Amycolatopsis endophytica (DSM 104006, CCTCC AA 2010003, JCM 31481)

Name: Amycolatopsis endophytica (DSM 104006, CCTCC AA 2010003, JCM 31481)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132133

Type strain

Culture col. no. DSM 104006 CCTCC AA 2010003 JCM 31481 KCTC 19776 KLBMP 1221

NCBI tax ID(s) 860233

Special Collections DSMZ JCM KCTC

History DSMZ <- CCTCC; CCTCC AA2010003 JCM <-- KCTC 19776 <-- S. Qin; Xuzhou Normal Univ., China; KLBMP 1221. KCTC <- S Qin, Xuzhou Normal Univ., China

Links

Amycolatopsis endophytica DSM 104006 is an aerobe, Gram-positive bacterium that was isolated from healthy oil-seed plant Jatrophacurcas L.

Gram-positive aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 408025

KCTC 19776,JCM 31481,DSM 104006

@ref 20215

Last LPSN update 2026-05-29 08:37:47

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Pseudonocardiales

Family Pseudonocardiaceae

Genus Amycolatopsis

Species Amycolatopsis endophytica

Full scientific name Amycolatopsis endophytica Miao et al. 2012

Morphology

Cell morphology

@ref	Gram stain	Confidence
67771	positive
125439	positive	98.701
125438	positive	92.342

Multimedia

@ref:	23923
multimedia content:	DSM_104006.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_104006.jpg
caption:	Medium 65 28°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
23923	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)		Medium recipe at MediaDive	Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
23923	positive	growth	28
67770	positive	growth	28
67771	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
67771	aerobe
125439	obligate aerobe	99.639

Observation

67770

Observationquinones: MK-9(H₄)

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Shrub (Scrub)

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
23923	healthy oil-seed plant Jatrophacurcas L	Jatropha curcas	Sichuan Province, Panzhihua	China	CHN	Asia
67770	Surface-sterilized seeds of Jatropha curcas L.	Jatropha curcas	Panzhihua, Sichuan Province, south-west China	China	CHN	Asia
67771	From surface-sterilized seeds of an oil-seed plant `Jatropha curcas L.`		Sichuan Province	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence HM153799 (>99% sequence identity) for Amycolatopsis from Microbeatlas

Aquatic Samples	0
Soil Samples	4
Animal Samples	1
Plant Samples	0
Total Samples	5

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
23923	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM1341040v1 assembly for Amycolatopsis endophytica DSM 104006	contig	GCA_013410405	860233.3	2856431239	860233	77.18

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
23923	Amycolatopsis endophytica strain KLBMP 1221 16S ribosomal RNA gene, partial sequence	HM153799	1443		860233

GC content

@ref	GC-content (mol%)	Method
23923	73.3	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1341040v1 assembly for Amycolatopsis endophytica DSM 104006
BV-BRC: 860233.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.64	no
125439	gram_stain	BacteriaNetⓘ	positive	98.70	no
125439	motility	BacteriaNetⓘ	no	87.98	no
125439	spore_formation	BacteriaNetⓘ	yes	64.26	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Amycolatopsis endophytica strain DSM 104006
PATRIC: 860233.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	92.34	yes
125438	anaerobic	anaerobicⓘ	no	98.42	yes
125438	aerobic	aerobicⓘ	yes	89.29	yes
125438	spore-forming	spore-formingⓘ	yes	79.36	no
125438	thermophilic	thermophileⓘ	no	95.49	no
125438	flagellated	motile2+ⓘ	no	88.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Amycolatopsis endophytica sp. nov., a novel endophytic actinomycete isolated from oil-seed plant Jatropha curcas L.	Miao Q, Qin S, Bian GK, Yuan B, Xing K, Zhang YJ, Li Q, Tang SK, Li WJ, Jiang JH	Antonie Van Leeuwenhoek	10.1007/s10482-011-9588-8	2011

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 )
#23923	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 104006
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Amycolatopsis endophytica (DSM 104006, CCTCC AA 2010003, JCM 31481)

Name and taxonomic classification

Morphology

Cell morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Observation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_013410405

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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