Archive BacDiveID:10.13145/bacdive13215.20201210.5

Strain identifier

BacDive ID: 13215

Type strain:

Species: Amycolatopsis orientalis

Strain Designation: M 43-05865, Pittinger M43-05865, CCTMLa 2924

Strain history: CIP <- 2001, CCM, Amycolatopsis orientalis subsp. orientalis <- R. E. Gordon <- E. B. Shirling <- R. C. Pittenger: strain M 43-05865

NCBI tax ID(s): 1125971 (strain), 31958 (species)

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

General

@ref: 9119

BacDive-ID: 13215

DSM-Number: 40040

keywords: mesophilic, spore-forming, Bacteria, 16S sequence, genome sequence, antibiotic compound production, human pathogen

description: Amycolatopsis orientalis M 43-05865 is a spore-forming, mesophilic human pathogen that builds an aerial mycelium and produces antibiotic compounds.

strain history: <- E.B. Shirling, ISP <- R.C. Pittenger, M 43-05865 (Streptomyces orientalis)

doi: 10.13145/bacdive13215.20201210.5

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/actinobacteria
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Pseudonocardiales
family: Pseudonocardiaceae
genus: Amycolatopsis
species: Amycolatopsis orientalis
full scientific name: Amycolatopsis orientalis (Pittenger and Brigham 1956) Lechevalier et al. 1986
synonyms
@ref synonym
20215 Nocardia orientalis
20215 Streptomyces orientalis

@ref	synonym
20215	Nocardia orientalis
20215	Streptomyces orientalis

@ref: 9119

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Amycolatopsis

species: Amycolatopsis orientalis

full scientific name: Amycolatopsis orientalis (Pittenger and Brigham 1956) Lechevalier et al. 1986 emend. Nouioui et al. 2018

strain designation: M 43-05865, Pittinger M43-05865

type strain: yes

Morphology

colony morphology

@ref	colony color	incubation period	medium used
19392	Yellow	10-14 days	ISP 2
19392	Beige	10-14 days	ISP 3
19392	Beige	10-14 days	ISP 4
19392	Beige	10-14 days	ISP 5
19392	Beige	10-14 days	ISP 6
19392	Beige	10-14 days	ISP 7

multicellular morphology

@ref	forms multicellular complex	complex name	complex color	medium name
19392	yes	Aerial Mycelium	White	ISP 2
19392	yes	Aerial Mycelium	White	ISP 3
19392	yes	Aerial Mycelium	White	ISP 4
19392	yes	Aerial Mycelium	White	ISP 5
19392	yes	Aerial Mycelium	White	ISP 6
19392	yes	Aerial Mycelium	White	ISP 7

multimedia

@ref: 9119
multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_40040.jpg
caption: Medium 65 28°C
license or copyright: (C) Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH
intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@ref	name	growth	composition	link
19392	ISP 2	yes	Name: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
19392	ISP 3	yes	Name: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19392	ISP 4	yes	Name: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19392	ISP 5	yes	Name: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19392	ISP 6	yes	Name: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19392	ISP 7	yes	Name: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
38186	MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulum	yes	Distilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g)
9119	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	yes		https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf
9119	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)	yes		https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium65.pdf

culture temp

@ref	growth	type	temperature	range
19392	positive	optimum	30	mesophilic
9119	positive	growth	28	mesophilic
38186	positive	growth	30	mesophilic

Physiology and metabolism

spore formation

@ref: 19392
spore description: spore surface: smooth, Fragmentation: +
spore formation: yes

compound production

@ref	compound
9119	vancomycin
20216	Vancomycin

halophily

@ref: 19392
salt: NaCl
growth: positive
tested relation: maximum
concentration: 5 %

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity
19392	62968	cellulose	-
19392	16634	raffinose	-
19392	26546	rhamnose	-
19392	28757	fructose	-
19392	29864	mannitol	+
19392	17268	myo-inositol	+
19392	18222	xylose	-
19392	17992	sucrose	-
19392	22599	arabinose	+
19392	17234	glucose	+

