Halomonas hamiltonii (DSM 21197, KCTC 22157, T68687)

Name: Halomonas hamiltonii (DSM 21197, KCTC 22157, T68687)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6074

Type strain

Strain Designation T68687

Culture col. no. DSM 21197 KCTC 22157 T68687

NCBI tax ID(s) 502829

Special Collections DSMZ KCTC Literature strains

History <- K. K. Kim, KCTC; T68687 <- D. A. Stevens, Santa Clara Valley Medical Center (SCVMC), San Jose, California, USA <- D A Stevens, Santa Clara Valley Medical Center, USA

Links

Halomonas hamiltonii T68687 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from waste handling option port of a dialysis machine.

Gram-negative motile rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 405345

KCTC 22157,DSM 21197

@ref 20215

Last LPSN update 2025-12-16 09:48:13

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Oceanospirillales

Family Halomonadaceae

Genus Halomonas

Species Halomonas hamiltonii

Full scientific name Halomonas hamiltonii Kim et al. 2010

Synonyms (2)

Vreelandella hamiltonii
Halomonas johnsoniae

BacDive ID	Other strains from **Halomonas hamiltonii** (1)	Type strain
6073	H. hamiltonii W1025, DSM 21196, KCTC 22154 (type strain)

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29031	negative	2.75 µm	0.8 µm	rod-shaped
67771	negative
125439	negative				99.5
125439					90.8
125438	negative				100

Pigmentation

29031

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
15439	TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)		Medium recipe at MediaDive	Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
15439	positive	growth	28	mesophilic
29031	positive	growth	10-40
29031	positive	optimum	32.5	mesophilic
67771	positive	growth	28	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
29031	positive	optimum	8.5
29031	positive	growth	07-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
29031	aerobe
67771	aerobe

Spore formation

@ref	Spore formation	Confidence
29031
125439		99.6

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29031	NaCl	positive	growth	0-20 %
29031	NaCl	positive	optimum	2.5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29031	17879 ChEBI	4-hydroxybenzoate	+	carbon source
29031	30089 ChEBI	acetate	+	carbon source
29031	16449 ChEBI	alanine	+	carbon source
29031	16947 ChEBI	citrate	+	carbon source
29031	16236 ChEBI	ethanol	+	carbon source
29031	28757 ChEBI	fructose	+	carbon source
29031	24265 ChEBI	gluconate	+	carbon source
29031	17234 ChEBI	glucose	+	carbon source
29031	17754 ChEBI	glycerol	+	carbon source
29031	25115 ChEBI	malate	+	carbon source
29031	17306 ChEBI	maltose	+	carbon source
29031	29864 ChEBI	mannitol	+	carbon source
29031	17632 ChEBI	nitrate	+	reduction
29031	26271 ChEBI	proline	+	carbon source
29031	17272 ChEBI	propionate	+	carbon source
29031	17822 ChEBI	serine	+	carbon source
29031	30911 ChEBI	sorbitol	+	carbon source
29031	30031 ChEBI	succinate	+	carbon source
29031	17992 ChEBI	sucrose	+	carbon source
29031	27082 ChEBI	trehalose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
29031	16136 ChEBI	hydrogen sulfide

Enzymes

@ref	Value	Activity	Ec
29031	catalase	+	1.11.1.6
29031	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Engineered	#Waste
#Infection	#Medical device

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
15439	waste handling option port of a dialysis machine	California, San Jose, Santa Clara Valley Medical Center	USA	USA	North America
67771	From dialysis center environment and machines		USA	USA	North America

Taxonmaps

69479

Global distribution of 16S sequence AM941399 (>99% sequence identity) for Halomonas from Microbeatlas

Aquatic Samples	3901
Soil Samples	614
Animal Samples	4865
Plant Samples	81
Total Samples	9461

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15439	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	ASM1465179v1 assembly for Vreelandella hamiltonii KCTC 22157	contig	GCA_014651795	502832.6	8109882043	502832	70.6

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
15439	Halomonas johnsoniae partial 16S rRNA gene, type strain T68687T	AM941399	1455	502832
124043	Halomonas johnsoniae strain KCTC 22157 16S ribosomal RNA gene, partial sequence.	MT759856	1351	502832
124043	Halomonas johnsoniae strain KCTC 22157 16S ribosomal RNA gene, partial sequence.	MT758078	1351	502832

GC content

@ref	GC-content (mol%)	Method
15439	64.4	high performance liquid chromatography (HPLC)
29031	64.4-65.2

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Halomonas johnsoniae KCTC 22157
NCBI: GCA_014651795

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.60	no
125439	motility	BacteriaNetⓘ	yes	90.80	no
125439	gram_stain	BacteriaNetⓘ	negative	99.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	83.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Halomonas johnsoniae strain KCTC 22157
PATRIC: 502832.6

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	100.00	yes
125438	anaerobic	anaerobicⓘ	no	97.19	yes
125438	spore-forming	spore-formingⓘ	no	88.93	yes
125438	thermophilic	thermophileⓘ	no	96.07	yes
125438	aerobic	aerobicⓘ	yes	80.74	yes
125438	flagellated	motile2+ⓘ	yes	81.70	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Identification and analysis of a clinically isolated strain of Halomonas based on whole-genome sequencing and comparative genomics.	Wang P, Xie C.	Lab Med	10.1093/labmed/lmad040	2024
Phylogeny	Halomonas montanilacus sp. nov., isolated from hypersaline Lake Pengyanco on the Tibetan Plateau.	Lu H, Xing P, Zhai L, Li H, Wu Q	Int J Syst Evol Microbiol	10.1099/ijsem.0.004109	2020
Phylogeny	Halomonas songnenensis sp. nov., a moderately halophilic bacterium isolated from saline and alkaline soils.	Jiang J, Pan Y, Hu S, Zhang X, Hu B, Huang H, Hong S, Meng J, Li C, Wang K	Int J Syst Evol Microbiol	10.1099/ijs.0.056499-0	2014
Phylogeny	Halomonas stevensii sp. nov., Halomonas hamiltonii sp. nov. and Halomonas johnsoniae sp. nov., isolated from a renal care centre.	Kim KK, Lee KC, Oh HM, Lee JS	Int J Syst Evol Microbiol	10.1099/ijs.0.004424-0	2009

References

#15439	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21197
#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 )
#25461	IJSEM 369 2010 ( DOI 10.1099/ijs.0.004424-0 , PubMed 19651714 )
#29031	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #25461
#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) .
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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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Halomonas hamiltonii (DSM 21197, KCTC 22157, T68687)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014651795

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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