Vibrio pomeroyi (DSM 17180, CAIM 578, CIP 108273)

Name: Vibrio pomeroyi (DSM 17180, CAIM 578, CIP 108273)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17301

Type strain

Culture col. no. DSM 17180 CAIM 578 CIP 108273 LMG 20537

NCBI tax ID(s) 198832

Special Collections DSMZ CIP

Links

Vibrio pomeroyi DSM 17180 is a facultative anaerobe, mesophilic, Gram-negative prokaryote that was isolated from bivalve larvae.

Gram-negative motile rod-shaped facultative anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 86191
CAIM 578,LMG 20537,DSM 17180,CIP 108273,CECT 8440

@ref 20215

Last LPSN update 2025-12-16 09:51:03

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order "Vibrionales"

Family Vibrionaceae

Genus Vibrio

Species Vibrio pomeroyi

Full scientific name Vibrio pomeroyi Thompson et al. 2003

Morphology

Cell morphology
@ref Gram stain Confidence
125438 negative 100
125439 negative 97.7
121935 negative

Culture and growth conditions

Culture medium
@ref Name Growth Medium link Composition
6713 BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Medium recipe at MediaDive Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
39989 Marine agar (MA) Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
121935 CIP Medium 13 Medium recipe at CIP

Culture temp
@ref Growth Type Temperature (°C) Range
6713 positive growth 28 mesophilic
39989 positive growth 25 mesophilic
121935 positive growth 5-30
121935 negative growth 37

Physiology and metabolism

Oxygen tolerance
@ref Oxygen tolerance
121935 facultative anaerobe
125439 obligate aerobe

Spore formation
@ref Spore formation Confidence
125439 96

Halophily
@ref Salt Growth Tested relation Concentration
121935 NaCl positive growth 2-10 %
121935 NaCl growth 0 %

Metabolite utilization
@ref Chebi-ID Metabolite Utilization activity Kind of utilization tested
68369 17128 ChEBI adipate - assimilation from API 20NE
68371 27613 ChEBI amygdalin - builds acid from from API 50CH acid
68371 18305 ChEBI arbutin - builds acid from from API 50CH acid
68369 29016 ChEBI arginine - hydrolysis from API 20NE
121935 16947 ChEBI citrate - carbon source
68371 17108 ChEBI D-arabinose - builds acid from from API 50CH acid
68371 18333 ChEBI D-arabitol - builds acid from from API 50CH acid
68371 28847 ChEBI D-fucose - builds acid from from API 50CH acid
68369 17634 ChEBI D-glucose + assimilation from API 20NE
68369 17634 ChEBI D-glucose + fermentation from API 20NE
68371 62318 ChEBI D-lyxose - builds acid from from API 50CH acid
68369 16899 ChEBI D-mannitol + assimilation from API 20NE
68369 16024 ChEBI D-mannose + assimilation from API 20NE
68371 17924 ChEBI D-sorbitol - builds acid from from API 50CH acid
68371 16443 ChEBI D-tagatose - builds acid from from API 50CH acid
68371 65327 ChEBI D-xylose - builds acid from from API 50CH acid
68369 27689 ChEBI decanoate + assimilation from API 20NE
68371 17113 ChEBI erythritol - builds acid from from API 50CH acid
121935 4853 ChEBI esculin + hydrolysis
68369 4853 ChEBI esculin + hydrolysis from API 20NE
68371 16813 ChEBI galactitol - builds acid from from API 50CH acid
68369 5291 ChEBI gelatin + hydrolysis from API 20NE
68371 28066 ChEBI gentiobiose - builds acid from from API 50CH acid
68369 24265 ChEBI gluconate + assimilation from API 20NE
121935 17234 ChEBI glucose + fermentation
68371 15443 ChEBI inulin - builds acid from from API 50CH acid
68371 30849 ChEBI L-arabinose - builds acid from from API 50CH acid
68369 30849 ChEBI L-arabinose - assimilation from API 20NE
68371 18403 ChEBI L-arabitol - builds acid from from API 50CH acid
68371 18287 ChEBI L-fucose - builds acid from from API 50CH acid
68371 62345 ChEBI L-rhamnose - builds acid from from API 50CH acid
68371 17266 ChEBI L-sorbose - builds acid from from API 50CH acid
68371 65328 ChEBI L-xylose - builds acid from from API 50CH acid
121935 17716 ChEBI lactose + fermentation
68369 25115 ChEBI malate + assimilation from API 20NE
68369 17306 ChEBI maltose + assimilation from API 20NE
68371 6731 ChEBI melezitose - builds acid from from API 50CH acid
68371 28053 ChEBI melibiose - builds acid from from API 50CH acid
68371 320061 ChEBI methyl alpha-D-glucopyranoside - builds acid from from API 50CH acid
68371 43943 ChEBI methyl alpha-D-mannoside - builds acid from from API 50CH acid
68371 74863 ChEBI methyl beta-D-xylopyranoside - builds acid from from API 50CH acid
68371 17268 ChEBI myo-inositol - builds acid from from API 50CH acid
68369 59640 ChEBI N-acetylglucosamine + assimilation from API 20NE
121935 17632 ChEBI nitrate + reduction
68369 17632 ChEBI nitrate + reduction from API 20NE
121935 16301 ChEBI nitrite - reduction
68371 Potassium 2-ketogluconate - builds acid from from API 50CH acid
68371 Potassium 5-ketogluconate - builds acid from from API 50CH acid
68371 16634 ChEBI raffinose - builds acid from from API 50CH acid
68371 15963 ChEBI ribitol - builds acid from from API 50CH acid
68371 17814 ChEBI salicin - builds acid from from API 50CH acid
121935 132112 ChEBI sodium thiosulfate - builds gas from
68371 17992 ChEBI sucrose - builds acid from from API 50CH acid
68369 27897 ChEBI tryptophan + energy source from API 20NE
68371 32528 ChEBI turanose - builds acid from from API 50CH acid
68369 16199 ChEBI urea - hydrolysis from API 20NE
68371 17151 ChEBI xylitol - builds acid from from API 50CH acid

