Shinella pollutisoli (KCTC 52677, CCTCC AB 2017242, AH-1)

Name: Shinella pollutisoli (KCTC 52677, CCTCC AB 2017242, AH-1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 159722

Type strain

Strain Designation AH-1

Culture col. no. KCTC 52677 CCTCC AB 2017242 AH-1

NCBI tax ID(s) 2250594

Special Collections KCTC Literature strains

History KCTC <- Qing Chen, Zaozhuang Univ.

Links

Shinella pollutisoli AH-1 is an aerobe, Gram-negative, motile bacterium that was isolated from TBBPA-contaminated soil sample.

Gram-negative motile rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 24942

KCTC 52677

@ref 20215

Last LPSN update 2026-05-29 08:44:15

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Rhizobiaceae

Genus Shinella

Species Shinella pollutisoli

Full scientific name Shinella pollutisoli Mu et al. 2018

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
66623	negative	1.8-2.5 µm	0.3-0.6 µm	rod-shaped
125438	negative					98.333

Colony morphology

@ref	Colony size	Colony color	Incubation period	Medium used
66623	1-2 mm	pale yellow	2 days	Tryptic Soy Agar

Culture and growth conditions

Culture medium

@ref	Name	Growth
66623	LB (Luria-Bertani) agar
66623	Nutrient agar (NA)
66623	Reasoner's 2A agar (R2A)
66623	tryptic soy agar (TSA)

Culture temp

@ref	Growth	Type	Temperature (°C)
66623	positive	optimum	30
66623	positive	growth	15-37
67771	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
66623	positive	optimum	7
66623	positive	growth	6.5-9	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
66623	aerobe
67771	aerobe
125439	obligate aerobe	97.942

Spore formation

@ref	Spore formation	Confidence
125439		98.755

Halophily

@ref	Salt	Growth	Tested relation	Concentration
66623	NaCl	positive	growth	0-2 %(w/v)
66623	NaCl	positive	optimum	1 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
66623	16193 ChEBI	3-hydroxybenzoate	-	carbon source
66623	17879 ChEBI	4-hydroxybenzoate	-	carbon source
66623	16411 ChEBI	acetic acid	-	carbon source
66623	17128 ChEBI	adipate	-	carbon source
66623	53258 ChEBI	citric acid	-	carbon source
66623	17634 ChEBI	D-glucose	+	carbon source
66623	17634 ChEBI	D-glucose	-	fermentation
66623	16899 ChEBI	D-mannitol	+	carbon source
66623	16988 ChEBI	D-ribose	+	carbon source
66623	17924 ChEBI	D-sorbitol	+	carbon source
66623	27689 ChEBI	decanoate	-	carbon source
66623	4853 ChEBI	esculin	-	hydrolysis
66623	5291 ChEBI	gelatin	-	hydrolysis
66623	24265 ChEBI	gluconate	-	carbon source
66623	28087 ChEBI	glycogen	-	carbon source
66623	17240 ChEBI	itaconate	-	carbon source
66623	16977 ChEBI	L-alanine	+	carbon source
66623	30849 ChEBI	L-arabinose	+	carbon source
66623	18287 ChEBI	L-fucose	-	carbon source
66623	15971 ChEBI	L-histidine	-	carbon source
66623	17203 ChEBI	L-proline	+	carbon source
66623	62345 ChEBI	L-rhamnose	+	carbon source
66623	17115 ChEBI	L-serine	-	carbon source
66623	24996 ChEBI	lactate	-	carbon source
66623	25115 ChEBI	malate	-	carbon source
66623	15792 ChEBI	malonate	-	carbon source
66623	17306 ChEBI	maltose	+	carbon source
66623	28053 ChEBI	melibiose	-	carbon source
66623	17268 ChEBI	myo-inositol	+	carbon source
66623	59640 ChEBI	N-acetylglucosamine	+	carbon source
66623	17632 ChEBI	nitrate	-	reduction
66623	18401 ChEBI	phenylacetate	-	carbon source
66623		potassium 2-dehydro-D-gluconate	-	carbon source
66623		potassium 5-dehydro-D-gluconate	-	carbon source
66623	17272 ChEBI	propionate	-	carbon source
66623	17814 ChEBI	salicin	-	carbon source
66623	28017 ChEBI	starch	-	hydrolysis
66623	9300 ChEBI	suberic acid	-	carbon source
66623	30031 ChEBI	succinate	-	carbon source
66623	17992 ChEBI	sucrose	+	carbon source
66623	31011 ChEBI	valerate	-	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
66623	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
66623	acid phosphatase	-	3.1.3.2
66623	alkaline phosphatase	-	3.1.3.1
66623	alpha-chymotrypsin	+	3.4.21.1
66623	alpha-fucosidase	+	3.2.1.51
66623	alpha-galactosidase	+	3.2.1.22
66623	alpha-glucosidase	-	3.2.1.20
66623	alpha-mannosidase	+	3.2.1.24
66623	arginine dihydrolase	-	3.5.3.6
66623	beta-galactosidase	+	3.2.1.23
66623	beta-glucosidase	+	3.2.1.21
66623	beta-glucuronidase	-	3.2.1.31
66623	catalase	+	1.11.1.6
66623	cystine aminopeptidase	-	3.4.11.3
66623	cytochrome oxidase	+	1.9.3.1
66623	esterase (C 4)	-
66623	esterase Lipase (C 8)	-
66623	leucine aminopeptidase	-	3.4.1.1
66623	lipase (C 14)	+
66623	N-acetyl-beta-glucosaminidase	+	3.2.1.52
66623	naphthol-AS-BI-phosphohydrolase	-
66623	urease	-	3.5.1.5
66623	valine aminopeptidase	-

