Name: Rhodohalobacter halophilus JZ3C29
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 133122

Type strain:

Species: Rhodohalobacter halophilus

Strain Designation: JZ3C29

Culture col. no.: MCCC 1H00131, KCTC 52046, JCM 31413

Strain history: <- Zong-Jun Du, Shandong Univ., China

NCBI tax ID(s): 1812810 (species)

Special Collections

Section

When using BacDive for research please cite our paper

Rhodohalobacter halophilus JZ3C29 is a facultative anaerobe, heterotroph, Gram-negative bacterium that forms circular colonies and was isolated from saltern.

colony-forming
Gram-negative
rod-shaped
facultative anaerobe
heterotroph
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Balneolota*
	Class	*Balneolia*
	Order	*Balneolales*
	Family	*Balneolaceae*
	Genus	*Rhodohalobacter*
	Species	**Rhodohalobacter halophilus**
	Full Scientific Name (LPSN)	Rhodohalobacter halophilus Xia et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #25304]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative

[Ref.: #25304]	Cell length	2.5-16.5 µm

[Ref.: #25304]	Cell width	0.3-0.6 µm

[Ref.: #25304]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #25304]	Motility	no
[Ref.: #67771]	Motility	no

[Ref.: #25304]	Colony size	1 mm
[Ref.: #25304]	Colony color	reddish
[Ref.: #25304]	Colony shape	circular
[Ref.: #25304]	Incubation period	3 days
[Ref.: #25304]	Cultivation medium used	modified marine agar 2216

Information on culture and growth conditions Culture and growth conditions

[Ref.: #25304]

Culture medium

modified marine agar 2216

[Ref.: #25304]

Culture medium growth

[Ref.: #25304]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #25304]	growth	20-50 °C
[Ref.: #25304]	optimum	40 °C
[Ref.: #67770]	growth	40 °C
[Ref.: #67771]	growth	33-37 °C

	pH	Kind of pH		pH
[Ref.: #25304]			optimum	7.5-8.5
[Ref.: #25304]			growth	7.0-9.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #25304]	Oxygen tolerance	facultative anaerobe
[Ref.: #67771]	Oxygen tolerance	facultative anaerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %91.7

[Ref.: #25304]

Nutrition type

heterotroph

[Ref.: #25304]

Ability of spore formation

[Ref.: #25304]

Halophily / tolerance level

halophilic

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #25304]		NaCl		growth	2.0-16.0	%
[Ref.: #25304]		NaCl		optimum	8-10	%(w/v)

