth: yes
link: https://mediadive.dsmz.de/medium/573
composition: Name: THIOTHRIX MEDIUM (DSMZ Medium 573) Composition: Agar 12.0 g/l Na2S x 9 H2O 0.3 g/l NH4Cl 0.2 g/l Na-acetate 0.1 g/l K2HPO4 0.01 g/l MgSO4 x 7 H2O 0.01 g/l FeSO4 x 7 H2O 0.0035 g/l EDTA 0.001 g/l ZnSO4 x 7 H2O 5e-05 g/l H3BO3 5e-05 g/l MnSO4 x 4 H2O 1e-05 g/l Co(NO3)2 5e-06 g/l Na2MoO4 x 2 H2O 5e-06 g/l CuSO4 x 5 H2O 2.5e-08 g/l CaSO4 Distilled water

culture temp

@ref	growth	type	temperature	range
15526	positive	growth	20-25
29249	positive	growth	05-32
29249	positive	optimum	24	psychrophilic

culture pH

@ref	ability	type	pH
29249	positive	growth	6.2-8.2
29249	positive	optimum	7

Physiology and metabolism

oxygen tolerance

@ref: 29249
oxygen tolerance: aerobe

spore formation

@ref	spore formation	confidence
69481	no	100
69480	no	99.864

halophily

@ref: 29249
salt: NaCl
growth: positive
tested relation: growth
concentration: <3 %

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
29249	30089	acetate	+	carbon source
29249	22653	asparagine	+	carbon source
29249	35391	aspartate	+	carbon source
29249	16947	citrate	+	carbon source
29249	29987	glutamate	+	carbon source
29249	24996	lactate	+	carbon source
29249	15792	malonate	+	carbon source
29249	15361	pyruvate	+	carbon source
29249	30031	succinate	+	carbon source
29249	16199	urea	+	carbon source
29249	17632	nitrate	+	reduction

enzymes

@ref	value	activity	ec
29249	cytochrome oxidase	+	1.9.3.1
29249	urease	+	3.5.1.5

Isolation, sampling and environmental information

isolation

@ref: 15526
sample type: shallow site of a low-temperature carstic lake
geographic location: Northern Caucasus, Kabardino-Balkaria, Blue lake system
country: Russia
origin.country: RUS
continent: Europe

isolation source categories

Cat1: #Environmental
Cat2: #Aquatic
Cat3: #Lake (large)

taxonmaps

@ref: 69479
File name: preview.99_8036.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_524;96_3712;97_4564;98_5857;99_8036&stattab=map
Last taxonomy: Thiothrix lacustris
16S sequence: EU642572
Sequence Identity:
Total samples: 2381
soil counts: 40
aquatic counts: 2295
animal counts: 44
plant counts: 2

Safety information

risk assessment

@ref: 15526
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 15526
description: Thiothrix lacustris strain BL 16S ribosomal RNA gene, partial sequence
accession: EU642572
length: 1399
database: ena
NCBI tax ID: 525917

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Thiothrix lacustris DSM 21227	GCA_000621325	scaffold	ncbi	1123401
66792	Thiothrix lacustris DSM 21227	1123401.3	wgs	patric	1123401
66792	Thiothrix lacustris DSM 21227	2556921650	draft	img	1123401

GC content

@ref	GC-content	method
15526	51.4	thermal denaturation, midpoint method (Tm)
29249	51.4

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	100	no
motile	no	83.118	yes
flagellated	no	89.79	yes
gram-positive	no	99.074	yes
anaerobic	no	94.162	yes
halophile	no	92.714	no
spore-forming	no	92.292	no
thermophile	no	99.414	yes
glucose-util	yes	63.379	no
aerobic	yes	81.06	yes
glucose-ferment	no	86.598	no

External links

@ref: 15526

culture collection no.: DSM 21227, VKM B-2521

straininfo link

@ref: 86084
straininfo: 401546

literature

topic: Phylogeny
Pubmed-ID: 19643883
title: Thiothrix caldifontis sp. nov. and Thiothrix lacustris sp. nov., gammaproteobacteria isolated from sulfide springs.
authors: Chernousova E, Gridneva E, Grabovich M, Dubinina G, Akimov V, Rossetti S, Kuever J
journal: Int J Syst Evol Microbiol
DOI: 10.1099/ijs.0.009456-0
year: 2009
mesh: DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Hot Springs/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sulfides/*metabolism, Thiothrix/*classification/genetics/*isolation & purification/metabolism
topic2: Genetics

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed
15526	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21227)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-21227
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
29249	Barberan A, Caceres Velazquez H, Jones S, Fierer N.		10.1128/mSphere.00237-17	Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information	25669	28776041
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)
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
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)
69481	Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch		10.21203/rs.3.rs-2527258/v1	Predictions based on the model GenomeNet Sporulation v. 1
86084	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID401546.1	StrainInfo: A central database for resolving microbial strain identifiers