Xanthomonas hyacinthi (DSM 19077, ATCC 19314, ICMP 189)

Name: Xanthomonas hyacinthi (DSM 19077, ATCC 19314, ICMP 189)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17589

Type strain

Culture col. no. DSM 19077 ATCC 19314 ICMP 189 LMG 739 NCPPB 599 2 more

NCBI tax ID(s) 1440765 56455

Special Collections DSMZ

History DSMZ <- NCPPB <- E. van Slogteren

Links

Xanthomonas hyacinthi DSM 19077 is a plant pathogen that was isolated from Hyacinthus orientalis.

plant pathogen genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 5617

LMG 739,ATCC 19314,ICMP 189,LMG 16016,NCPPB 599,PDDCC 189,ATCC 193314,CFBP 1156,DSM 19077

@ref 20215

Last LPSN update 2026-05-29 08:29:03

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Lysobacterales

Family Lysobacteraceae

Genus Xanthomonas

Species Xanthomonas hyacinthi

Full scientific name Xanthomonas hyacinthi (ex Wakker 1883) Vauterin et al. 1995

BacDive ID	Other strains from **Xanthomonas hyacinthi** (2)	Type strain
17590	X. hyacinthi DSM 50855, ICPB XH 110, LMG 742
141435	X. hyacinthi CCUG 1830, CCM 1896

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	96.102
125438	negative	97.994

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7869	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)
7869	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	98.921

Spore formation

@ref	Spore formation	Confidence
125439		99.741

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
7869	Hyacinthus orientalis	Netherlands	NLD	Europe

Taxonmaps

69479

Global distribution of 16S sequence Y10754 (>99% sequence identity) for Xanthomonas from Microbeatlas

Aquatic Samples	3769
Soil Samples	5101
Animal Samples	5827
Plant Samples	5320
Total Samples	20017

Interaction and safety

Risk assessment

@ref	Pathogenicity plant	Biosafety level	Biosafety level comment
7869		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
124043	ASM4264802v1 assembly for Xanthomonas hyacinthi ICMP 189	contig	GCA_042648025			56455	70.27
66792	ASM101043v1 assembly for Xanthomonas hyacinthi DSM 19077	contig	GCA_001010435	1440765.4	2651869672	1440765	0

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
7869	X.hyacinthi 16S rRNA gene	Y10754	1500	56455
124043	Xanthomonas hyacinthi strain LMG739 16S-23S ribosomal RNA intergenic spacer, complete sequence.	AF209759	493	56455
124043	Xanthomonas hyacinthi strain ICMP 189 16S ribosomal RNA gene, partial sequence.	MT760330	1379	56455

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM4264802v1 assembly for Xanthomonas hyacinthi ICMP 189
NCBI: GCA_042648025

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.92	no
125439	motility	BacteriaNetⓘ	yes	85.59	no
125439	gram_stain	BacteriaNetⓘ	negative	96.10	no
125439	spore_formation	BacteriaNetⓘ	no	99.74	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Xanthomonas hyacinthi DSM 19077
PATRIC: 1440765.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.99	no
125438	anaerobic	anaerobicⓘ	no	95.96	no
125438	spore-forming	spore-formingⓘ	no	86.44	no
125438	aerobic	aerobicⓘ	yes	88.12	no
125438	thermophilic	thermophileⓘ	no	97.50	yes
125438	flagellated	motile2+ⓘ	yes	76.84	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Phylogenetic Distribution and Evolution of Type VI Secretion System in the Genus Xanthomonas.	Liyanapathiranage P, Wagner N, Avram O, Pupko T, Potnis N.	Front Microbiol	10.3389/fmicb.2022.840308	2022
Enzymology	Differences in hyporheic-zone microbial community structure along a heavy-metal contamination gradient.	Feris K, Ramsey P, Frazar C, Moore JN, Gannon JE, Holben WE.	Appl Environ Microbiol	10.1128/aem.69.9.5563-5573.2003	2003

References

#7869	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19077
#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 hyacinthi (DSM 19077, ATCC 19314, ICMP 189)

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_042648025

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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