Archive BacDiveID:10.13145/bacdive24045.20230509.8.1

Strain identifier

BacDive ID: 24045

Type strain:

Species: Chryseobacterium zeae

Strain Designation: JM-1085

Strain history: CIP <- 2013, P. Kämpfer, Giessen Univ., Giessen, Germany: strain JM-1085

NCBI tax ID(s): 1416779 (species)

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

General

@ref: 20940

BacDive-ID: 24045

DSM-Number: 27623

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

description: Chryseobacterium zeae JM-1085 is a mesophilic, Gram-negative bacterium that was isolated from surface-sterilized stem of 10-week-old sweet corn .

NCBI tax id

NCBI tax id: 1416779
Matching level: species

strain history

@ref	history
20940	<- P. Kämpfer, Justus-Liebig-Universität, Giessen, Germany; JM-1085 <- J. Mcinroy
124023	CIP <- 2013, P. Kämpfer, Giessen Univ., Giessen, Germany: strain JM-1085

doi: 10.13145/bacdive24045.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/bacteroidota
domain: Bacteria
phylum: Bacteroidota
class: Flavobacteriia
order: Flavobacteriales
family: Weeksellaceae
genus: Chryseobacterium
species: Chryseobacterium zeae
full scientific name: Chryseobacterium zeae Kämpfer et al. 2014
synonyms
- @ref: 20215
- synonym: Epilithonimonas zeae

@ref: 20940

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Weeksellaceae

genus: Chryseobacterium

species: Chryseobacterium zeae

full scientific name: Chryseobacterium zeae Kämpfer et al. 2014

strain designation: JM-1085

type strain: yes

Morphology

cell morphology

@ref	gram stain	confidence	cell shape	motility
69480	negative	99.979
124023	negative		rod-shaped	no

Culture and growth conditions

culture medium

@ref	name	growth	composition	link
32771	MEDIUM 72- for trypto casein soja agar	yes	Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
20940	CASO AGAR (MERCK 105458) (DSMZ Medium 220)	yes	Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water	https://mediadive.dsmz.de/medium/220
124023	CIP Medium 72	yes		https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@ref	growth	type	temperature	range
20940	positive	growth	28	mesophilic
32771	positive	growth	30	mesophilic

Physiology and metabolism

spore formation

@ref	spore formation	confidence
69481	no	100
69480	no	99.991

Isolation, sampling and environmental information

isolation

@ref	sample type	host species	geographic location	country	origin.country	continent
20940	surface-sterilized stem of 10-week-old sweet corn (Zea mays)	Zea mays	Alabama, Macon county, Tallassee, E.V. Smith Research Center, Plant Breeding Unit facility	USA	USA	North America
124023	Environment, Soil sample			United States of America	USA	North America

isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Stem (Branch)
#Host Body-Site	#Plant	#Sterilized plant part

taxonmaps

@ref: 69479
File name: preview.99_6432.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_76;96_206;97_225;98_657;99_6432&stattab=map
Last taxonomy: Chryseobacterium
16S sequence: HG738135
Sequence Identity:
Total samples: 36
soil counts: 8
aquatic counts: 8
animal counts: 17
plant counts: 3

Safety information

risk assessment

@ref	biosafety level	biosafety level comment
20940	1	Risk group (German classification)
124023	1	Risk group (French classification)

Sequence information

16S sequences

@ref: 20940
description: Chryseobacterium zeae partial 16S rRNA gene, type strain JM-1085T
accession: HG738135
length: 1440
database: ena
NCBI tax ID: 1416779

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Epilithonimonas zeae DSM 27623	GCA_900141765	contig	ncbi	1416779
66792	Chryseobacterium zeae strain DSM 27623	1416779.3	wgs	patric	1416779
66792	Chryseobacterium zeae DSM 27623	2695421044	draft	img	1416779

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	100	no
motile	no	90.941	no
gram-positive	no	98.06	no
anaerobic	no	99.621	no
halophile	no	94.216	no
spore-forming	no	96.075	no
thermophile	no	99.819	yes
glucose-util	yes	87.168	no
aerobic	yes	90.817	no
flagellated	no	96.611	no
glucose-ferment	no	90.777	no

External links

@ref: 20940

culture collection no.: DSM 27623, CCM 8491, LMG 27809, CIP 110648

straininfo link

@ref: 88018
straininfo: 390471

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	24379020	Chryseobacterium zeae sp. nov., Chryseobacterium arachidis sp. nov., and Chryseobacterium geocarposphaerae sp. nov. isolated from the rhizosphere environment.	Kampfer P, McInroy JA, Glaeser SP	Antonie Van Leeuwenhoek	10.1007/s10482-013-0101-4	2013	Bacteriophage Typing, Chryseobacterium/classification/genetics/isolation & purification/metabolism, Cluster Analysis, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizosphere, *Soil Microbiology	Metabolism
Phylogeny	25450189	Chryseobacterium polytrichastri sp. nov., isolated from a moss (Polytrichastrum formosum), and emended description of the genus Chryseobacterium.	Chen XY, Zhao R, Chen ZL, Liu L, Li XD, Li YH	Antonie Van Leeuwenhoek	10.1007/s10482-014-0338-6	2014	Bacterial Typing Techniques, Base Composition, Bryophyta/growth & development/microbiology, Chryseobacterium/classification/genetics/*isolation & purification, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Ice Cover, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tibet, Vitamin K 2/analysis	Genetics
Phylogeny	25878202	Chryseobacterium solani sp. nov., isolated from field-grown eggplant rhizosphere soil.	Du J, Ngo HTT, Won K, Kim KY, Jin FX, Yi TH	Int J Syst Evol Microbiol	10.1099/ijs.0.000266	2015	Bacterial Typing Techniques, Base Composition, Chryseobacterium/classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhizosphere, Sequence Analysis, DNA, Soil Microbiology, Solanum melongena/*microbiology, Vitamin K 2/analogs & derivatives/chemistry	Genetics
Phylogeny	29264617	Chryseobacterium chungangensis sp. nov., a bacterium isolated from soil of sweet gourd garden.	Huq MA	Arch Microbiol	10.1007/s00203-017-1469-8	2017	Base Composition, Chryseobacterium/cytology/*genetics/isolation & purification/metabolism, Cucurbitaceae, DNA, Bacterial/genetics, Fatty Acids/metabolism, Gardens, Molecular Typing, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Vitamin K 2/analogs & derivatives/metabolism	Metabolism

Reference

@id	authors	title	doi/url	catalogue
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
20940	Curators of the DSMZ		https://www.dsmz.de/collection/catalogue/details/culture/DSM-27623	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27623)
32771	Curators of the CIP		https://brclims.pasteur.fr/brcWeb/souche/detail/1/30452
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
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
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
88018	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-ID390471.1
124023	Curators of the CIP		https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110648	Collection of Institut Pasteur (CIP 110648)

General

NCBI tax id

strain history

Name and taxonomic classification

LPSN

synonyms

Morphology

cell morphology

Culture and growth conditions

culture medium

culture temp

Physiology and metabolism

spore formation

Isolation, sampling and environmental information

isolation

isolation source categories

taxonmaps

Safety information

risk assessment

Sequence information

16S sequences

Genome sequences

Genome-based predictions

predictions

External links

straininfo link

literature

Reference