[Ref.: #67770]	Observation	quinones: MK-7
[Ref.: #67771]	Observation	quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25304]	(S)-lactate ChEBI	+	carbon source
[Ref.: #25304]	3-O-methyl-D-glucose ChEBI	+	carbon source
[Ref.: #25304]	acetoacetate ChEBI	+	carbon source
[Ref.: #25304]	alginate ChEBI	-	hydrolysis
[Ref.: #25304]	alpha-D-glucose ChEBI	+	carbon source
[Ref.: #25304]	amygdalin ChEBI	+/-	builds acid from
[Ref.: #25304]	arbutin ChEBI	+	builds acid from
[Ref.: #25304]	aspartate ChEBI	-	carbon source
[Ref.: #25304]	carboxymethylcellulose ChEBI	-	hydrolysis
[Ref.: #25304]	citrate ChEBI	+	carbon source
[Ref.: #25304]	D-arabitol ChEBI	+	carbon source
[Ref.: #25304]	D-fructose ChEBI	+	carbon source
[Ref.: #25304]	D-fructose ChEBI	+	builds acid from
[Ref.: #25304]	D-galactose ChEBI	+/-	builds acid from
[Ref.: #25304]	D-galacturonic acid ChEBI	+	carbon source
[Ref.: #25304]	D-glucarate ChEBI	+	carbon source
[Ref.: #25304]	D-gluconate ChEBI	+	carbon source
[Ref.: #25304]	D-glucose ChEBI	+	builds acid from
[Ref.: #25304]	D-glucose 6-phosphate ChEBI	+	carbon source
[Ref.: #25304]	D-glucuronate ChEBI	+	carbon source
[Ref.: #25304]	D-mannitol ChEBI	+	carbon source
[Ref.: #25304]	D-mannitol ChEBI	+	builds acid from
[Ref.: #25304]	D-mannose ChEBI	+	carbon source
[Ref.: #25304]	D-mannose ChEBI	+/-	builds acid from
[Ref.: #25304]	D-ribose ChEBI	+	builds acid from
[Ref.: #25304]	D-sorbitol ChEBI	+	carbon source
[Ref.: #25304]	D-tagatose ChEBI	-	builds acid from
[Ref.: #25304]	D-xylose ChEBI	+	builds acid from
[Ref.: #25304]	dextrin ChEBI	+	carbon source
[Ref.: #25304]	esculin ChEBI	-	hydrolysis
[Ref.: #25304]	esculin ChEBI	+	builds acid from
[Ref.: #25304]	gelatin ChEBI	+	hydrolysis
[Ref.: #25304]	gentiobiose ChEBI	+	carbon source
[Ref.: #25304]	glucuronamide ChEBI	+	carbon source
[Ref.: #25304]	glycerol ChEBI	+	carbon source
[Ref.: #25304]	glycerol ChEBI	+	builds acid from
[Ref.: #25304]	glycogen ChEBI	+	builds acid from
[Ref.: #25304]	inosine ChEBI	+	carbon source
[Ref.: #25304]	L-alanine ChEBI	+	carbon source
[Ref.: #25304]	L-arabinose ChEBI	+	builds acid from
[Ref.: #25304]	L-arginine ChEBI	+	carbon source
[Ref.: #25304]	L-histidine ChEBI	+	carbon source
[Ref.: #25304]	L-malate ChEBI	+	carbon source
[Ref.: #25304]	L-pyroglutamic acid ChEBI	+	carbon source
[Ref.: #25304]	L-rhamnose ChEBI	+	carbon source
[Ref.: #25304]	L-rhamnose ChEBI	+	builds acid from
[Ref.: #25304]	lactose ChEBI	+	carbon source
[Ref.: #25304]	maltose ChEBI	-	carbon source
[Ref.: #25304]	maltose ChEBI	+	builds acid from
[Ref.: #25304]	melibiose ChEBI	+	carbon source
[Ref.: #25304]	melibiose ChEBI	+	builds acid from
[Ref.: #25304]	methyl (R)-lactate ChEBI	+	carbon source
[Ref.: #25304]	methyl alpha-D-glucopyranoside ChEBI	+/-	builds acid from
[Ref.: #25304]	myo-inositol ChEBI	+	carbon source
[Ref.: #25304]	myo-inositol ChEBI	+/-	builds acid from
[Ref.: #25304]	N-acetyl-beta-D-mannosamine ChEBI	+	carbon source
[Ref.: #25304]	N-acetylgalactosamine ChEBI	+	carbon source
[Ref.: #25304]	N-acetylglucosamine ChEBI	+/-	builds acid from
[Ref.: #25304]	n-acetylneuraminate ChEBI	+	carbon source
[Ref.: #25304]	nitrate ChEBI	-	reduction
[Ref.: #25304]	potassium 5-dehydro-D-gluconate	+/-	builds acid from
[Ref.: #25304]	raffinose ChEBI	+	carbon source
[Ref.: #25304]	raffinose ChEBI	+	builds acid from
[Ref.: #25304]	ribitol ChEBI	+/-	builds acid from
[Ref.: #25304]	salicin ChEBI	+	builds acid from
[Ref.: #25304]	stachyose ChEBI	+	carbon source
[Ref.: #25304]	starch ChEBI	+	hydrolysis
[Ref.: #25304]	starch ChEBI	+	builds acid from
[Ref.: #25304]	sucrose ChEBI	+	carbon source
[Ref.: #25304]	sucrose ChEBI	+	builds acid from
[Ref.: #25304]	trehalose ChEBI	+	carbon source
[Ref.: #25304]	trehalose ChEBI	+	builds acid from
[Ref.: #25304]	turanose ChEBI	+	carbon source
[Ref.: #25304]	tween 20 ChEBI	-	hydrolysis
[Ref.: #25304]	tween 40 ChEBI	-	hydrolysis
[Ref.: #25304]	tween 80 ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #25304]	acetylspiramycin ChEBI	yes	30	µg
[Ref.: #25304]	ampicillin ChEBI	yes	10	µg
[Ref.: #25304]	cefotaxime ChEBI	yes	30	µg
[Ref.: #25304]	ceftriaxone ChEBI	yes	30	µg
[Ref.: #25304]	chloramphenicol ChEBI	yes	30	µg
[Ref.: #25304]	clindamycin ChEBI	yes	2	µg
[Ref.: #25304]	erythromycin ChEBI	yes	15	µg
[Ref.: #25304]	gentamicin ChEBI				yes	30	µg
[Ref.: #25304]	kanamycin ChEBI				yes	30	µg
[Ref.: #25304]	lincomycin ChEBI	yes	2	µg
[Ref.: #25304]	nalidixic acid ChEBI				yes	30	µg
[Ref.: #25304]	neomycin ChEBI				yes	30	µg
[Ref.: #25304]	penicillin g ChEBI	yes	10	µg
[Ref.: #25304]	rifampicin ChEBI	yes	5	µg
[Ref.: #25304]	streptomycin ChEBI				yes	10	µg
[Ref.: #25304]	tetracycline ChEBI				yes	30	µg
[Ref.: #25304]	tobramycin ChEBI				yes	10	µg
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #25304]	acetoin ChEBI	no
[Ref.: #25304]	hydrogen sulfide ChEBI	no
[Ref.: #25304]	indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test
[Ref.: #25304]		acetoin ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #25304]	acid phosphatase	+	3.1.3.2
[Ref.: #25304]	alpha-chymotrypsin	+	3.4.21.1
[Ref.: #25304]	catalase	+	1.11.1.6
[Ref.: #25304]	cystine arylamidase	-	3.4.11.3
[Ref.: #25304]	cytochrome oxidase	-	1.9.3.1
[Ref.: #25304]	esterase (C 4)	+/-
[Ref.: #25304]	lipase (C 14)	-
[Ref.: #25304]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #25304]	naphthol-AS-BI-phosphohydrolase	-
[Ref.: #25304]	trypsin	+	3.4.21.4
[Ref.: #25304]	urease	-	3.5.1.5
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #25304]

