Archive BacDiveID:10.13145/bacdive24744.20240916.9.1

Strain identifier

BacDive ID: 24744

Type strain:

Species: Aminivibrio pyruvatiphilus

Strain Designation: 4F6E

Strain history: A. Tonouchi 4F6E.

NCBI tax ID(s): 1005740 (species)

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

General

@ref: 21278

BacDive-ID: 24744

DSM-Number: 25964

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

description: Aminivibrio pyruvatiphilus 4F6E is an anaerobe, Gram-negative, motile bacterium that was isolated from soil from a rice paddy field.

NCBI tax id

NCBI tax id: 1005740
Matching level: species

strain history

@ref	history
21278	<- A. Tonouchi, Faculty Agriculture and Life Sci., Hirosaki Univ., Japan; 4F6E <- T. Honda {2010}
67770	A. Tonouchi 4F6E.

doi: 10.13145/bacdive24744.20240916.9.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/synergistota
domain: Bacteria
phylum: Synergistota
class: Synergistia
order: Synergistales
family: Synergistaceae
genus: Aminivibrio
species: Aminivibrio pyruvatiphilus
full scientific name: Aminivibrio pyruvatiphilus Honda et al. 2013

@ref: 21278

domain: Bacteria

phylum: Synergistetes

class: Synergistia

order: Synergistales

family: Synergistaceae

genus: Aminivibrio

species: Aminivibrio pyruvatiphilus

full scientific name: Aminivibrio pyruvatiphilus Honda et al. 2013

strain designation: 4F6E

type strain: yes

Morphology

cell morphology

@ref: 31105
gram stain: negative
cell length: 2.25 µm
cell width: 0.8 µm
cell shape: rod-shaped
motility: yes

colony morphology

@ref: 21278
incubation period: 3-7 days

pigmentation

@ref: 31105
production: yes

Culture and growth conditions

culture medium

@ref: 21278
name: ANAEROBIC FRESHWATER (FWM) MEDIUM (DSMZ Medium 503)
growth: yes
link: https://mediadive.dsmz.de/medium/503
composition: Name: ANAEROBIC FRESHWATER (FWM) MEDIUM (DSMZ Medium 503; with strain-specific modifications) Composition: Na2CO3 1.49551 g/l NaCl 0.997008 g/l KCl 0.498505 g/l Na-pyruvate 0.498504 g/l MgCl2 x 6 H2O 0.398803 g/l Na2S x 9 H2O 0.299103 g/l NH4Cl 0.249252 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149552 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498505 g/l NaOH 0.000498504 g/l Pyridoxine hydrochloride 0.000299103 g/l Nicotinic acid 0.000199402 g/l Thiamine-HCl x 2 H2O 0.000199402 g/l CoCl2 x 6 H2O 0.000189432 g/l Calcium pantothenate 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l Vitamin B12 9.97009e-05 g/l p-Aminobenzoic acid 7.97607e-05 g/l ZnCl2 6.97906e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l D-(+)-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 Distilled water

culture temp

@ref	growth	type	temperature
21278	positive	growth	37
31105	positive	growth	20-42
31105	positive	optimum	38.5
67770	positive	growth	37

culture pH

@ref	ability	type	pH
31105	positive	growth	6.4-8.4
31105	positive	optimum	7.3

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
21278	anaerobe
31105	anaerobe
69480	anaerobe	93.853

spore formation

@ref	spore formation	confidence
31105	no
69481	no	100

halophily

@ref: 31105
salt: NaCl
growth: positive
tested relation: growth
concentration: 0-1.5 %

observation

@ref: 31105
observation: aggregates in clumps

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
31105	16449	alanine	+	carbon source
31105	22653	asparagine	+	carbon source
31105	35391	aspartate	+	carbon source
31105	16947	citrate	+	carbon source
31105	29987	glutamate	+	carbon source
31105	15428	glycine	+	carbon source
31105	27570	histidine	+	carbon source
31105	25017	leucine	+	carbon source
31105	15361	pyruvate	+	carbon source
31105	17822	serine	+	carbon source

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
21278	soil from a rice paddy field	Aomori Prefecture, Asino, Kanagi, Goshogawara city	Japan	JPN	Asia
67770	Soil of a rice field in Japan

isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)

Safety information

risk assessment

@ref: 21278
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 21278
description: Aminivibrio pyruvatiphilus gene for 16S ribosomal RNA, partial sequence
accession: AB623229
length: 1441
database: nuccore
NCBI tax ID: 1005740

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Aminivibrio pyruvatiphilus strain DSM 25964	1005740.3	wgs	patric	1005740
66792	Aminivibrio pyruvatiphilus DSM 25964	2756170234	draft	img	1005740
67770	Aminivibrio pyruvatiphilus DSM 25964	GCA_004366815	scaffold	ncbi	1005740

GC content

@ref	GC-content	method
21278	61.9	high performance liquid chromatography (HPLC)
31105	61.9

Genome-based predictions

predictions

@ref	trait	model	description	prediction	confidence	training_data
69481	spore-forming	spore-forming	Ability to form endo- or exospores	no	100	no
69480	gram-positive	gram-positive	Positive reaction to Gram-staining	no	76.957	yes
69480	anaerobic	anaerobic	Ability to grow under anoxygenic conditions (including facultative anaerobes)	yes	93.853	no
69480	spore-forming	spore-forming	Ability to form endo- or exospores	no	79.3	yes
69480	aerobic	aerobic	Ability to grow under oxygenic conditions (including facultative aerobes)	no	92.502	yes
69480	thermophilic	thermophile	Ability to grow at temperatures above or equal to 45°C	no	72.729	yes
69480	flagellated	motile2+	Ability to perform flagellated movement	yes	61.297	no

External links

@ref: 21278

culture collection no.: DSM 25964, JCM 18417

straininfo link

@ref: 88572
straininfo: 407815

literature

topic: Phylogeny
Pubmed-ID: 23625260
title: Aminivibrio pyruvatiphilus gen. nov., sp. nov., an anaerobic, amino-acid-degrading bacterium from soil of a Japanese rice field.
authors: Honda T, Fujita T, Tonouchi A
journal: Int J Syst Evol Microbiol
DOI: 10.1099/ijs.0.052225-0
year: 2013
mesh: Amino Acids/metabolism, Bacteria, Anaerobic/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Coculture Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Japan, Molecular Sequence Data, Oryza/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology
topic2: Genetics

Reference

@id	authors	title	doi/url	catalogue	ID_cross_reference	pubmed	journal
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
21278	Curators of the DSMZ		https://www.dsmz.de/collection/catalogue/details/culture/DSM-25964	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25964)
31105	Barberan A, Caceres Velazquez H, Jones S, Fierer N.	Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information	10.1128/mSphere.00237-17		27434	28776041
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			33211880	Nucleic Acids Res. 49: D498-D508 2020
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
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
69481	Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch	Predictions based on the model GenomeNet Sporulation v. 1	10.21203/rs.3.rs-2527258/v1
88572	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-ID407815.1