API zym

@ref	Alkaline phosphatase	Esterase	Esterase Lipase	Lipase	Leucine arylamidase	Valine arylamidase	Cystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
19392	+	+	+	-	-	-	-	-	+	+	+	-	-	-	-	-	+	-	-

API 20E

@ref	ONPG	ADH Arg	LDC Lys	ODC	CIT	H2S	URE	TDA Trp	IND	VP	GEL
19392	-	+	-	-	+	-	-	-	-	-	+

Isolation, sampling and environmental information

isolation

@ref: 9119
sample type: soil
geographic location: Asia

isolation source categories

Cat1: #Environmental
Cat2: #Terrestrial
Cat3: #Soil

Safety information

risk assessment

@ref	biosafety level	biosafety level comment	pathogenicity human
19392	1	Risk group (German classification)
9119	1	Risk group (German classification)	yes

Sequence information

16S sequences

@ref	description	accession	length	database	NCBI tax ID
20218	Amycolatopsis orientalis partial 16S rRNA gene, strain IMSNU 20058T	AJ400711	1458	ena	31958
20218	Amycolatopsis orientalis gene for 16S ribosomal RNA, partial sequence, strain: JCM 4235	D44036	120	ena	31958
20218	Amycolatopsis orientalis gene for 16S ribosomal RNA, partial sequence	D86935	1467	ena	31958
20218	A.orientalis (ssp. orientalis DSM 40040) 16S ribosomal RNA (partial)	X76958	1444	ena	31958

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Amycolatopsis orientalis B-37	GCA_000943515	complete	ncbi	31958
66792	Amycolatopsis orientalis DSM 40040 = KCTC 9412	GCA_000478275	contig	ncbi	1125971
66792	Amycolatopsis orientalis DSM 40040 = KCTC 9412	1125971.3	wgs	patric	1125971
66792	Amycolatopsis orientalis strain B-37	31958.7	wgs	patric	31958

External links

@ref: 9119

culture collection no.: DSM 40040, ATCC 19795, CBS 547.68, CCM 2778, IAM 14281, IFO 12360, IFO 12806, IMET 7510, IMET 7653, IMSNU 20058, ISP 5040, JCM 4235, JCM 4600, KCC S-0235, KCC S-0600, NBRC 12360, NBRC 12806, NIHJ 483, NRRL 2450, RIA 1074

straininfo link

@ref	passport
20218	http://www.straininfo.net/strains/164569
20218	http://www.straininfo.net/strains/119664
20218	http://www.straininfo.net/strains/230419
20218	http://www.straininfo.net/strains/164571
20218	http://www.straininfo.net/strains/164572
20218	http://www.straininfo.net/strains/164573
20218	http://www.straininfo.net/strains/119667
20218	http://www.straininfo.net/strains/164574
20218	http://www.straininfo.net/strains/119668
20218	http://www.straininfo.net/strains/279007
20218	http://www.straininfo.net/strains/119665
20218	http://www.straininfo.net/strains/164575
20218	http://www.straininfo.net/strains/164576
20218	http://www.straininfo.net/strains/164577
20218	http://www.straininfo.net/strains/164578
20218	http://www.straininfo.net/strains/486258
20218	http://www.straininfo.net/strains/334260
20218	http://www.straininfo.net/strains/804511
20218	http://www.straininfo.net/strains/116669
20218	http://www.straininfo.net/strains/119670

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
9119	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40040)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-40040
19392	Wink, J.		http://www.dsmz.de/microorganisms/wink_pdf/DSM40040.pdf	Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
20216	Curators of the HKI		http://www.leibniz-hki.de/de/	Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI)
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
38186	Curators of the CIP		https://brclims.pasteur.fr/brcWeb/souche/detail/1/4513
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)

General

Name and taxonomic classification

LPSN

synonyms

Morphology

colony morphology

multicellular morphology

multimedia

Culture and growth conditions

culture medium

culture temp

Physiology and metabolism

spore formation

compound production

halophily

metabolite utilization

API zym

API 20E

Isolation, sampling and environmental information

isolation

isolation source categories

Safety information

risk assessment

Sequence information

16S sequences

Genome sequences

External links

straininfo link

Reference