Name: Emticicia oligotrophica GPTSA100-15
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 3783

Type strain:

Species: Emticicia oligotrophica

Strain Designation: GPTSA100-15

Culture col. no.: DSM 17448, CIP 109782, MTCC 6937

Strain history: <- MTCC <- P. Saha and T. Chakrabarti; GPTSA100-15

NCBI tax ID(s): 929562 (strain), 312279 (species)

SI-ID 396940

DSM 17448

Section

Emticicia oligotrophica GPTSA100-15 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from warm spring water.

Gram-negative
rod-shaped
aerobe
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	*Bacteroidota*
	Class	*Cytophagia*
	Order	*Cytophagales*
	Family	*Spirosomataceae*
	Genus	*Emticicia*
	Species	**Emticicia oligotrophica**
	Full Scientific Name (LPSN)	Emticicia oligotrophica Saha and Chakrabarti 2006

Information on morphological and physiological properties Morphology

[Ref.: #31704]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.993

[Ref.: #31704]	Cell length	02-05 µm

[Ref.: #31704]	Cell width	0.3-0.4 µm

[Ref.: #31704]	Cell shape	rod-shaped

[Ref.: #31704]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %95.187

[Ref.: #31704]

Pigment production

yes

Multimedia content

[Ref.: #66793]

Caption:

electron microscopic image

[Ref.: #66793]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6989]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #6989]

Culture medium growth

[Ref.: #6989]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6989]

Culture medium composition

expand / minimize

[Ref.: #6989]

Culture medium

DILUTED TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545a)

[Ref.: #6989]

Culture medium growth

[Ref.: #6989]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6989]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #6989]	growth	28 °C
[Ref.: #31704]	growth	15-42 °C
[Ref.: #31704]	optimum	37 °C

[Ref.: #6989]	Temperature range	mesophilic
[Ref.: #31704]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31704]			optimum	08-11
[Ref.: #31704]			growth	05-11

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31704]

Oxygen tolerance

aerobe

[Ref.: #31704]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.99

[Ref.: #31704]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31704]	arabinose ChEBI	+	carbon source
[Ref.: #31704]	cellobiose ChEBI	+	carbon source
[Ref.: #31704]	fructose ChEBI	+	carbon source
[Ref.: #31704]	galactose ChEBI	+	carbon source
[Ref.: #31704]	glucose ChEBI	+	carbon source
[Ref.: #31704]	glycerol ChEBI	+	carbon source
[Ref.: #31704]	lactose ChEBI	+	carbon source
[Ref.: #31704]	melibiose ChEBI	+	carbon source
[Ref.: #31704]	nitrate ChEBI	+	reduction
[Ref.: #31704]	raffinose ChEBI	+	carbon source
[Ref.: #31704]	sucrose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #31704]	catalase	+	1.11.1.6
[Ref.: #31704]	cytochrome oxidase	+	1.9.3.1
[Ref.: #31704]	gelatinase	+
[Ref.: #31704]	urease	+	3.5.1.5

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

[Ref.: #6989]	Sample type/isolated from	warm spring water
[Ref.: #6989]	Geographic location (country and/or sea, region)	Assam, Jorhat
[Ref.: #6989]	Country	India
[Ref.: #6989]	Country ISO 3 Code	IND
[Ref.: #6989]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Thermal spring

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AY904352 (>99% sequence identity) for Emticicia oligotrophica subclade from Microbeatlas

Aquatic Samples	1267
Soil Samples	68
Animal Samples	102
Plant Samples	62
Total Samples	1499

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

[Ref.: #6989]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #6989]	Emticicia oligotrophica strain GPTSA100-15 16S ribosomal RNA gene, partial sequence	AY904352	1385	ENA	929562 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Emticicia oligotrophica GPTSA100-15, DSM 17448	2506485001	complete	JGI IMG/M	929562 tax ID	*
[Ref.: #66792]	Emticicia oligotrophica DSM 17448	929562.9	plasmid	PATRIC	929562 tax ID	*
[Ref.: #66792]	Emticicia oligotrophica DSM 17448	929562.8	plasmid	PATRIC	929562 tax ID	*
[Ref.: #66792]	Emticicia oligotrophica DSM 17448	929562.7	plasmid	PATRIC	929562 tax ID	*
[Ref.: #66792]	Emticicia oligotrophica DSM 17448	929562.6	plasmid	PATRIC	929562 tax ID	*
[Ref.: #66792]	Emticicia oligotrophica DSM 17448	929562.10	plasmid	PATRIC	929562 tax ID	*

