Name: Actinomadura chibensis DSM 45038
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 16994

Type strain:

Species: Actinomadura chibensis

Culture col. no.: DSM 45038, IFM 10266, JCM 14158, NBRC 106107

Strain history: Y. Mikami IFM 10266 <-- Chiba Univ. Hosp., Japan.

NCBI tax ID(s): 1220554 (strain), 392828 (species)

SI-ID 297503

DSM 45038, JCM 14158

Section

Actinomadura chibensis DSM 45038 is a mesophilic bacterium that was isolated from human.

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	*Streptosporangiales*
	Family	*Thermomonosporaceae*
	Genus	*Actinomadura*
	Species	**Actinomadura chibensis**
	Full Scientific Name (LPSN)	Actinomadura chibensis Hanafy et al. 2008

Information on culture and growth conditions Culture and growth conditions

[Ref.: #12265]

Culture medium

N-Z-AMINE-MEDIUM (DSMZ Medium 554)

[Ref.: #12265]

Culture medium growth

[Ref.: #12265]

Culture medium link

Medium recipe at MediaDive

[Ref.: #12265]

Culture medium composition

expand / minimize

[Ref.: #12265]

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

[Ref.: #12265]

Culture medium growth

[Ref.: #12265]

Culture medium link

Medium recipe at MediaDive

[Ref.: #12265]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #12265]			growth	37 °C
[Ref.: #67770]			growth	28 °C

[Ref.: #12265]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67770]

Observation

quinones: MK-9(H₆), MK-9(H₄), MK-9(H₈)

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

[Ref.: #12265]	Sample type/isolated from	human
[Ref.: #12265]	Country	Japan
[Ref.: #12265]	Country ISO 3 Code	JPN
[Ref.: #12265]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Sputum
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host

#Human

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB264086 (>99% sequence identity) for Actinomadura from Microbeatlas

Aquatic Samples	34
Soil Samples	208
Animal Samples	4
Plant Samples	47
Total Samples	293

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

[Ref.: #12265]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #20218]	Actinomadura chibensis gene for 16S rRNA, partial sequence	AB264086	1466	ENA	392828 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Actinomadura chibensis NBRC 106107	GCA_001552135	contig	GenBank	1220554 tax ID
[Ref.: #67770]	Actinomadura chibensis JCM 14158	GCA_008085895	contig	GenBank	392828 tax ID
[Ref.: #66792]	Actinomadura chibensis NBRC 106107	1220554.3	wgs	PATRIC	1220554 tax ID	*
[Ref.: #66792]	Actinomadura chibensis strain JCM 14158	392828.3	wgs	PATRIC	392828 tax ID	*
[Ref.: #66792]	Actinomadura chibensis NBRC 106107	2675903560	draft	JGI IMG/M	1220554 tax ID	*

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Actinomadura chibensis NBRC 106107 PATRIC: 1220554.3
[Ref.: #69480]	motile	no	92.842	no
[Ref.: #69480]	gram-positive	yes	89.715	no
[Ref.: #69480]	anaerobic	no	98.069	no
[Ref.: #69480]	aerobic	yes	89.847	no
[Ref.: #69480]	halophile	no	93.347	no
[Ref.: #69480]	spore-forming	yes	91.561	no
[Ref.: #69480]	glucose-util	yes	89.719	no
[Ref.: #69480]	flagellated	no	98.452	no
[Ref.: #69480]	thermophile	no	92.256	yes
[Ref.: #69480]	glucose-ferment	no	88.844	no

Availability in culture collections External links

[Ref.: #12265]

Culture collection no.

DSM 45038, IFM 10266, JCM 14158, NBRC 106107

[Ref.: #85996]

SI-ID 297503

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Actinomadura decatromicini sp. nov., isolated from mountain soil in Thailand.	Songsumanus A, Kuncharoen N, Kudo T, Yuki M, Ohkuma M, Igarashi Y, Tanasupawat S	J Antibiot (Tokyo)	10.1038/s41429-020-0353-y	2020	*
Phylogeny	Actinomadura syzygii sp. nov., an endophytic actinomycete isolated from the roots of a jambolan plum tree (Syzygium cumini L. Skeels).	Rachniyom H, Matsumoto A, Indananda C, Duangmal K, Takahashi Y, Thamchaipenet A	Int J Syst Evol Microbiol	10.1099/ijs.0.000203	2015	*

References

#12265

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45038

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#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) .

#85996

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-ID297503.1 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Actinomadura chibensis in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Actinomadura chibensis NBRC 106107

Change proposal

Change proposal