Archive BacDiveID:10.13145/bacdive14099.20211221.6

Strain identifier

BacDive ID: 14099

Type strain:

Species: Pedobacter caeni

Strain history: CIP <- 2005, DSMZ

NCBI tax ID(s): 288992 (species)

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

General

@ref: 6593

BacDive-ID: 14099

DSM-Number: 16990

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

description: Pedobacter caeni DSM 16990 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from nitrifying inoculum.

NCBI tax id

NCBI tax id: 288992
Matching level: species

strain history

<- B. Vanparys, LMG

2005, DSMZ

doi: 10.13145/bacdive14099.20211221.6

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/bacteroidetes
domain: Bacteria
phylum: Bacteroidetes
class: Sphingobacteriia
order: Sphingobacteriales
family: Sphingobacteriaceae
genus: Pedobacter
species: Pedobacter caeni
full scientific name: Pedobacter caeni Vanparys et al. 2005

@ref: 6593

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Pedobacter

species: Pedobacter caeni

full scientific name: Pedobacter caeni Vanparys et al. 2005

type strain: yes

Morphology

cell morphology

@ref: 31473
gram stain: negative
cell length: 6.5 µm
cell width: 0.75 µm
cell shape: rod-shaped
motility: no

Culture and growth conditions

culture medium

@ref	name	growth	link	composition
6593	TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)	yes	https://bacmedia.dsmz.de/medium/545	Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water
34022	MEDIUM 72- for trypto casein soja agar	yes		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)

culture temp

@ref	growth	type	temperature	range
6593	positive	growth	28	mesophilic
31473	positive	growth	28-37	mesophilic
31473	positive	optimum	28	mesophilic
34022	positive	growth	30	mesophilic

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance
6593	aerobe
31473	aerobe

spore formation

@ref: 31473
spore formation: no

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
31473	16634	raffinose	+	carbon source
31473	17151	xylitol	+	carbon source

enzymes

@ref	value	activity	ec
31473	catalase	+	1.11.1.6
31473	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

isolation

@ref: 6593
sample type: nitrifying inoculum
geographic location: Gent
country: Belgium
origin.country: BEL
continent: Europe

isolation source categories

Cat1: #Engineered
Cat2: #Laboratory
Cat3: #Lab enrichment

Safety information

risk assessment

@ref: 6593
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 6593
description: Pedobacter caeni partial 16S rRNA gene, type strain LMG 22862T
accession: AJ786798
length: 1337
database: ena
NCBI tax ID: 288992

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Pedobacter caeni DSM 16990	GCA_900129215	scaffold	ncbi	288992
66792	Pedobacter caeni strain DSM 16990	288992.5	wgs	patric	288992
66792	Pedobacter caeni DSM 16990	2622736434	draft	img	288992

GC content

@ref: 31473
GC-content: 42.7

External links

@ref: 6593

culture collection no.: DSM 16990, CIP 109035, LMG 22862

straininfo link

@ref	passport
20218	http://www.straininfo.net/strains/387818
20218	http://www.straininfo.net/strains/691176
20218	http://www.straininfo.net/strains/383926

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed	ID_cross_reference
6593	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16990)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-16990
20215	D.Gleim, M.Kracht, N.Weiss et. al.		http://www.dsmz.de/bacterial-diversity/prokaryotic-nomenclature-up-to-date.html	Prokaryotic Nomenclature Up-to-date - compilation of all names of Bacteria and Archaea, validly published according to the Bacteriological Code since 1. Jan. 1980, and validly published nomenclatural changes since
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
27773			10.1099/ijs.0.63635-0			15879274
31473	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		28776041	27773
34022	Curators of the CIP		https://brclims.pasteur.fr/brcWeb/souche/detail/1/6732
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)