[Ref.: #6989]	GC-content	36.9 mol%
[Ref.: #6989]	GC-content	35.6 mol%	sequence analysis

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: Emticicia oligotrophica DSM 17448 DSM 17448 NCBI: GCA_000263195.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Emticicia oligotrophica DSM 17448 DSM 17448 NCBI: GCA_000263195.1
[Ref.: #69480]	motile	no	94.608	yes
[Ref.: #69480]	flagellated	no	97.126	yes
[Ref.: #69480]	gram-positive	no	97.686	yes
[Ref.: #69480]	anaerobic	no	99.03	yes
[Ref.: #69480]	aerobic	yes	85.535	yes
[Ref.: #69480]	halophile	no	96.382	no
[Ref.: #69480]	spore-forming	no	94.822	yes
[Ref.: #69480]	glucose-util	yes	85.745	yes
[Ref.: #69480]	thermophile	no	96.228	no
[Ref.: #69480]	glucose-ferment	no	90.234	no

Availability in culture collections External links

[Ref.: #6989]

Culture collection no.

DSM 17448, CIP 109782, MTCC 6937

[Ref.: #73295]

SI-ID 396940

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Emticicia aquatilis sp. nov., isolated from a freshwater sample.	Ngo HTT, Trinh H, Yang JE, Won KH, Chu DH, Kook M, Yi TH	Int J Syst Evol Microbiol	10.1099/ijsem.0.001840	2017	*
Phylogeny	Emticiciafontis sp. nov., isolated from a freshwater pond.	Nam GG, Joung Y, Song J, Lim Y, Cho JC	Int J Syst Evol Microbiol	10.1099/ijsem.0.001490	2016	*
Phylogeny	Emticicia paludis sp. nov., isolated from wetland freshwater.	Kang H, Kim H, Joung Y, Joh K	Int J Syst Evol Microbiol	10.1099/ijsem.0.001205	2016	*
Phylogeny	Emticicia aquatica sp. nov., a species of the family Cytophagaceae isolated from fresh water.	Joung Y, Seo MA, Kang H, Kim H, Ahn TS, Cho JC, Joh K	Int J Syst Evol Microbiol	10.1099/ijsem.0.000577	2015	*
Phylogeny	Taeseokella kangwonensis gen. nov., sp. nov., isolated from a freshwater reservoir.	Joung Y, Hong S, Kim H, Kang H, Farrance CE, Joh K	Int J Syst Evol Microbiol	10.1099/ijsem.0.000582	2015	*
Phylogeny	Emticicia sediminis sp. nov. isolated from sediment of a shallow stream.	Park SE, Lee S, Kim H, Ahn TY	Int J Syst Evol Microbiol	10.1099/ijs.0.000292	2015	*
Phylogeny	Lacihabitans soyangensis gen. nov., sp. nov., a new member of the family Cytophagaceae, isolated from a freshwater reservoir.	Joung Y, Kim H, Kang H, Lee BI, Ahn TS, Joh K	Int J Syst Evol Microbiol	10.1099/ijs.0.058511-0	2014	*
Phylogeny	Emticicia ginsengisoli sp. nov., a species of the family 'Flexibacteraceae' isolated from soil of a ginseng field.	Liu QM, Ten LN, Yu HS, Jin FX, Im WT, Lee ST	Int J Syst Evol Microbiol	10.1099/ijs.0.65386-0	2008	*
Phylogeny	Emticicia oligotrophica gen. nov., sp. nov., a new member of the family 'Flexibacteraceae', phylum Bacteroidetes.	Saha P, Chakrabarti T	Int J Syst Evol Microbiol	10.1099/ijs.0.64086-0	2006	*

References

#6989

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17448

#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 )

#31704

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 #27981 (see below)

#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) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#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 )

#73295

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-ID396940.1 )

#27981

IJSEM 991 2006 ( DOI 10.1099/ijs.0.64086-0 , PubMed 16627643 )

* These data were automatically processed and therefore are not curated

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Emticicia oligotrophica DSM 17448 DSM 17448

Emticicia oligotrophica DSM 17448 DSM 17448

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