Emticicia agri (KCTC 62270, JCM 33056, 17J42-9)

Name: Emticicia agri (KCTC 62270, JCM 33056, 17J42-9)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 164447

Type strain

Strain Designation 17J42-9

Culture col. no. KCTC 62270 JCM 33056 17J42-9

NCBI tax ID(s) 2492393

Special Collections JCM KCTC Literature strains

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Emticicia agri 17J42-9 is an aerobe, mesophilic, Gram-negative prokaryote that forms circular colonies and was isolated from Soil on Jeju Island.

Gram-negative motile rod-shaped colony-forming aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 25477

KCTC 62270,JCM 33056

@ref 20215

Last LPSN update 2025-12-16 10:09:28

Domain Pseudomonadati

Phylum Bacteroidota

Class Cytophagia

Order Cytophagales

Family Spirosomataceae

Genus Emticicia

Species Emticicia agri

Full scientific name Emticicia agri Ten et al. 2019

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Flagellum arrangement	Confidence
68212	negative	4.7-10.8 µm	0.8-1.1 µm	rod-shaped	gliding
125439	negative					99.3
125438	negative					97.774

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
68212	2 mm	orange	circular	3 days	Reasoner's 2A agar (R2A)

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
67770	positive	growth	25	mesophilic
68212	positive	growth	10-37

Culture pH

@ref	Ability	Type	PH	PH range
68212	positive	growth	6.0-8.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
68212	aerobe
125439	obligate aerobe	98.4

Spore formation

@ref	Spore formation	Confidence
125439		95.5

Halophily

@ref	Salt	Growth	Tested relation	Concentration
68212	NaCl	positive	growth	0.5 %(w/v)
68212	NaCl		growth	1 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68212	16808 ChEBI	2-dehydro-D-gluconate	-	assimilation
68212	16193 ChEBI	3-hydroxybenzoate	-	assimilation
68212	37054 ChEBI	3-hydroxybutyrate	-	assimilation
68212	17879 ChEBI	4-hydroxybenzoate	-	assimilation
68212	58143 ChEBI	5-dehydro-D-gluconate	-	assimilation
68212	30089 ChEBI	acetate	-	assimilation
68212	17128 ChEBI	adipate	-	assimilation
68212	16947 ChEBI	citrate	-	assimilation
68212	17634 ChEBI	D-glucose	-	assimilation
68212	16899 ChEBI	D-mannitol	+	assimilation
68212	16024 ChEBI	D-mannose	-	assimilation
68212	16988 ChEBI	D-ribose	-	assimilation
68212	17924 ChEBI	D-sorbitol	-	assimilation
68212	27689 ChEBI	decanoate	-	assimilation
68212	4853 ChEBI	esculin	+	hydrolysis
68212	24265 ChEBI	gluconate	-	assimilation
68212	17234 ChEBI	glucose	-	builds acid from
68212	28087 ChEBI	glycogen	-	assimilation
68212	17120 ChEBI	hexanoate	-	assimilation
68212	35581 ChEBI	indole	-	hydrolysis
68212	17240 ChEBI	itaconate	-	assimilation
68212	16977 ChEBI	L-alanine	-	assimilation
68212	30849 ChEBI	L-arabinose	-	assimilation
68212	18287 ChEBI	L-fucose	-	assimilation
68212	15971 ChEBI	L-histidine	-	assimilation
68212	15589 ChEBI	L-malate	-	assimilation
68212	17203 ChEBI	L-proline	+	assimilation
68212	62345 ChEBI	L-rhamnose	+	assimilation
68212	17115 ChEBI	L-serine	-	assimilation
68212	24996 ChEBI	lactate	-	assimilation
68212	15792 ChEBI	malonate	-	assimilation
68212	17306 ChEBI	maltose	-	assimilation
68212	28053 ChEBI	melibiose	-	assimilation
68212	17268 ChEBI	myo-inositol	-	assimilation
68212	506227 ChEBI	N-acetyl-D-glucosamine	+	assimilation
68212	17632 ChEBI	nitrate	-	reduction
68212	18401 ChEBI	phenylacetate	-	assimilation
68212	17272 ChEBI	propionate	-	assimilation
68212	17814 ChEBI	salicin	-	assimilation
68212	76282 ChEBI	suberate	-	assimilation
68212	17992 ChEBI	sucrose	+	assimilation
68212	53426 ChEBI	tween 80	+/-	hydrolysis
68212	16199 ChEBI	urea	-	hydrolysis
68212	31011 ChEBI	valerate	-	assimilation

