Amycolatopsis palatopharyngis (DSM 44832, AS 4.1729, PCM 2600)

Name: Amycolatopsis palatopharyngis (DSM 44832, AS 4.1729, PCM 2600)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13254

Type strain

Strain Designation 1BDZ

Culture col. no. DSM 44832 AS 4.1729 PCM 2600 1BDZ CIP 108399 2 more

NCBI tax ID(s) 187982

Special Collections DSMZ JCM CIP Literature strains

History <- CGMCC 2004, PCM AS 4.1729 AS 4.1729 <-- Y. Huang 1BDZ. CIP <- 2004, PCM AS 4.1729

Links

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

rod-shaped facultative anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 131412

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

@ref 20215

Last LPSN update 2026-02-09 11:21:05

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Pseudonocardiales

Family Pseudonocardiaceae

Genus Amycolatopsis

Species Amycolatopsis palatopharyngis

Full scientific name Amycolatopsis palatopharyngis Huang et al. 2004

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
29926		rod-shaped
121505	negative	rod-shaped
125439	positive		95.3

Colony morphology

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
12014	N-Z-AMINE-MEDIUM (DSMZ Medium 554)	Medium recipe at MediaDive	Name: N-Z-AMINE-MEDIUM (DSMZ Medium 554) Composition: Starch 20.0 g/l Agar 20.0 g/l Glucose 10.0 g/l N-Z amine 5.0 g/l Yeast extract 5.0 g/l CaCO3 1.0 g/l Distilled water
33960	MEDIUM 29- Brain heart agar		Distilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
121505	CIP Medium 29	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
12014	positive	growth	28
29926	positive	growth	10-40
33960	positive	growth	37
67770	positive	growth	37
121505	positive	growth	25-45
121505	negative	growth	10

Culture pH

@ref	Ability	Type	PH	PH range
29926	positive	growth	06-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29926	facultative anaerobe
121505	obligate aerobe
125438	aerobe	90.612
125439	obligate aerobe	97.3

Spore formation

29926

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29926	NaCl	positive	growth	0.5-10 %
121505	NaCl	positive	growth	6 %
121505	NaCl		growth	0 %
121505	NaCl		growth	2 %
121505	NaCl		growth	4 %
121505	NaCl		growth	8 %
121505	NaCl		growth	10 %

Observation

67770

Observationquinones: MK-9(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29926	22599 ChEBI	arabinose	+	carbon source
29926	17057 ChEBI	cellobiose	+	carbon source
121505	16947 ChEBI	citrate	-	carbon source
121505	4853 ChEBI	esculin	+	hydrolysis
29926	28757 ChEBI	fructose	+	carbon source
29926	28260 ChEBI	galactose	+	carbon source
121505	606565 ChEBI	hippurate	-	hydrolysis
29926	17306 ChEBI	maltose	+	carbon source
29926	28053 ChEBI	melibiose	+	carbon source
29926	17632 ChEBI	nitrate	+	reduction
121505	17632 ChEBI	nitrate	-	reduction
121505	16301 ChEBI	nitrite	-	reduction
29926	16634 ChEBI	raffinose	+	carbon source
29926	30911 ChEBI	sorbitol	+	carbon source
29926	17992 ChEBI	sucrose	+	carbon source
29926	18222 ChEBI	xylose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
121505	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
121505	15688 ChEBI	acetoin	-
121505	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
121505	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	+	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
121505	amylase	+
68382	beta-galactosidase	-	3.2.1.23	from API zym
121505	beta-galactosidase	-	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
121505	caseinase	-	3.4.21.50
121505	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
121505	DNase	+
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
121505	gamma-glutamyltransferase	+	2.3.2.2
29926	gelatinase	+
121505	gelatinase	-
121505	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
121505	lipase	-
68382	lipase (C 14)	-		from API zym
121505	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
121505	ornithine decarboxylase	-	4.1.1.17
121505	oxidase	+
68382	trypsin	+	3.4.21.4	from API zym
121505	tryptophan deaminase	-
121505	tween esterase	-
29926	urease	+	3.5.1.5
121505	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
121505	-	+	+	+	-	+	-	-	+	+	+	+	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Infection	#Disease	-
#Infection	#Patient	-
#Host	#Human	#Male

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent	Isolation date
12014	from the infected palatopharyngeal mucosa of a 70-year-old male patient	Poland	POL	Europe
67770	Palatopharyngeal mucosa of a patient
121505	Human, Infected palatopharyngeal mucosa	Poland	POL	Europe	2001

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Biosafety level	Biosafety level comment
12014	yes, in single cases	1	Risk group (German classification) According to TRBA 466
121505		1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM338518v1 assembly for Amycolatopsis palatopharyngis DSM 44832	contig	GCA_003385185	187982.4	2866120936	187982	47.71

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
12014	Amycolatopsis palatopharyngis strain 1Bdz 16S ribosomal RNA gene, partial sequence	AF479268	1427		187982

GC content

12014

GC-content (mol%)65.8

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Amycolatopsis palatopharyngis DSM 44832
NCBI: GCA_003385185

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	50.50	no
125439	motility	BacteriaNetⓘ	no	80.20	no
125439	gram_stain	BacteriaNetⓘ	positive	95.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Amycolatopsis palatopharyngis strain DSM 44832
PATRIC: 187982.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	86.42	no
125438	anaerobic	anaerobicⓘ	no	95.60	yes
125438	spore-forming	spore-formingⓘ	yes	77.42	no
125438	aerobic	aerobicⓘ	yes	90.61	no
125438	thermophilic	thermophileⓘ	no	95.37	yes
125438	flagellated	motile2+ⓘ	no	89.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	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
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

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 )
#26297	IJSEM 359 2004 ( DOI 10.1099/ijs.0.02685-0 , PubMed 15023943 )
#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
#33960	; Curators of the CIP;
#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 .
#121505	Collection of Institut Pasteur ; Curators of the CIP; CIP 108399
#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 palatopharyngis (DSM 44832, AS 4.1729, PCM 2600)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003385185

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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