Archive BacDiveID:10.13145/bacdive6794.20230509.8.1

Strain identifier

BacDive ID: 6794

Type strain:

Species: Leptonema illini

Strain Designation: 3055

Strain history: <- R. Galloway, CDC; 3055 {2008} <- L.E. Hanson

NCBI tax ID(s): 929563 (strain), 183 (species)

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

General

@ref: 15764

BacDive-ID: 6794

DSM-Number: 21528

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

description: Leptonema illini 3055 is a mesophilic, Gram-negative bacterium that was isolated from urine of a bull.

NCBI tax id

NCBI tax id	Matching level
183	species
929563	strain

strain history

@ref: 15764
history: <- R. Galloway, CDC; 3055 {2008} <- L.E. Hanson

doi: 10.13145/bacdive6794.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/spirochaetota
domain: Bacteria
phylum: Spirochaetota
class: Spirochaetia
order: Leptospirales
family: Leptospiraceae
genus: Leptonema
species: Leptonema illini
full scientific name: Leptonema illini Hovind-Hougen 1983

@ref: 15764

domain: Bacteria

phylum: Spirochaetes

class: Spirochaetia

order: Spirochaetales

family: Leptospiraceae

genus: Leptonema

species: Leptonema illini

full scientific name: Leptonema illini Hovind-Hougen 1983

strain designation: 3055

type strain: yes

Morphology

cell morphology

@ref: 69480
gram stain: negative
confidence: 99.964

colony morphology

@ref: 15764
incubation period: >14 days

multimedia

@ref: 66793
multimedia content: EM_DSM_21528_1.jpg
caption: electron microscopic image
intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@ref: 15764
name: LEPTOSPIRA-MEDIUM (DSMZ Medium 1113)
growth: yes
link: https://mediadive.dsmz.de/medium/1113
composition: Name: LEPTOSPIRA-MEDIUM (DSMZ Medium 1113) Composition: Leptospira Medium Base EMJH 2.3 g/l Agarose 1.5 g/l Leptospira Enrichment EMJH Distilled water

culture temp

@ref: 15764
growth: positive
type: growth
temperature: 30
range: mesophilic

Physiology and metabolism

spore formation

@ref: 69480
spore formation: no
confidence: 99.992

Isolation, sampling and environmental information

isolation

@ref: 15764
sample type: urine of a bull
country: USA
origin.country: USA
continent: North America

isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Bovinae (Cow, Cattle)
#Host Body Product	#Fluids	#Urine

taxonmaps

@ref: 69479
File name: preview.99_4613.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16024;96_2298;97_2789;98_3462;99_4613&stattab=map
Last taxonomy: Leptonema illini subclade
16S sequence: AY714984
Sequence Identity:
Total samples: 9140
soil counts: 3028
aquatic counts: 4214
animal counts: 807
plant counts: 1091

Safety information

risk assessment

@ref: 15764
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 15764
description: Leptonema illini serovar Illini strain 3055 16S ribosomal RNA gene, partial sequence
accession: AY714984
length: 1428
database: ena
NCBI tax ID: 929563

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Leptonema illini DSM 21528	GCA_000243335	scaffold	ncbi	929563
66792	Leptonema illini DSM 21528	929563.3	wgs	patric	929563
66792	Leptonema illini 3055, DSM 21528	2506783010	draft	img	929563

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	86	no
motile	yes	77.893	no
flagellated	no	72.425	no
gram-positive	no	98.504	no
anaerobic	no	87.434	no
aerobic	yes	62.771	no
halophile	no	89.702	no
spore-forming	no	88.958	no
thermophile	no	96.478	yes
glucose-util	yes	69.981	no
glucose-ferment	no	89.451	no

External links

@ref: 15764

culture collection no.: DSM 21528, NCTC 11301

straininfo link

@ref: 76264
straininfo: 401315

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
15764	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21528)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-21528
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
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)
66793	Mukherjee et al.		10.1038/nbt.3886	GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life	35: 676-683 2017	28604660
66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg		10.1093/nar/gkaa1025	BRENDA, the ELIXIR core data resource in 2021: new developments and updates	Nucleic Acids Res. 49: D498-D508 2020	33211880
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)
76264	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID401315.1	StrainInfo: A central database for resolving microbial strain identifiers