Name: Amycolatopsis palatopharyngis 1BDZ
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13254

Type strain:

Species: Amycolatopsis palatopharyngis

Strain Designation: 1BDZ

Culture col. no.: DSM 44832, AS 4.1729, PCM 2600, JCM 12460, CGMCC 4.1729, CIP 108399

Strain history: CIP <- 2004, PCM AS 4.1729

NCBI tax ID(s): 187982 (species)

SI-ID 131412

AS 4.1729, DSM 44832, JCM 12460, CGMCC 4.1729, CIP 108399

Section

Amycolatopsis palatopharyngis 1BDZ is a facultative anaerobe, mesophilic, rod-shaped human pathogen that was isolated from from the infected palatopharyngeal mucosa of a 70-year-old male patient.

rod-shaped
facultative anaerobe
human pathogen
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	*Pseudonocardiales*
	Family	*Pseudonocardiaceae*
	Genus	*Amycolatopsis*
	Species	**Amycolatopsis palatopharyngis**
	Full Scientific Name (LPSN)	Amycolatopsis palatopharyngis Huang et al. 2004

Information on morphological and physiological properties Morphology

[Ref.: #121505]	Gram stain	negative
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #121505]	Cell shape	rod-shaped
[Ref.: #29926]	Cell shape	rod-shaped

[Ref.: #121505]	Motility	yes
[Ref.: #29926]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %90.458

Information on culture and growth conditions Culture and growth conditions

[Ref.: #12014]

Culture medium

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

[Ref.: #12014]

Culture medium growth

[Ref.: #12014]

Culture medium link

Medium recipe at MediaDive

[Ref.: #12014]

Culture medium composition

expand / minimize

[Ref.: #33960]

Culture medium

MEDIUM 29- Brain heart agar

[Ref.: #33960]

Culture medium growth

[Ref.: #33960]

Culture medium composition

expand / minimize

[Ref.: #121505]

Culture medium

CIP Medium 29

[Ref.: #121505]

Culture medium growth

[Ref.: #121505]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #12014]		growth	28 °C
[Ref.: #29926]		growth	10-40 °C
[Ref.: #33960]		growth	37 °C
[Ref.: #67770]		growth	37 °C
[Ref.: #121505]		growth	25-45 °C
[Ref.: #121505]	no	growth	10 °C

[Ref.: #12014]	Temperature range	mesophilic
[Ref.: #33960]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #121505]	Temperature range	psychrophilic

	pH	Kind of pH		pH
[Ref.: #29926]			growth	06-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29926]	Oxygen tolerance	facultative anaerobe
[Ref.: #121505]	Oxygen tolerance	obligate aerobe

[Ref.: #29926]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %96
[Ref.: #69480]	Ability of spore formation	yes Confidence in %99.998

	Salt	Tested relation		Salt conc.
[Ref.: #29926]	NaCl		growth	0.5-10	%
[Ref.: #121505]	NaCl		growth	6	%
[Ref.: #121505]	NaCl	no	growth	0	%
[Ref.: #121505]	NaCl	no	growth	2	%
[Ref.: #121505]	NaCl	no	growth	4	%
[Ref.: #121505]	NaCl	no	growth	8	%
[Ref.: #121505]	NaCl	no	growth	10	%

[Ref.: #67770]

Observation

quinones: MK-9(H₄)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29926]	arabinose ChEBI	+	carbon source
[Ref.: #29926]	cellobiose ChEBI	+	carbon source
[Ref.: #121505]	citrate ChEBI	-	carbon source
[Ref.: #121505]	esculin ChEBI	+	hydrolysis
[Ref.: #29926]	fructose ChEBI	+	carbon source
[Ref.: #29926]	galactose ChEBI	+	carbon source
[Ref.: #121505]	hippurate ChEBI	-	hydrolysis
[Ref.: #29926]	maltose ChEBI	+	carbon source
[Ref.: #29926]	melibiose ChEBI	+	carbon source
[Ref.: #29926]	nitrate ChEBI	+	reduction
[Ref.: #121505]	nitrate ChEBI	-	reduction
[Ref.: #121505]	nitrite ChEBI	-	reduction
[Ref.: #29926]	raffinose ChEBI	+	carbon source
[Ref.: #29926]	sorbitol ChEBI	+	carbon source
[Ref.: #29926]	sucrose ChEBI	+	carbon source
[Ref.: #29926]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #121505]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #121505]		acetoin ChEBI	-
[Ref.: #121505]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #121505]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	+	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #121505]	amylase	+
[Ref.: #121505]	beta-galactosidase	-	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #121505]	caseinase	-	3.4.21.50
[Ref.: #121505]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #121505]	DNase	+
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #121505]	gamma-glutamyltransferase	+	2.3.2.2
[Ref.: #29926]	gelatinase	+
[Ref.: #121505]	gelatinase	-
[Ref.: #121505]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #121505]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #121505]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #121505]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #121505]	oxidase	+
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #121505]	tryptophan deaminase	-
[Ref.: #121505]	tween esterase	-
[Ref.: #29926]	urease	+	3.5.1.5
[Ref.: #121505]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #121505]	11150	-	+	+	+	-	+	-	-	+	+	+	+	-	-	-	-	-	-	-	-

