Name: Nocardioides zeae JM-1068
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 24254

Type strain:

Species: Nocardioides zeae

Strain Designation: JM-1068

Culture col. no.: DSM 28163, CIP 110696, LMG 28079, JCM 30728

Strain history: CIP <- 2013, P. Kämpfer, Justus Liebig Giessen Univ., Giessen, Germany: strain JM-1068

NCBI tax ID(s): 1457234 (species)

SI-ID 404056

DSM 28163, CIP 110696

Section

Nocardioides zeae JM-1068 is a mesophilic, Gram-positive bacterium that was isolated from internal stem tissue of field grown healthy corn, Zea mays cultivar 'Sweet Belle'.

Gram-positive
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Propionibacteriales*
	Family	*Nocardioidaceae*
	Genus	*Nocardioides*
	Species	**Nocardioides zeae**
	Full Scientific Name (LPSN)	Nocardioides zeae Glaeser et al. 2014

Information on morphological and physiological properties Morphology

[Ref.: #124028]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #124028]	Cell shape	rod-shaped

[Ref.: #124028]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #36247]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #36247]

Culture medium growth

[Ref.: #36247]

Culture medium composition

expand / minimize

[Ref.: #20687]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #20687]

Culture medium growth

[Ref.: #20687]

Culture medium link

Medium recipe at MediaDive

[Ref.: #20687]

Culture medium composition

expand / minimize

[Ref.: #20687]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #20687]

Culture medium growth

[Ref.: #20687]

Culture medium link

Medium recipe at MediaDive

[Ref.: #20687]

Culture medium composition

expand / minimize

[Ref.: #124028]

Culture medium

CIP Medium 72

[Ref.: #124028]

Culture medium growth

[Ref.: #124028]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #20687]	growth	28 °C
[Ref.: #36247]	growth	30 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #20687]	Temperature range	mesophilic
[Ref.: #36247]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %90
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.973

[Ref.: #67770]

Observation

quinones: MK-8(H₄)

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #20687]	Sample type/isolated from	internal stem tissue of field grown healthy corn, Zea mays cultivar 'Sweet Belle'
[Ref.: #20687]	Host species	Zea mays
[Ref.: #20687]	Geographic location (country and/or sea, region)	E.V. Smith Research Center, Alabama, Tallassee
[Ref.: #20687]	Country	USA
[Ref.: #20687]	Country ISO 3 Code	USA
[Ref.: #20687]	Continent	North America

[Ref.: #67770]	Sample type/isolated from	Healthy stem of a Zea mays plant
[Ref.: #67770]	Host species	Zea mays

[Ref.: #124028]	Sample type/isolated from	Plant, Field grown corn root tissue
[Ref.: #124028]	Geographic location (country and/or sea, region)	Tallassee, Alabama, USA
[Ref.: #124028]	Country	United States of America
[Ref.: #124028]	Country ISO 3 Code	USA
[Ref.: #124028]	Continent	North America
[Ref.: #124028]	Isolation date	2005
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Stem (Branch)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KF900163 (>99% sequence identity) for Nocardioides zeae subclade from Microbeatlas

Aquatic Samples	2245
Soil Samples	5821
Animal Samples	5517
Plant Samples	1975
Total Samples	15558

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #20687]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #124028]	Biosafety level	1	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #20687]	Nocardioides zeae strain JM-1068 16S ribosomal RNA gene, partial sequence	KF900163	1438	ENA	1457234 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Nocardioides zeae JCM 30728	GCA_010686755	scaffold	GenBank	1457234 tax ID
[Ref.: #66792]	Nocardioides zeae strain JCM 30728	1457234.3	wgs	PATRIC	1457234 tax ID	*
[Ref.: #66792]	Nocardioides zeae JCM 30728	2902192801	draft	JGI IMG/M	1457234 tax ID	*

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Nocardioides zeae JCM 30728 NCBI: GCA_010686755.1
[Ref.: #69481]	spore-forming	no	90	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Nocardioides zeae strain JCM 30728 PATRIC: 1457234.3
[Ref.: #69480]	motile	no	95.99	no
[Ref.: #69480]	gram-positive	yes	88.379	no
[Ref.: #69480]	anaerobic	no	99.122	no
[Ref.: #69480]	halophile	no	92.387	no
[Ref.: #69480]	spore-forming	no	83.124	no
[Ref.: #69480]	glucose-util	yes	89.902	no
[Ref.: #69480]	thermophile	no	98.887	yes
[Ref.: #69480]	aerobic	yes	94.87	no
[Ref.: #69480]	flagellated	no	97.709	no
[Ref.: #69480]	glucose-ferment	no	91.987	no

Availability in culture collections External links

[Ref.: #20687]

Culture collection no.

DSM 28163, CIP 110696, LMG 28079, JCM 30728

[Ref.: #88196]

SI-ID 404056

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nocardioides zeae sp. nov., isolated from the stem of Zea mays.	Glaeser SP, McInroy JA, Busse HJ, Kampfer P	Int J Syst Evol Microbiol	10.1099/ijs.0.061481-0	2014	*

References

#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. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#20687

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28163

#36247 ; Curators of the CIP;

#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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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 .

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#88196

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 . ( DOI 10.60712/SI-ID404056.1 )

#124028 Collection of Institut Pasteur ; Curators of the CIP; CIP 110696
* These data were automatically processed and therefore are not curated

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Nocardioides zeae JCM 30728

Nocardioides zeae strain JCM 30728

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