Name: Shinella zoogloeoides 1-16M
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13901

Type strain:

Species: Shinella zoogloeoides

Strain Designation: 1-16M

Culture col. no.: DSM 287, ATCC 19623, CCM 2456, NCIB 10340, NCTC 10482, CCUG 35204, NCIMB 10340, LMG 4433, IAM 12669, JCM 20728, NBRC 102405

Strain history: IAM 12669 <-- ATCC 19623 <-- K. Crabtree I-16-M.

NCBI tax ID(s): 352475 (species)

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

Section

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

Gram-negative
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	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Rhizobiaceae*
	Genus	*Shinella*
	Species	**Shinella zoogloeoides**
	Full Scientific Name (LPSN)	Shinella zoogloeoides An et al. 2006

Synonym

Crabtreella saccharophila

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.972

Information on culture and growth conditions Culture and growth conditions

[Ref.: #24]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #24]

Culture medium growth

[Ref.: #24]

Culture medium link

Medium recipe at MediaDive

[Ref.: #24]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #24]	growth	30 °C
[Ref.: #52590]	growth	30 °C
[Ref.: #67770]	growth	25 °C

[Ref.: #24]	Temperature range	mesophilic
[Ref.: #52590]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #52590]

Oxygen tolerance

aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.997

[Ref.: #24]

Name of produced compound

PHB synthase

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

[Ref.: #24]	Sample type/isolated from	activated sludge

[Ref.: #52590]	Sample type/isolated from	Sludge,activated

[Ref.: #67770]	Sample type/isolated from	Flocs in sewage sludge (activated)
* marker position based on {}

Isolation sources categories

#Engineered

#Waste

#Activated sludge

What are isolation sources categories?

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

[Ref.: #24]

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.: #20218]	Rhizobiales bacterium ROi51 16S ribosomal RNA gene, partial sequence	EF219048	1441	ENA	441051 tax ID	*
[Ref.: #20218]	Z.ramigera gene for 16S rRNA (ATCC 19623)	X74915	1477	ENA	352475 tax ID	*
[Ref.: #20218]	Crabtreella saccharophila gene for 16S rRNA, partial sequence	AB238789	1458	ENA	352475 tax ID	*
[Ref.: #20218]	Zoogloea ramigera gene for 16S ribosomal RNA	D14255	1407	ENA	350 tax ID	*
[Ref.: #20218]	Shinella zoogloeoides gene for 16S rRNA, partial sequence, strain: NBRC 102405	AB681761	1403	ENA	352475 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Shinella zoogloeoides DSM 287	GCA_009826855	contig	GenBank	352475 tax ID	*
[Ref.: #66792]	Shinella zoogloeoides strain DSM 287	352475.7	wgs	PATRIC	352475 tax ID	*
[Ref.: #66792]	Shinella zoogloeoides ATCC 19623	GCA_020883495	complete	GenBank	352475 tax ID	*
[Ref.: #66792]	Shinella zoogloeoides strain ATCC 19623	352475.12	complete	PATRIC	352475 tax ID	*
[Ref.: #66792]	Shinella zoogloeoides strain ATCC 19623	352475.11	complete	PATRIC	352475 tax ID	*

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: Shinella zoogloeoides strain DSM 287 PATRIC: 352475.5
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Shinella zoogloeoides ATCC 19623 NCBI: GCA_020883495.1
[Ref.: #69480]	flagellated	no	63.33	no
[Ref.: #69480]	gram-positive	no	98.011	no
[Ref.: #69480]	anaerobic	no	96.766	yes
[Ref.: #69480]	aerobic	yes	83.348	no
[Ref.: #69480]	halophile	no	93.363	no
[Ref.: #69480]	spore-forming	no	95.761	no
[Ref.: #69480]	motile	yes	86.435	no
[Ref.: #69480]	thermophile	no	98.916	yes
[Ref.: #69480]	glucose-util	yes	91.842	no
[Ref.: #69480]	glucose-ferment	no	89.057	no

Availability in culture collections External links

[Ref.: #24]

Culture collection no.

DSM 287, ATCC 19623, CCM 2456, NCIB 10340, NCTC 10482, CCUG 35204, NCIMB 10340, LMG 4433, IAM 12669, JCM 20728, NBRC 102405

[Ref.: #83076]

SI-ID 6465

Literature:

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

	Title	Authors	Journal	DOI	Year
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	*
	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	*

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;

#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 )

#83076

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-ID6465.1 )

* These data were automatically processed and therefore are not curated

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Shinella zoogloeoides strain DSM 287

Shinella zoogloeoides ATCC 19623

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