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68212	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68212	acid phosphatase	+	3.1.3.2
68212	alkaline phosphatase	+	3.1.3.1
68212	alpha-chymotrypsin	+	3.4.21.1
68212	alpha-fucosidase	+	3.2.1.51
68212	alpha-galactosidase	+	3.2.1.22
68212	alpha-glucosidase	+	3.2.1.20
68212	alpha-mannosidase	+	3.2.1.24
68212	arginine dihydrolase	-	3.5.3.6
68212	beta-galactosidase	+	3.2.1.23
68212	beta-glucosidase	+	3.2.1.21
68212	beta-glucuronidase	-	3.2.1.31
68212	catalase	+	1.11.1.6
68212	cystine arylamidase	+	3.4.11.3
68212	cytochrome oxidase	+	1.9.3.1
68212	esterase (C 4)	+
68212	esterase Lipase (C 8)	+/-
68212	gelatinase	-
68212	leucine arylamidase	+	3.4.11.1
68212	lipase (C 14)	-
68212	N-acetyl-beta-glucosaminidase	+	3.2.1.52
68212	naphthol-AS-BI-phosphohydrolase	+
68212	trypsin	+	3.4.21.4
68212	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@ref

68212

Fatty acid	Percentage
C16:1 w7c/C16:1 w6c	34.1
C15:0 iso	23.4
C17:0 iso 3OH	10.8
C16:0	5.7
C16:1 w5c	5.7
C15:0 iso 3OH	4.7
C16:0 N alcohol	4.7
C16:0 3OH	3
C18:0	1.8
C15:1 iso G	1.2
C14:0	1

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture
67770	Soil on Jeju Island		Republic of Korea	KOR	Asia
68212	soil	Jeju Island	Republic of Korea	KOR	Asia	33.3259	126.842 33.3259/126.842	Reasoner's 2A

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
68212	ASM416828v1 assembly for Emticicia agri 17J42-9	contig	GCA_004168285	2492393.4	2883663913	2492393	44.21

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
67770	Emticicia sp. 17J42-9 gene for 16S ribosomal RNA, partial sequence	LC434627	1431		2492393

GC content

@ref	GC-content (mol%)	Method
68212	38.6	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Emticicia agri 17J42-9
NCBI: GCA_004168285

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	95.50	no
125439	motility	BacteriaNetⓘ	no	79.30	no
125439	gram_stain	BacteriaNetⓘ	negative	99.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Emticicia agri 17J42-9
NCBI: GCA_004168285.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.77	yes
125438	anaerobic	anaerobicⓘ	no	96.18	no
125438	aerobic	aerobicⓘ	yes	87.63	no
125438	spore-forming	spore-formingⓘ	no	86.83	no
125438	thermophilic	thermophileⓘ	no	94.65	yes
125438	flagellated	motile2+ⓘ	no	88.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Emticicia agri sp. nov., a novel member of the family Cytophagaceae.	Ten LN, Li W, Ha A, Kim MK, Rooney AP, Jung HY	Int J Syst Evol Microbiol	10.1099/ijsem.0.003651	2019

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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68212	Leonid N. Ten, Weilan Li, Aeri Ha, Myung Kyum Kim, Alejandro P. Rooney and Hee-Young Jung: Emticicia agri sp. nov., a novel member of the family Cytophagaceae. IJSEM 69: 3492 - 3499 2019 ( DOI 10.1099/ijsem.0.003651 )
#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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Emticicia agri (KCTC 62270, JCM 33056, 17J42-9)

Name and taxonomic classification