Fatty acid	Percentage
C16:1ω7c / C15:0 iso 2OH	46.5
C15:0 iso	27.3
C17:1 iso ω9c	8.8
C15:0 anteiso	6.9
C16:0	6.5
C14:0	2.4
C16:1ω5c	1.7

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

[Ref.: #25304]	Sample type/isolated from	saltern
[Ref.: #25304]	Geographic location (country and/or sea, region)	Feicheng, China
[Ref.: #25304]	Country	China
[Ref.: #25304]	Country ISO 3 Code	CHN
[Ref.: #25304]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Saltern located in Feicheng
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From marine solar saltern
[Ref.: #67771]	Geographic location (country and/or sea, region)	near the city of Feicheng, the coastal area of Weihai
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Condition	#Saline	-
#Environmental	#Aquatic	#Non-marine Saline and Alkaline
#Environmental	#Terrestrial	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KU862657 (>99% sequence identity) for Rhodohalobacter halophilus subclade from Microbeatlas

Aquatic Samples	25
Soil Samples	4
Animal Samples	4
Plant Samples
Total Samples	33

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.: #25304]	Rhodohalobacter halophilus strain JZ3C29 16S ribosomal RNA gene, partial sequence	KU862657	1456	GenBank ENA	1812810 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Rhodohalobacter halophilus JZ3C29	GCA_001715195	contig	GenBank ENA	1812810 tax ID
[Ref.: #66792]	Rhodohalobacter halophilus JZ3C29	2751185588	draft	JGI IMG/M	1812810 tax ID	*

[Ref.: #25304]	GC-content	44.4 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67771]	GC-content	44.4 mol%
[Ref.: #67770]	GC-content	44.4 mol%	genome sequence analysis

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

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Rhodohalobacter halophilus JZ3C29 NCBI: GCA_001715195
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	yes	54.2
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	58
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	variable	71.1
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	91.7

Availability in culture collections External links

[Ref.: #25304]

Culture collection no.

MCCC 1H00131, KCTC 52046, JCM 31413

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rhodohalobacter mucosus sp. nov., isolated from a marine solar saltern.	Wang TJ, Liu ZW, Feng X, Zou QH, Du ZJ	Arch Microbiol	10.1007/s00203-021-02254-1	2021	*
Phylogeny	Rhodohalobacter barkolensis sp. nov., isolated from a saline lake and emended description of the genus Rhodohalobacter.	Han SB, Yu YH, Ju Z, Li Y, Zhang R, Hou XJ, Ma XY, Yu XY, Sun C, Wu M	Int J Syst Evol Microbiol	10.1099/ijsem.0.002775	2018	*
Phylogeny	Rhodohalobacter halophilus gen. nov., sp. nov., a moderately halophilic member of the family Balneolaceae.	Xia J, Xie ZH, Dunlap CA, Rooney AP, Du ZJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.001806	2017	*

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 )

#25304

J. X. Xia, Z. H.,Dunlap, C. A.,Rooney, A. P.,Du, Z. J.: Rhodohalobacter halophilus gen. nov., sp. nov., a moderately halophilic member of the family Balneolaceae. IJSEM 67: 1281 - 1287 2017 ( DOI 10.1099/ijsem.0.001806 , PubMed 28109207 )

#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;
#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 .

#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 .

* These data were automatically processed and therefore are not curated

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