Name: Agrobacterium sp. H13-3
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 158834

Type strain:

Species: Agrobacterium sp.

Strain Designation: H13-3

Culture col. no.: DSM 110110

Strain history: <- J. Wittmann, DSMZ and R. Schmitt, Uni Regensburg <-

NCBI tax ID(s): 361 (species)

SI-ID 399074

DSM 110110

Other strains from Agrobacterium sp.

A. sp. S2, DSM 5681
A. sp. LK, DSM 11401
A. sp. D97, DSM 13150
A. sp. 0362, DSM 30201, DSM 60578
A. sp. B 2326, KGR, DSM 30203, DSM 60566, ...
A. sp. IMI 379938
A. sp. JCM 17895, FERM AP-21298
A. sp. JCM 20916, DSM 30202, DSM 60563, ...
A. sp. JCM 20989, IAM 13936, NCPPB 2604
A. sp. JCM 20992, IAM 13941, LMG 294
A. sp. JCM 20993, IAM 13942, LMG 29, NCPPB ...
A. sp. JCM 20994, CFBP 5506, IAM 13943, ...
A. sp. JCM 21077, IAM 14219, NCPPB 2561
A. sp. JCM 21079, IAM 14221, NCPPB 3268
A. sp. JCM 21236, IAM 14465

Section

Agrobacterium sp. H13-3 is a mesophilic bacterium that was isolated from rhizosphere of Lupinus luteus.

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	*Agrobacterium*
	Full Scientific Name (LPSN)	Agrobacterium Conn 1942 (Approved Lists 1980)

Information on culture and growth conditions Culture and growth conditions

[Ref.: #65656]

Culture medium

TRYPTONE YEAST EXTRACT AGAR (TYG) (DSMZ Medium 680)

[Ref.: #65656]

Culture medium growth

[Ref.: #65656]

Culture medium link

Medium recipe at MediaDive

[Ref.: #65656]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #65656]			growth	30 °C

[Ref.: #65656]

Temperature range

mesophilic

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

[Ref.: #65656]	Sample type/isolated from	rhizosphere of Lupinus luteus
[Ref.: #65656]	Host species	Lupinus luteus
[Ref.: #65656]	Geographic location (country and/or sea, region)	unknown
[Ref.: #65656]	Country	Hungary
[Ref.: #65656]	Country ISO 3 Code	HUN
[Ref.: #65656]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Rhizosphere

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence CP002248 (>99% sequence identity) for Agrobacterium from Microbeatlas

Aquatic Samples	6
Soil Samples	7
Animal Samples	33
Plant Samples	42
Total Samples	88

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.: #65656]	Agrobacterium sp. H13-3 circular chromosome, complete sequence	CP002248	2823930	ENA	861208 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Agrobacterium sp. H13-3	861208.11	plasmid	PATRIC	1183401 tax ID	*
[Ref.: #66792]	Agrobacterium sp. H13-3	861208.3	complete	PATRIC	1183401 tax ID	*
[Ref.: #66792]	Agrobacterium sp. H13-3	650716007	complete	JGI IMG/M	861208 tax ID	*

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Agrobacterium sp. H13-3 PATRIC: 861208.3
[Ref.: #69480]	motile	yes	85.015	no
[Ref.: #69480]	flagellated	no	68.13	no
[Ref.: #69480]	gram-positive	no	98.11	no
[Ref.: #69480]	anaerobic	no	97.659	no
[Ref.: #69480]	halophile	no	85.821	no
[Ref.: #69480]	spore-forming	no	96.86	no
[Ref.: #69480]	thermophile	no	99.521	yes
[Ref.: #69480]	glucose-util	yes	90.407	no
[Ref.: #69480]	aerobic	yes	89.385	no
[Ref.: #69480]	glucose-ferment	no	89.842	no

Availability in culture collections External links

[Ref.: #65656]

Culture collection no.

DSM 110110

[Ref.: #111353]

SI-ID 399074

Literature:

Topic	Title	Authors	Journal	DOI	Year
Metabolism	More than Rotating Flagella: Lipopolysaccharide as a Secondary Receptor for Flagellotropic Phage 7-7-1.	Gonzalez F, Helm RF, Broadway KM, Scharf BE	J Bacteriol	10.1128/JB.00363-18	2018	*
Pathogenicity	Diversity of bacterial lactase genes in intestinal contents of mice with antibiotics-induced diarrhea.	Long CX, He L, Guo YF, Liu YW, Xiao NQ, Tan ZJ	World J Gastroenterol	10.3748/wjg.v23.i42.7584	2017	*
Genetics	Genome and proteome analysis of 7-7-1, a flagellotropic phage infecting Agrobacterium sp H13-3.	Kropinski AM, Van den Bossche A, Lavigne R, Noben JP, Babinger P, Schmitt R	Virol J	10.1186/1743-422X-9-102	2012	*
Genetics	Complete genome sequencing of Agrobacterium sp. H13-3, the former Rhizobium lupini H13-3, reveals a tripartite genome consisting of a circular and a linear chromosome and an accessory plasmid but lacking a tumor-inducing Ti-plasmid.	Wibberg D, Blom J, Jaenicke S, Kollin F, Rupp O, Scharf B, Schneiker-Bekel S, Sczcepanowski R, Goesmann A, Setubal JC, Schmitt R, Puhler A, Schluter A	J Biotechnol	10.1016/j.jbiotec.2011.01.010	2011	*
	Minimum requirements of flagellation and motility for infection of Agrobacterium sp. strain H13-3 by flagellotropic bacteriophage 7-7-1.	Yen JY, Broadway KM, Scharf BE	Appl Environ Microbiol	10.1128/AEM.01082-12	2012	*

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 )

#65656

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 110110

#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) .

#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) .

#111353

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-ID399074.1 )

* These data were automatically processed and therefore are not curated

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