Escherichia marmotae (DSM 28771, CGMCC 1.12862, HT073016)

Name: Escherichia marmotae (DSM 28771, CGMCC 1.12862, HT073016)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 131363

Type strain

Strain Designation HT073016

Culture col. no. DSM 28771 CGMCC 1.12862 HT073016

NCBI tax ID(s) 1499973

Special Collections DSMZ

History <- S. Liu, Nat. Inst. for Communicable Disease Control and Prevention, Beijing, China; HT073016

Links

Escherichia marmotae HT073016 is a bacterium that was isolated from fresh faeces of wild marmot Marmota himalayana.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 403821

DSM 28771

@ref 20215

Last LPSN update 2026-02-09 11:31:26

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Enterobacterales

Family Enterobacteriaceae

Genus Escherichia

Species Escherichia marmotae

Full scientific name Escherichia marmotae Liu et al. 2015

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	99.75

Multimedia

@ref:	22590
multimedia content:	DSM_28771.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_28771.jpg
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
22590	NUTRIENT AGAR (DSMZ Medium 1)		Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
22590	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	92.6

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68368	27613 ChEBI	amygdalin	-	fermentation	from API 20E
68368	29016 ChEBI	arginine	-	hydrolysis	from API 20E
68368	16947 ChEBI	citrate	-	assimilation	from API 20E
68368	17634 ChEBI	D-glucose	+	fermentation	from API 20E
68368	16899 ChEBI	D-mannitol	+	fermentation	from API 20E
68368	5291 ChEBI	gelatin	-	hydrolysis	from API 20E
68368	30849 ChEBI	L-arabinose	+	fermentation	from API 20E
68368	62345 ChEBI	L-rhamnose	+	fermentation	from API 20E
68368	25094 ChEBI	lysine	+	degradation	from API 20E
68368	28053 ChEBI	melibiose	-	fermentation	from API 20E
68368	17268 ChEBI	myo-inositol	-	fermentation	from API 20E
68368	17632 ChEBI	nitrate	+	reduction	from API 20E
68368	18257 ChEBI	ornithine	-	degradation	from API 20E
68368	30911 ChEBI	sorbitol	+	fermentation	from API 20E
68368	17992 ChEBI	sucrose	-	fermentation	from API 20E
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68368	16199 ChEBI	urea	-	hydrolysis	from API 20E

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
68368	17997 ChEBI	dinitrogen	from API 20E
68368	16136 ChEBI	hydrogen sulfide	from API 20E
68368	35581 ChEBI	indole	from API 20E
68368	16301 ChEBI	nitrite	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Indole test
68368	15688 ChEBI	acetoin	-		from API 20E
68368	35581 ChEBI	indole		-	from API 20E

Enzymes

@ref	Value	Activity	Ec
68368	arginine dihydrolase	-	3.5.3.6	from API 20E
68368	beta-galactosidase	-	3.2.1.23	from API 20E
68368	cytochrome oxidase	-	1.9.3.1	from API 20E
68368	gelatinase	-		from API 20E
68368	lysine decarboxylase	+	4.1.1.18	from API 20E
68368	ornithine decarboxylase	-	4.1.1.17	from API 20E
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
68368	urease	-	3.5.1.5	from API 20E

API 20E

@ref	ONPG	ADH (Arg)	LDC (Lys)	ODC	CIT	H2S productionH2S	URE	TDA (Trp)	IND	Acetoin production (Voges Proskauer test)VP	GEL	GLU	MAN	INO	Sor	RHA	SAC	MEL	AMY	ARA	OX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	OF-O	OF-F
22590	-	-	+	-	-	-	-	-	-	-	-	+	+	-	+	+	-	-	-	+	-	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Rodentia (Other)
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
22590	fresh faeces of wild marmot Marmota himalayana	Marmota himalayana	Qinghai province, Yushu Tibetan autonomous prefecture, 4525 m above sea level	China	CHN	Asia	33.425	96.375 33.425/96.375

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
22590	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM290036v1 assembly for Escherichia marmotae HT073016	complete	GCA_002900365	1499973.6	2917408641	1499973	98.02
66792	ASM80769v3 assembly for Escherichia marmotae HT073016	scaffold	GCA_000807695	1499973.3	2630968558	1499973	33.96

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
22590	Escherichia marmotae strain HT073016 16S ribosomal RNA gene, partial sequence	KJ787692	1504		1499973

GC content

@ref	GC-content (mol%)	Method
22590	53.8	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Escherichia marmotae HT073016
NCBI: GCA_002900365

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	79.30	no
125439	motility	BacteriaNetⓘ	yes	67.60	no
125439	gram_stain	BacteriaNetⓘ	negative	70.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	92.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Escherichia marmotae HT073016
NCBI: GCA_002900365.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.75	no
125438	anaerobic	anaerobicⓘ	no	95.87	no
125438	aerobic	aerobicⓘ	no	71.75	no
125438	spore-forming	spore-formingⓘ	no	87.45	no
125438	thermophilic	thermophileⓘ	no	97.50	yes
125438	flagellated	motile2+ⓘ	yes	77.30	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genomic dissection of Escherichia marmotae provides insights into diversity and pathogenic potential.	Binsker U, Deneke C, Hamid HM, Gadicherla AK, Gohler A, Kasbohrer A, Hammerl JA.	ISME Commun	10.1093/ismeco/ycae126	2024
Phylogeny	Escherichia marmotae sp. nov., isolated from faeces of Marmota himalayana.	Liu S, Jin D, Lan R, Wang Y, Meng Q, Dai H, Lu S, Hu S, Xu J	Int J Syst Evol Microbiol	10.1099/ijs.0.000228	2015

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 )
#22590	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28771
#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) .
#68368	Automatically annotated from API 20E .
#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 )

Rate our new design

Content

About us

Escherichia marmotae (DSM 28771, CGMCC 1.12862, HT073016)

Name and taxonomic classification

Morphology

Cell morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20E

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002900365

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media