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

[Ref.: #12014]	Sample type/isolated from	from the infected palatopharyngeal mucosa of a 70-year-old male patient
[Ref.: #12014]	Country	Poland
[Ref.: #12014]	Country ISO 3 Code	POL
[Ref.: #12014]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Palatopharyngeal mucosa of a patient

[Ref.: #121505]	Sample type/isolated from	Human, Infected palatopharyngeal mucosa
[Ref.: #121505]	Country	Poland
[Ref.: #121505]	Country ISO 3 Code	POL
[Ref.: #121505]	Continent	Europe
[Ref.: #121505]	Isolation date	2001
* marker position based on {}

Isolation sources categories

#Infection	#Disease	-
#Infection	#Patient	-
#Host	#Human	#Male

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AF479268 (>99% sequence identity) for Amycolatopsis marina from Microbeatlas

Aquatic Samples	28
Soil Samples	157
Animal Samples	183
Plant Samples	90
Total Samples	458

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

[Ref.: #12014]	Pathogenicity (human)	yes, in single cases
[Ref.: #12014]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #121505]	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.: #12014]	Amycolatopsis palatopharyngis strain 1Bdz 16S ribosomal RNA gene, partial sequence	AF479268	1427	ENA	187982 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Amycolatopsis palatopharyngis DSM 44832	GCA_003385185	contig	GenBank	187982 tax ID
[Ref.: #66792]	Amycolatopsis palatopharyngis strain DSM 44832	187982.4	wgs	PATRIC	187982 tax ID	*
[Ref.: #66792]	Amycolatopsis palatopharyngis DSM 44832	2866120936	draft	JGI IMG/M	187982 tax ID	*

[Ref.: #12014]

GC-content

65.8 mol%

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: Amycolatopsis palatopharyngis strain DSM 44832 PATRIC: 187982.4
[Ref.: #69481]	spore-forming	no	96	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Amycolatopsis palatopharyngis strain DSM 44832 PATRIC: 187982.4
[Ref.: #69480]	motile	no	91.273	yes
[Ref.: #69480]	gram-positive	yes	90.105	no
[Ref.: #69480]	anaerobic	no	99.244	no
[Ref.: #69480]	aerobic	yes	94.596	no
[Ref.: #69480]	halophile	yes	60.704	no
[Ref.: #69480]	spore-forming	yes	63.156	yes
[Ref.: #69480]	glucose-util	yes	90.21	no
[Ref.: #69480]	flagellated	no	97.614	yes
[Ref.: #69480]	thermophile	no	96.691	yes
[Ref.: #69480]	glucose-ferment	no	93.437	no

Availability in culture collections External links

[Ref.: #12014]

Culture collection no.

DSM 44832, AS 4.1729, PCM 2600, JCM 12460, CGMCC 4.1729, CIP 108399

[Ref.: #82458]

SI-ID 131412

Literature:

	Title	Authors	Journal	DOI	Year
Phylogeny	Amycolatopsis flava sp. nov., a halophilic actinomycete isolated from Dead Sea.	Wei X, Jiang Y, Chen X, Jiang Y, Lai H	Antonie Van Leeuwenhoek	10.1007/s10482-015-0542-z	2015	*
Phylogeny	Amycolatopsis marina sp. nov., an actinomycete isolated from an ocean sediment.	Bian J, Li Y, Wang J, Song FH, Liu M, Dai HQ, Ren B, Gao H, Hu X, Liu ZH, Li WJ, Zhang LX	Int J Syst Evol Microbiol	10.1099/ijs.0.000026-0	2009	*
Phylogeny	Amycolatopsis palatopharyngis sp. nov., a potentially pathogenic actinomycete isolated from a human clinical source.	Huang Y, Pasciak M, Liu Z, Xie Q, Gamian A	Int J Syst Evol Microbiol	10.1099/ijs.0.02685-0	2004	*
	Revisiting the Taxonomic Status of the Biomedically and Industrially Important Genus Amycolatopsis, Using a Phylogenomic Approach.	Sangal V, Goodfellow M, Blom J, Tan GYA, Klenk HP, Sutcliffe IC	Front Microbiol	10.3389/fmicb.2018.02281	2018	*

References

#12014

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44832

#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 )

#29926

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26297 (see below)

#33960 ; 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;

#68382

Automatically annotated from API zym .

#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 )

#82458

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-ID131412.1 )

#121505 Collection of Institut Pasteur ; Curators of the CIP; CIP 108399

#26297

IJSEM 359 2004 ( DOI 10.1099/ijs.0.02685-0 , PubMed 15023943 )

* These data were automatically processed and therefore are not curated

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Amycolatopsis palatopharyngis strain DSM 44832

Amycolatopsis palatopharyngis strain DSM 44832

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