Antibiotic resistance
@ref Metabolite Is antibiotic Is sensitive Is resistant
121935 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production
@ref Chebi-ID Metabolite Production
68369 35581 ChEBI indole from API 20NE
121935 35581 ChEBI indole

Metabolite tests
@ref Chebi-ID Metabolite Voges-proskauer-test
121935 15688 ChEBI acetoin -
121935 17234 ChEBI glucose
68369 35581 ChEBI indole from API 20NE

Enzymes
@ref Value Activity Ec
68382 acid phosphatase + 3.1.3.2 from API zym
121935 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
121935 amylase +
68369 arginine dihydrolase - 3.5.3.6 from API 20NE
68382 beta-galactosidase - 3.2.1.23 from API zym
121935 beta-galactosidase + 3.2.1.23
68382 beta-glucosidase - 3.2.1.21 from API zym
68369 beta-glucosidase + 3.2.1.21 from API 20NE
68382 beta-glucuronidase - 3.2.1.31 from API zym
121935 caseinase + 3.4.21.50
121935 catalase + 1.11.1.6
68382 cystine arylamidase - 3.4.11.3 from API zym
68369 cytochrome oxidase + 1.9.3.1 from API 20NE
68382 esterase (C 4) + from API zym
68382 esterase lipase (C 8) + from API zym
121935 gamma-glutamyltransferase + 2.3.2.2
121935 gelatinase +
68369 gelatinase + from API 20NE
121935 lecithinase +
68382 leucine arylamidase + 3.4.11.1 from API zym
121935 lipase +
68382 lipase (C 14) - from API zym
121935 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
121935 ornithine decarboxylase - 4.1.1.17
121935 oxidase +
121935 protease +
68382 trypsin + 3.4.21.4 from API zym
121935 tryptophan deaminase -
121935 tween esterase +
121935 urease - 3.5.1.5
68369 urease - 3.5.1.5 from API 20NE
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

121935 - + + + - + - - + - + + - - - - - - - -

API 20NE

@ref Reduction of nitratesNO3 TRP GLU_ Ferm ADH (Arg) URE ESC GEL PNPG GLU_ Assim ARA MNE MAN NAG MAL GNT CAP ADI MLT CIT PAC OX

6713 + + + - - + + + + - + + + + + + - + + - +

API 50CHac

@ref ControlQ GLY ERY DARA LARA RIB DXYL LXYL ADO MDX GAL GLU FRU MNE SBE RHA DUL INO MAN SOR MDM MDG NAG AMY ARB ESC SAL CEL MAL LAC MEL SAC TRE INU MLZ RAF AMD GLYG XLT GEN TUR LYX TAG DFUC LFUC DARL LARL GNT 2KG 5KG

121935 not determinedn.d. +/- - - - +/- - - - - +/- +/- +/- +/- - - - - +/- - - - +/- - - +/- - +/- +/- +/- - - +/- - - - +/- +/- - - - - - - - - - +/- - -

