Shinella zoogloeoides (DSM 287, ATCC 19623, CCM 2456)

Name: Shinella zoogloeoides (DSM 287, ATCC 19623, CCM 2456)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13901

Type strain

Strain Designation 1-16M

Culture col. no. DSM 287 ATCC 19623 CCM 2456 NCIB 10340 NCTC 10482 7 more

NCBI tax ID(s) 352475

Special Collections DSMZ CCUG JCM

History DSMZ <- L. Hartmann <- ATCC (Zoogloea ramigera) <- K.T. Crabtree, 1-16M JCM <-- IAM 12669 <-- ATCC 19623 <-- K. Crabtree I-16-M.

Links

Shinella zoogloeoides 1-16M is an aerobe bacterium that was isolated from activated sludge.

aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 6465

LMG 4433,ATCC 19623,CCM 2456,CCUG 35204,DSM 287,IAM 12669,NCIMB 10340,NCTC 10482,NCIB 10340,KCTC 2531,BCRC 11043,CCRC 11043,NCAIM B.01953,NRRL B-3303,KCTC 12503,NBRC 102405,JCM 20728

@ref 20215

Last LPSN update 2026-05-29 08:28:09

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Rhizobiaceae

Genus Shinella

Species Shinella zoogloeoides

Full scientific name Shinella zoogloeoides An et al. 2006

Synonyms (1)

Crabtreella saccharophila

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	91.968
125438	negative	98.833

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
24	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)
24	positive	growth	30
52590	positive	growth	30
67770	positive	growth	25

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
52590	aerobe
125439	obligate aerobe	90.753

Spore formation

@ref	Spore formation	Confidence
125438		92.942
125439		99.41

Compound production

CompoundPHB synthase

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Waste	#Activated sludge

Isolation

@ref	Sample type
24	activated sludge
52590	Sludge,activated
67770	Flocs in sewage sludge (activated)

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
24	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM2088349v1 assembly for Shinella zoogloeoides ATCC 19623	complete	GCA_020883495	352475.11	8111611443	352475	92.25
66792	Shinella zoogloeoides strain ATCC 19623	complete		352475.12		352475	80.47
124043	ASM4266036v1 assembly for Shinella zoogloeoides CCUG 35204	contig	GCA_042660365			352475	56.1
66792	ASM982685v1 assembly for Shinella zoogloeoides DSM 287	contig	GCA_009826855	352475.7	8002197218	352475	53.11

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Rhizobiales bacterium ROi51 16S ribosomal RNA gene, partial sequence	EF219048	1441	441051
20218	Z.ramigera gene for 16S rRNA (ATCC 19623)	X74915	1477	352475
20218	Crabtreella saccharophila gene for 16S rRNA, partial sequence	AB238789	1458	352475
20218	Zoogloea ramigera gene for 16S ribosomal RNA	D14255	1407	350
20218	Shinella zoogloeoides gene for 16S rRNA, partial sequence, strain: NBRC 102405	AB681761	1403	352475

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM2088349v1 assembly for Shinella zoogloeoides ATCC 19623
BV-BRC: 352475.11

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	90.75	no
125439	gram_stain	BacteriaNetⓘ	negative	91.97	no
125439	motility	BacteriaNetⓘ	yes	61.90	no
125439	spore_formation	BacteriaNetⓘ	no	99.41	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Shinella zoogloeoides ATCC 19623
NCBI: GCA_020883495.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.83	no
125438	anaerobic	anaerobicⓘ	no	95.99	yes
125438	aerobic	aerobicⓘ	yes	79.69	yes
125438	spore-forming	spore-formingⓘ	no	92.94	no
125438	thermophilic	thermophileⓘ	no	98.00	no
125438	flagellated	motile2+ⓘ	yes	71.80	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Complete Genome Sequences of Kinneretia sp. Strain XES5, Shinella sp. Strain XGS7, and Vogesella sp. Strain XCS3, Isolated from Xenopus laevis Skin.	Hudson DT, Chapman PA, Day RC, Morgan XC, Beck CW.	Microbiol Resour Announc	10.1128/mra.01050-21	2021
Enzymology	Isolation and Characterization of Levoglucosan-Metabolizing Bacteria.	Arya AS, Hang MTH, Eiteman MA.	Appl Environ Microbiol	10.1128/aem.01868-21	2022
Metabolism	Functions and Unique Diversity of Genes and Microorganisms Involved in Arsenite Oxidation from the Tailings of a Realgar Mine.	Zeng XC, E G, Wang J, Wang N, Chen X, Mu Y, Li H, Yang Y, Liu Y, Wang Y.	Appl Environ Microbiol	10.1128/aem.02190-16	2016
	Phylogeny and Phylogeography of Rhizobial Symbionts Nodulating Legumes of the Tribe Genisteae.	Stepkowski T, Banasiewicz J, Granada CE, Andrews M, Passaglia LMP.	Genes (Basel)	10.3390/genes9030163	2018
	A persistent and diverse airway microbiota present during chronic obstructive pulmonary disease exacerbations.	Huang YJ, Kim E, Cox MJ, Brodie EL, Brown R, Wiener-Kronish JP, Lynch SV.	OMICS	10.1089/omi.2009.0100	2010
	Cellulose-mediated floc formation by the activated sludge bacterium Shinella zoogloeoides ATCC 19623.	Gao N, Dai J, Liu Y, Li S, Wang J, Lu W, Qiu D	BMC Microbiol	10.1186/s12866-022-02516-y	2022
Phylogeny	Shinella oryzae sp. nov., a novel zearalenone-resistant bacterium isolated from rice paddy soil.	Gao R, Zheng J, Lu W, Ke X, Chen M, Lin M, Zhang W, Zhou Z	Antonie Van Leeuwenhoek	10.1007/s10482-022-01724-w	2022
Phylogeny	Shinella kummerowiae sp. nov., a symbiotic bacterium isolated from root nodules of the herbal legume Kummerowia stipulacea.	Lin DX, Wang ET, Tang H, Han TX, He YR, Guan SH, Chen WX	Int J Syst Evol Microbiol	10.1099/ijs.0.65723-0	2008
Phylogeny	Zoogloea oryzae sp. nov., a nitrogen-fixing bacterium isolated from rice paddy soil, and reclassification of the strain ATCC 19623 as Crabtreella saccharophila gen. nov., sp. nov.	Xie CH, Yokota A	Int J Syst Evol Microbiol	10.1099/ijs.0.63755-0	2006
Phylogeny	Shinella granuli gen. nov., sp. nov., and proposal of the reclassification of Zoogloea ramigera ATCC 19623 as Shinella zoogloeoides sp. nov.	An DS, Im WT, Yang HC, Lee ST	Int J Syst Evol Microbiol	10.1099/ijs.0.63942-0	2006
Phylogeny	Shinella lacus sp. nov., a novel microcystin-degrading alphaproteobacterium containing the bla carbapenemase gene.	Gong ZL, Deng Y, Jiang ZM, Liu LQ, Yu LY, Su J, Zhang YQ	Int J Syst Evol Microbiol	10.1099/ijsem.0.005659	2022

References

#24	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 287
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#52590	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 35204
#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) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 zoogloeoides (DSM 287, ATCC 19623, CCM 2456)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Compound production

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_020883495

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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