Archive BacDiveID:10.13145/bacdive23331.20230509.8.1

Strain identifier

BacDive ID: 23331

Type strain:

Species: Brockia lithotrophica

Strain Designation: Kam1851

Strain history: <- A. Perevalova, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; Kam1851 <- A. Perevalova {2009}

NCBI tax ID(s): 933949 (species)

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

General

@ref: 19226

BacDive-ID: 23331

DSM-Number: 22653

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

description: Brockia lithotrophica Kam1851 is an anaerobe, spore-forming, thermophilic bacterium that was isolated from sediment-water mixture from a terrestrial hot spring.

NCBI tax id

NCBI tax id: 933949
Matching level: species

strain history

@ref: 19226
history: <- A. Perevalova, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; Kam1851 <- A. Perevalova {2009}

doi: 10.13145/bacdive23331.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/bacillota
domain: Bacteria
phylum: Bacillota
class: Clostridia
order: Thermoanaerobacterales
family: Thermoanaerobacteraceae
genus: Brockia
species: Brockia lithotrophica
full scientific name: Brockia lithotrophica Perevalova et al. 2013

@ref: 19226

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Thermoanaerobacterales

family: Thermoanaerobacteraceae

genus: Brockia

species: Brockia lithotrophica

full scientific name: Brockia lithotrophica Perevalova et al. 2013

strain designation: Kam1851

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell length	cell width	cell shape	motility	confidence
30656	positive	2.25 µm	0.35 µm	rod-shaped	yes
69480	positive					98.533

colony morphology

@ref: 19226
incubation period: 2-3 days

Culture and growth conditions

culture medium

@ref: 19226
name: BROCKIA LITHOTROPHICA MEDIUM (DSMZ Medium 395a)
growth: yes
link: https://mediadive.dsmz.de/medium/395a
composition: Name: BROCKIA MEDIUM (DSMZ Medium 395a) Composition: Sulfur 9.98004 g/l NaHCO3 0.798403 g/l MgCl2 x 6 H2O 0.698603 g/l Na2S x 9 H2O 0.499002 g/l NaCl 0.499002 g/l CaCl2 x 2 H2O 0.439122 g/l NH4Cl 0.329341 g/l KH2PO4 0.329341 g/l KCl 0.329341 g/l HCl 0.00249501 g/l FeCl2 x 4 H2O 0.00149701 g/l Sodium resazurin 0.000499002 g/l CoCl2 x 6 H2O 0.000189621 g/l Pyridoxine hydrochloride 9.98004e-05 g/l MnCl2 x 4 H2O 9.98004e-05 g/l ZnCl2 6.98603e-05 g/l Thiamine HCl 4.99002e-05 g/l (DL)-alpha-Lipoic acid 4.99002e-05 g/l p-Aminobenzoic acid 4.99002e-05 g/l Calcium D-(+)-pantothenate 4.99002e-05 g/l Nicotinic acid 4.99002e-05 g/l Riboflavin 4.99002e-05 g/l Na2MoO4 x 2 H2O 3.59281e-05 g/l NiCl2 x 6 H2O 2.39521e-05 g/l Folic acid 1.99601e-05 g/l Biotin 1.99601e-05 g/l H3BO3 5.98802e-06 g/l CuCl2 x 2 H2O 1.99601e-06 g/l Vitamin B12 9.98004e-07 g/l Distilled water

culture temp

@ref	growth	type	temperature	range	confidence
19226	positive	growth	65	thermophilic
30656	positive	growth	46-78	thermophilic
30656	positive	optimum	62.5	thermophilic
69480				thermophilic	99.999

culture pH

@ref	ability	type	pH	PH range
30656	positive	growth	5.5-8.5	alkaliphile
30656	positive	optimum	6.5

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
19226	anaerobe
30656	anaerobe
69480	anaerobe	98.001

spore formation

@ref	spore formation	confidence
30656	yes
69481	yes	99
69480	no	92.459

Isolation, sampling and environmental information

isolation

@ref: 19226
sample type: sediment-water mixture from a terrestrial hot spring
geographic location: Kamchatka, Uzon Caldera, East Thermal Field, Zavarzin Pool (54°49' 81.0'' N, 160°01'46.0'' E)
country: Russia
origin.country: RUS
continent: Asia
latitude: 54.8392
longitude: 160.029

isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Sediment
#Environmental	#Aquatic	#Thermal spring
#Condition	#Thermophilic (>45°C)

taxonmaps

@ref: 69479
File name: preview.99_101320.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9488;96_41075;97_52421;98_69192;99_101320&stattab=map
Last taxonomy: Brockia lithotrophica subclade
16S sequence: HQ540553
Sequence Identity:
Total samples: 122
soil counts: 16
aquatic counts: 61
animal counts: 45

Safety information

risk assessment

@ref: 19226
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 19226
description: Brockia lithotrophica strain Kam1851 16S ribosomal RNA gene, partial sequence
accession: HQ540553
length: 1458
database: ena
NCBI tax ID: 933949

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Brockia lithotrophica DSM 22653	GCA_003633725	scaffold	ncbi	933949
66792	Brockia lithotrophica strain DSM 22653	933949.26	wgs	patric	933949
66792	Brockia lithotrophica DSM 22653	2757320359	draft	img	933949

GC content

@ref	GC-content	method
19226	63	fluorimetric
30656	63

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	yes	99	no
flagellated	no	86.818	no
gram-positive	yes	83.706	yes
anaerobic	yes	93.386	yes
aerobic	no	95.505	yes
halophile	no	88.769	no
spore-forming	no	58.194	no
glucose-util	yes	79.289	no
thermophile	yes	99.999	no
motile	yes	86.347	yes
glucose-ferment	no	53.938	no

External links

@ref: 19226

culture collection no.: DSM 22653, VKM B-2685

straininfo link

@ref: 87548
straininfo: 401606

literature

topic: Phylogeny
Pubmed-ID: 22493174
title: Brockia lithotrophica gen. nov., sp. nov., an anaerobic thermophilic bacterium from a terrestrial hot spring.
authors: Perevalova AA, Kublanov IV, Baslerov RV, Zhang G, Bonch-Osmolovskaya EA
journal: Int J Syst Evol Microbiol
DOI: 10.1099/ijs.0.041285-0
year: 2012
mesh: Bacteria, Anaerobic/*classification/genetics/metabolism, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Hot Springs/*microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Russia, Sequence Analysis, DNA
topic2: Genetics

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed
19226	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22653)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-22653
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
30656	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	26987	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
87548	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID401606.1	StrainInfo: A central database for resolving microbial strain identifiers