Archive BacDiveID:10.13145/bacdive24818.20230509.8.1

Strain identifier

BacDive ID: 24818

Type strain:

Species: Hydrogenispora ethanolica

Strain Designation: LX-B

Strain history: Y Liu et al. strain LX-B.

NCBI tax ID(s): 1082276 (species)

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

General

@ref: 21333

BacDive-ID: 24818

DSM-Number: 25471

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

description: Hydrogenispora ethanolica LX-B is an anaerobe, spore-forming, mesophilic bacterium that was isolated from anaerobic, mesophilic sludge treating herbicide wastewater.

NCBI tax id

NCBI tax id: 1082276
Matching level: species

strain history

@ref	history
21333	<- L. Yi, Qingdao Institute of Bioenergy & Bioprocess Technology, Chinese Academy of Sciences (CAS), Qingdao; LX-B <- L. Yi {2011}
67770	Y Liu et al. strain LX-B.

doi: 10.13145/bacdive24818.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/bacillota
domain: Bacteria
phylum: Bacillota
class: Clostridia
order: Eubacteriales
family: Clostridiaceae
genus: Hydrogenispora
species: Hydrogenispora ethanolica
full scientific name: Hydrogenispora ethanolica Liu et al. 2014

@ref: 21333

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Firmicutes, not assigned to order

family: Clostridiaceae

genus: Hydrogenispora

species: Hydrogenispora ethanolica

full scientific name: Hydrogenispora ethanolica Liu et al. 2014

strain designation: LX-B

type strain: yes

Morphology

cell morphology

@ref	motility	confidence	gram stain
69480	yes	95.341
69480		99.867	negative

Culture and growth conditions

culture medium

@ref: 21333
name: DESULFOVIBRIO (MV) MEDIUM (DSMZ Medium 641)
growth: yes
link: https://mediadive.dsmz.de/medium/641
composition: Name: DESULFOVIBRIO (MV) MEDIUM (DSMZ Medium 641; with strain-specific modifications) Composition: D-Glucose 1.99402 g/l Na2SO4 1.99402 g/l Na2S2O3 x 5 H2O 0.997009 g/l MgSO4 x 7 H2O 0.997009 g/l NH4Cl 0.997009 g/l Yeast extract 0.997009 g/l Na2CO3 0.997009 g/l KH2PO4 0.498504 g/l Na2S x 9 H2O 0.0997009 g/l CaCl2 x 2 H2O 0.0997009 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 Pyridoxine hydrochloride 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 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
21333	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
21333	anaerobe
69480	anaerobe	100

spore formation

@ref: 69480
spore formation: yes
confidence: 99.448

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
21333	anaerobic, mesophilic sludge treating herbicide wastewater	Qingdao	China	CHN	Asia
67770	Anaerobic sludge treating herbicide wastewater

isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Waste	#Wastewater
#Environmental	#Terrestrial	#Mud (Sludge)
#Condition	#Anoxic (anaerobic)

taxonmaps

@ref: 69479
File name: preview.99_177608.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_882;96_65790;97_85414;98_115988;99_177608&stattab=map
Last taxonomy: Hydrogenispora ethanolica subclade
16S sequence: AB669474
Sequence Identity:
Total samples: 1051
soil counts: 574
aquatic counts: 236
animal counts: 191
plant counts: 50

Safety information

risk assessment

@ref: 21333
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 21333
description: Hydrogenispora ethanolica gene for 16S rRNA, partial sequence
accession: AB669474
length: 1443
database: ena
NCBI tax ID: 1082276

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Hydrogenispora ethanolica LX-B	GCA_004340685	scaffold	ncbi	1082276
66792	Hydrogenispora ethanolica strain LX-B	1082276.3	wgs	patric	1082276
66792	Hydrogenispora ethanolica DSM 25471	2788499852	draft	img	1082276

GC content

@ref: 21333
GC-content: 56.1
method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	yes	72	no
motile	yes	86.503	no
flagellated	no	55.104	no
gram-positive	no	91.454	no
anaerobic	yes	98.708	yes
aerobic	no	97.795	no
halophile	no	96.382	no
spore-forming	yes	74.217	no
thermophile	no	86.042	no
glucose-util	yes	82.749	no
glucose-ferment	no	62.667	no

External links

@ref: 21333

culture collection no.: DSM 25471, CGMCC 1.5175, JCM 18117

straininfo link

@ref: 88639
straininfo: 400228

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	24554637	Hydrogenispora ethanolica gen. nov., sp. nov., an anaerobic carbohydrate-fermenting bacterium from anaerobic sludge.	Liu Y, Qiao JT, Yuan XZ, Guo RB, Qiu YL	Int J Syst Evol Microbiol	10.1099/ijs.0.060186-0	2014	Bacteria, Anaerobic/classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Carbohydrate Metabolism, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fermentation, Molecular Sequence Data, Phosphatidylglycerols/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/microbiology, Waste Water/microbiology	Genetics
Metabolism	27023388	Bioaugmentation of Hydrogenispora ethanolica LX-B affects hydrogen production through altering indigenous bacterial community structure.	Yang Z, Guo R, Shi X, He S, Wang L, Dai M, Qiu Y, Dang X	Bioresour Technol	10.1016/j.biortech.2016.03.097	2016	Bioreactors/microbiology, Firmicutes/metabolism, Hydrogen/analysis/metabolism, Sewage/microbiology	Biotechnology
Phylogeny	33724176	Capillibacterium thermochitinicola gen. nov., sp. nov., a novel anaerobic thermophilic chitinolytic bacterium from compost.	Ungkulpasvich U, Baramee S, Uke A, Kosugi A	Int J Syst Evol Microbiol	10.1099/ijsem.0.004693	2021

Reference

@id	authors	title	doi/url	catalogue	journal	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
21333	Curators of the DSMZ		https://www.dsmz.de/collection/catalogue/details/culture/DSM-25471	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25471)
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
66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg	BRENDA, the ELIXIR core data resource in 2021: new developments and updates	10.1093/nar/gkaa1025		Nucleic Acids Res. 49: D498-D508 2020	33211880
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
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
88639	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-ID400228.1