Laribacter hongkongensis (DSM 14985, LMG 21516, CCUG 45813)

Name: Laribacter hongkongensis (DSM 14985, LMG 21516, CCUG 45813)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 10465

Type strain

Strain Designation HKU1, HKUI

Culture col. no. DSM 14985 LMG 21516 CCUG 45813 CIP 107139 HKU1 1 more

NCBI tax ID(s) 1122157 168471

Special Collections DSMZ CCUG CIP

History DSMZ <- K.-Y. Yuen CIP <- 2001, R. Leung, HKU Pasteur Research Centre, Hong kong, China: strain HKUI CIP <- 2001, R. Leung, HKU Pasteur Research Centre, Hong Kong, China: strain HKUI

Links

Laribacter hongkongensis HKU1 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from blood of a patient with empyema.

Gram-negative rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 86622

LMG 21516,DSM 14985,CCUG 45813,CIP 107139

@ref 20215

Last LPSN update 2026-05-29 08:27:20

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Neisseriales

Family Aquaspirillaceae

Genus Laribacter

Species Laribacter hongkongensis

Full scientific name Laribacter hongkongensis Yuen et al. 2002

BacDive ID	Other strains from **Laribacter hongkongensis** (3)	Type strain
152170	L. hongkongensis CCUG 45965
152171	L. hongkongensis CCUG 45966
152172	L. hongkongensis CCUG 45967

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
119961	negative	rod-shaped
125438	negative		98.911
125439	negative		98.056

Colony morphology

119961

Hemolysis ability0

Multimedia

@ref:	66793
multimedia content:	EM_DSM_14985_1.jpg
multimedia.multimedia content:	EM_DSM_14985_1.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_14985_2.jpg
multimedia.multimedia content:	EM_DSM_14985_2.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_14985_3.jpg
multimedia.multimedia content:	EM_DSM_14985_3.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_14985_4.jpg
multimedia.multimedia content:	EM_DSM_14985_4.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_14985_5.jpg
multimedia.multimedia content:	EM_DSM_14985_5.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_14985_6.jpg
multimedia.multimedia content:	EM_DSM_14985_6.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
5653	BHI MEDIUM (DSMZ Medium 215)	Medium recipe at MediaDive	Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
5653	COLUMBIA BLOOD AGAR (DSMZ Medium 429)	Medium recipe at MediaDive	Name: COLUMBIA BLOOD AGAR (DSMZ Medium 429) Composition: Horse blood 40.0 g/l Columbia agar base
33633	MEDIUM 6 - Columbia agar with 10 % horse blood		Distilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
119961	CIP Medium 6	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
5653	positive	growth	37
33633	positive	growth	37
56931	positive	growth	37-42
119961	positive	growth	30-41
119961	negative	growth	5
119961	negative	growth	10
119961	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
56931	aerobe
119961	facultative anaerobe

Spore formation

@ref	Spore formation	Confidence
125439		99.779
125438		92.684

Halophily

@ref	Salt	Growth	Tested relation	Concentration
119961	NaCl	positive	growth	0-2 %
119961	NaCl		growth	4 %
119961	NaCl		growth	6 %
119961	NaCl		growth	8 %
119961	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
119961	16947 ChEBI	citrate	-	carbon source
119961	15792 ChEBI	malonate	-	assimilation
119961	17632 ChEBI	nitrate	+	reduction
119961	17632 ChEBI	nitrate	+	respiration
119961	16301 ChEBI	nitrite	-	reduction

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
119961	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
119961	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
119961	alcohol dehydrogenase	+	1.1.1.1
68382	alkaline phosphatase	-	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
119961	amylase	-
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
119961	caseinase	+	3.4.21.50
119961	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
119961	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
119961	lipase	-
68382	lipase (C 14)	-		from API zym
119961	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
119961	ornithine decarboxylase	-	4.1.1.17
119961	oxidase	+
119961	protease	-
68382	trypsin	-	3.4.21.4	from API zym
119961	tween esterase	-
119961	urease	+	3.5.1.5
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
119961	-	-	+	+	-	+	-	-	-	-	-	+	-	-	-	-	-	-	-	-

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
119961	not determinedn.d.	+	+	+	-	-	-	-	+	-	+	+	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	+	+	-	-	-	-	-	-	-	+	-	+	+	-	-	-	-	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Human	-
#Host Body Product	#Fluids	#Blood
#Infection	#Disease	-
#Infection	#Patient	-

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
5653	blood of a patient with empyema	Homo sapiens	Hongkong	China	CHN	Asia
56931	Human blood,bacteremia,empyema,cirrhotic patient	Homo sapiens	Hong Kong	China	CHN	Asia
119961	Human, Blood	Homo sapiens	Hong Kong	China	CHN	Asia	2001

Taxonmaps

69479

Global distribution of 16S sequence AB017489 (>99% sequence identity) for Chromobacterium from Microbeatlas

Aquatic Samples	118
Soil Samples	15
Animal Samples	41
Plant Samples	61
Total Samples	235

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5653	2	Risk group (German classification) According to TRBA 466
119961	1	Risk group (French 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	ASM42328v1 assembly for Laribacter hongkongensis DSM 14985	scaffold	GCA_000423285	1122157.5	2524023164	1122157	68.72

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
5653	Beta proteobacterium MBIC3903 gene for 16S rRNA, partial sequence	AB017489	1474		82200

GC content

5653

GC-content (mol%)68±2.43

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM42328v1 assembly for Laribacter hongkongensis DSM 14985
NCBI: GCA_000423285

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	82.85	no
125439	gram_stain	BacteriaNetⓘ	negative	98.06	no
125439	motility	BacteriaNetⓘ	yes	88.38	no
125439	spore_formation	BacteriaNetⓘ	no	99.78	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Laribacter hongkongensis DSM 14985 DSM 14985
NCBI: GCA_000423285.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.91	no
125438	anaerobic	anaerobicⓘ	no	91.87	yes
125438	aerobic	aerobicⓘ	yes	57.22	no
125438	spore-forming	spore-formingⓘ	no	92.68	no
125438	thermophilic	thermophileⓘ	no	97.10	no
125438	flagellated	motile2+ⓘ	yes	78.15	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Verrucosispora fiedleri sp. nov., an actinomycete isolated from a fjord sediment which synthesizes proximicins.	Goodfellow M, Brown R, Ahmed L, Pathom-Aree W, Bull AT, Jones AL, Stach JE, Zucchi TD, Zhang L, Wang J.	Antonie Van Leeuwenhoek	10.1007/s10482-012-9831-y	2013
Phylogeny	Verrucosispora maris sp. nov., a novel deep-sea actinomycete isolated from a marine sediment which produces abyssomicins.	Goodfellow M, Stach JE, Brown R, Bonda AN, Jones AL, Mexson J, Fiedler HP, Zucchi TD, Bull AT.	Antonie Van Leeuwenhoek	10.1007/s10482-011-9651-5	2012

References

#5653	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 14985
#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 )
#33633	; Curators of the CIP;
#56931	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 45813
#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) .
#66793	Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )
#68382	Automatically annotated from API zym .
#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 .
#119961	Collection of Institut Pasteur ; Curators of the CIP; CIP 107139
#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 )

Content

About us

Laribacter hongkongensis (DSM 14985, LMG 21516, CCUG 45813)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Antibiotic resistance

Metabolite production

Enzymes

API zym

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000423285

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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