Xanthomonas pisi (DSM 18956, ICMP 570, NCPPB 762)

Name: Xanthomonas pisi (DSM 18956, ICMP 570, NCPPB 762)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17609

Type strain

Strain Designation VdM 111, Xa1

Culture col. no. DSM 18956 ICMP 570 NCPPB 762 VdM 111 Xa1 2 more

NCBI tax ID(s) 1440766 56457

Special Collections DSMZ

History <- NCPPB <- D. Dye; XA1 <- N. Okabe

Links

Xanthomonas pisi VdM 111 is a mesophilic plant pathogen that was isolated from Pisum sativum, leaf spot.

mesophilic plant pathogen genome sequence 16S sequence

Name and taxonomic classification

SI-ID 5910

LMG 847,ICMP 570,NCPPB 762,PDDCC 570,ATCC 35936,NCAIM B.01393,DSM 18956,CFBP 4643

@ref 20215

Last LPSN update 2025-12-16 09:51:08

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Lysobacterales

Family Lysobacteraceae

Genus Xanthomonas

Species Xanthomonas pisi

Full scientific name Xanthomonas pisi (ex Goto and Okabe 1958) Vauterin et al. 1995

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	92.994
125439	negative	99.3

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7802	REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)		Medium recipe at MediaDive	Name: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) 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)	Range
7802	positive	growth	28	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	97.3

Spore formation

@ref	Spore formation	Confidence
125439		98.5

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Leaf (Phyllosphere)

Isolation

@ref	Sample type	Host species	Country	Country ISO 3 Code	Continent
7802	Pisum sativum, leaf spot	Pisum sativum	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence Y10758 (>99% sequence identity) for Xanthomonas from Microbeatlas

Aquatic Samples	6826
Soil Samples	10026
Animal Samples	28252
Plant Samples	7048
Total Samples	52152

Interaction and safety

Risk assessment

@ref	Pathogenicity plant	Biosafety level	Biosafety level comment
7802		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
66792	ASM101041v1 assembly for Xanthomonas pisi DSM 18956	contig	GCA_001010415	1440766.4	2636415828	1440766

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
7802	X.pisi 16S rRNA gene	Y10758	1502	56457
124043	Xanthomonas pisi strain ICMP 570 16S ribosomal RNA gene, partial sequence.	MT758039	1363	56457
124043	Xanthomonas pisi strain ICMP 570 16S ribosomal RNA gene, partial sequence.	MT759992	1361	56457

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Xanthomonas pisi DSM 18956
NCBI: GCA_001010415

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.50	no
125439	motility	BacteriaNetⓘ	yes	89.50	no
125439	gram_stain	BacteriaNetⓘ	negative	99.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Xanthomonas pisi DSM 18956
PATRIC: 1440766.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	92.99	no
125438	anaerobic	anaerobicⓘ	no	93.66	no
125438	spore-forming	spore-formingⓘ	no	88.07	no
125438	aerobic	aerobicⓘ	yes	80.27	no
125438	thermophilic	thermophileⓘ	no	95.33	yes
125438	flagellated	motile2+ⓘ	yes	59.55	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rhizobium pisi sv. trifolii K3.22 harboring nod genes of the Rhizobium leguminosarum sv. trifolii cluster.	Marek-Kozaczuk M, Leszcz A, Wielbo J, Wdowiak-Wrobel S, Skorupska A.	Syst Appl Microbiol	10.1016/j.syapm.2013.01.005	2013
Metabolism	Metabolic Promiscuity of an Orphan Small Alarmone Hydrolase Facilitates Bacterial Environmental Adaptation.	Fung DK, Bai K, Yang J, Xu X, Stevenson DM, Amador-Noguez D, Luo L, Wang JD.	mBio	10.1128/mbio.02422-22	2022

References

#7802	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18956
#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 )
#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 .
#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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Xanthomonas pisi (DSM 18956, ICMP 570, NCPPB 762)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001010415

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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