Fatty acid profile

Metadata FA analysis

@ref

66623

Fatty acid	Percentage
C18:1 w6c and/or C18:1 w7c	78.9
C16:0	5
C12:0 aldehyde	4.5
C18:0	3.1
C18:0 3OH	2.5
C19:0 cyclo w8c	2.3
C19:0 10-methyl	2
C16:1 w6c and/or C16:1 w7c	0.8
C16:0 3OH	0.6

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Enrichment culture	Enrichment culture duration	Enrichment culture temperature	Isolation procedure
66623	TBBPA-contaminated soil sample	Suqian City, Jiangsu Province	China	CHN	Asia	tryptic soy agar	3 days	30	A tetrabro-mobisphenol A (TBBPA)-contaminated soil sample (5.0 g) was added to a 250 ml flask containing 100 ml minimal medium (1.0 g NH4NO3, 1.6 g K2HPO4, 0.5 g KH2PO4, 0.2 g MgSO4 and 1.0 g NaCl per litre water at pH 7.0) supplemented with 0.1 mM TBBPA (TMM). The culture was incubated at 30°C at 150 r.p.m. for 5 days. A 5 ml aliquot of the enriched culture was subsequently transferred into 100 ml of fresh TMM. After three rounds of enrichment, the mixture was diluted in a tenfold series, and a 100 µl sample of each dilution was spread onto trypticase soy agar plates. The plates were incubated at 30°C for 3 days, and then all colonies were isolated.
67771	From halogenated aromatics-contaminated soil	City of Zaozhuang, Shandong Province	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence KY054581 (>99% sequence identity) for Shinella from Microbeatlas

Aquatic Samples	58
Soil Samples	6
Animal Samples	6
Plant Samples	5
Total Samples	75

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM4264330v1 assembly for Shinella pollutisoli KCTC 52677	scaffold	GCA_042643305			2250594	65.6
66792	ASM2460976v1 assembly for Shinella pollutisoli KCTC 52677	scaffold	GCA_024609765	2250594.3	8055573482	2250594	58.25

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
66623	Shinella pollutisoli strain AH-1 16S ribosomal RNA gene, partial sequence	KY054581	1441		2250594

GC content

@ref	GC-content (mol%)	Method
66623	68.2	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: ASM4264330v1 assembly for Shinella pollutisoli KCTC 52677
NCBI: GCA_042643305

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	negative	78.74	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.94	no
125439	motility	BacteriaNetⓘ	yes	66.08	no
125439	spore_formation	BacteriaNetⓘ	no	98.76	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Shinella pollutisoli KCTC 52677
NCBI: GCA_024609765.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.33	yes
125438	anaerobic	anaerobicⓘ	no	97.45	yes
125438	aerobic	aerobicⓘ	yes	82.49	yes
125438	spore-forming	spore-formingⓘ	no	89.97	no
125438	thermophilic	thermophileⓘ	no	97.99	no
125438	flagellated	motile2+ⓘ	yes	67.90	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Shinella pollutisoli sp. nov., isolated from tetrabromobisphenol A-contaminated soil.	Mu Y, Jia WB, Ke Z, Zhuang W, Wang HM, Jiang JD, Chen K, Chen Q	Int J Syst Evol Microbiol	10.1099/ijsem.0.002883	2018

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 )
#66623	Yang Mu, Wei-Bin Jia, Zhuang Ke, Wen Zhuang, Hong-Mei Wang, Jian-Dong Jiang, Kai Chen, Qing Chen: Shinella pollutisoli sp. nov., isolated from tetrabromobisphenol A-contaminated soil. IJSEM 68: 2602 - 2606 2018 ( DOI 10.1099/ijsem.0.002883 , PubMed 29949500 )
#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) .
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Shinella pollutisoli (KCTC 52677, CCTCC AB 2017242, AH-1)

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

Metabolite utilization

Metabolite production

Enzymes

Fatty acid profile

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_042643305

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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