Archive BacDiveID:10.13145/bacdive11860.20230509.8.1

Strain identifier

BacDive ID: 11860

Type strain:

Species: Aminobacter niigataensis

Strain Designation: DM-81

Strain history: T. Urakami DM-81.

NCBI tax ID(s): 83265 (species)

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

General

@ref: 2960

BacDive-ID: 11860

DSM-Number: 7050

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

description: Aminobacter niigataensis DM-81 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

NCBI tax id: 83265
Matching level: species

strain history

@ref	history
2960	<- JCM <- T. Urakami, DM-81
67770	T. Urakami DM-81.

doi: 10.13145/bacdive11860.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Alphaproteobacteria
order: Hyphomicrobiales
family: Phyllobacteriaceae
genus: Aminobacter
species: Aminobacter niigataensis
full scientific name: Aminobacter niigataensis Urakami et al. 1992

@ref: 2960

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Phyllobacteriaceae

genus: Aminobacter

species: Aminobacter niigataensis

full scientific name: Aminobacter niigataensis Urakami et al. 1992

strain designation: DM-81

type strain: yes

Morphology

cell morphology

@ref: 69480
gram stain: negative
confidence: 99.992

colony morphology

@ref: 58342
incubation period: 2 days

Culture and growth conditions

culture medium

@ref: 2960
name: NUTRIENT AGAR (DSMZ Medium 1)
growth: yes
link: https://mediadive.dsmz.de/medium/1
composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@ref	growth	type	temperature	range
2960	positive	growth	30	mesophilic
58342	positive	growth	30	mesophilic
67770	positive	growth	30	mesophilic

Physiology and metabolism

oxygen tolerance

@ref: 58342
oxygen tolerance: aerobe

spore formation

@ref	spore formation	confidence
69481	no	100
69480	no	99.997

observation

@ref: 67770
observation: quinones: Q-10

Isolation, sampling and environmental information

isolation

@ref	sample type
2960	soil
58342	Soil
67770	Soil

isolation source categories

Cat1: #Environmental
Cat2: #Terrestrial
Cat3: #Soil

taxonmaps

@ref: 69479
File name: preview.99_1038.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_220;97_697;98_812;99_1038&stattab=map
Last taxonomy: Mesorhizobium
16S sequence: AJ011761
Sequence Identity:
Total samples: 1264
soil counts: 780
aquatic counts: 308
animal counts: 145
plant counts: 31

Safety information

risk assessment

@ref: 2960
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 20218
description: Aminobacter niigataensis strain DSM7050T, 16S rRNA gene, partial
accession: AJ011761
length: 1466
database: ena
NCBI tax ID: 83265

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Aminobacter niigataensis DSM 7050	GCA_014200015	contig	ncbi	83265
66792	Aminobacter niigataensis strain DSM 7050	83265.3	wgs	patric	83265
66792	Aminobacter niigataensis DSM 7050	2829772224	draft	img	83265

GC content

@ref: 67770
GC-content: 63.2
method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	100	no
motile	yes	90.181	no
flagellated	no	69.65	no
gram-positive	no	97.921	no
anaerobic	no	98.786	yes
halophile	no	87.077	no
spore-forming	no	95.266	no
thermophile	no	98.075	no
glucose-util	yes	93.872	no
aerobic	yes	94.977	yes
glucose-ferment	no	90.724	no

External links

@ref: 2960

culture collection no.: DSM 7050, ATCC 49932, JCM 7853, CCUG 48820, CCM 4330, IAM 15265

straininfo link

@ref: 81078
straininfo: 42762

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
2960	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7050)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-7050
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
20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.		10.1016/j.syapm.2013.11.002	StrainInfo introduces electronic passports for microorganisms.	Syst Appl Microbiol. 37: 42-50 2014	24321274
58342	Curators of the CCUG	Culture Collection University of Gothenburg (CCUG) (CCUG 48820)	https://www.ccug.se/strain?id=48820
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)
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.		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
81078	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID42762.1	StrainInfo: A central database for resolving microbial strain identifiers