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

121935 not determinedn.d. + + + + + - - - - + + + - + - + - - + + - - - - - - - - - - - + - + - - - - - - - - - - - - - - - + - - - - - - - - - + + - - - - - - - - - - - - - - + - - + + + - - - - - + - - + + + + + + - - + +

Isolation, sampling and environmental information

Isolation source categories
Cat1 Cat2 Cat3
#Environmental #Aquatic #Marine
#Host #Invertebrates (Other) #Mollusca

Isolation
@ref Sample type Host species Geographic location Country Country ISO 3 Code Continent
6713 bivalve (Nodipecten nodosus) larvae Nodipecten nodosus LCMM Florianópolis Brazil BRA Middle and South America
121935 Animal, Bivalue larvae, Nodipecten nodosus Florianopolis Brazil BRA Middle and South America

Taxonmaps

69479

Global distribution of 16S sequence AJ491290 (>99% sequence identity) for Vibrio from Microbeatlas

Aquatic Samples 6829

Soil Samples 499

Animal Samples 1668

Plant Samples 1105

Total Samples 10101

Interaction and safety

Risk assessment
@ref Biosafety level Biosafety level comment
6713 1 Risk group (German classification)
According to TRBA 466
121935 2 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 ASM2434759v1 assembly for Vibrio pomeroyi LMG 20537 complete
GCA_024347595

198832.3

8048071933

198832
98.84

Genome browser: GCA_024347595

16S sequences
@ref Description Accession Length Database NCBI tax ID
6713 Vibrio pomeroyi partial 16S rRNA gene, type strain LMG 20537T AJ491290 1507

198832
124043 Vibrio pomeroyi strain LMG 20537(T) 16S ribosomal RNA gene, partial sequence. OQ147516 1098
198832
124043 Vibrio pomeroyi strain CAIM 578 16S ribosomal RNA gene, partial sequence. MT759944 1395
198832
124043 Vibrio pomeroyi strain CAIM 578 16S ribosomal RNA gene, partial sequence. MT757987 1399
198832
124043 Vibrio pomeroyi strain LMG 20537 16S ribosomal RNA gene, partial sequence. MW198186 601
198832

GC content
6713 GC-content (mol%)44.1

Genome-based predictions

Predictions
Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Vibrio pomeroyi LMG 20537
NCBI: GCA_024347595

@ref Trait Model Prediction Confidence in % In training data

125439 spore_formation BacteriaNetⓘ no 96.00 no

125439 motility BacteriaNetⓘ yes 72.70 no

125439 gram_stain BacteriaNetⓘ negative 97.70 no

125439 oxygen_tolerance BacteriaNetⓘ obligate aerobe 97.50 no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Vibrio pomeroyi LMG 20537
NCBI: GCA_024347595.1

@ref Trait Model Prediction Confidence in % In training data

125438 gram-positive gram-positiveⓘ no 100.00 no

125438 anaerobic anaerobicⓘ no 96.43 yes

125438 aerobic aerobicⓘ no 66.11 no

125438 spore-forming spore-formingⓘ no 89.18 no

125438 thermophilic thermophileⓘ no 99.50 yes

125438 flagellated motile2+ⓘ yes 87.67 no

Literature

Literature
Title Authors Journal DOI Year
Characterization of bacteria in ballast water using MALDI-TOF mass spectrometry. Emami K, Askari V, Ullrich M, Mohinudeen K, Anil AC, Khandeparker L, Burgess JG, Mesbahi E. PLoS One 10.1371/journal.pone.0038515 2012
A persistent and diverse airway microbiota present during chronic obstructive pulmonary disease exacerbations. Huang YJ, Kim E, Cox MJ, Brodie EL, Brown R, Wiener-Kronish JP, Lynch SV. OMICS 10.1089/omi.2009.0100 2010
Vibrio kanaloae sp. nov., Vibrio pomeroyi sp. nov. and Vibrio chagasii sp. nov., from sea water and marine animals. Thompson FL, Thompson CC, Li Y, Gomez-Gil B, Vandenberghe J, Hoste B, Swings J Int J Syst Evol Microbiol 10.1099/ijs.0.02490-0 2003

References

#6713 Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17180

#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 )

#39989 ; Curators of the CIP;

#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) .

#68369 Automatically annotated from API 20NE .

#68371 Automatically annotated from API 50CH acid .

#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 .

#121935 Collection of Institut Pasteur ; Curators of the CIP; CIP 108273

#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 )

@ref	Name	Medium link	Composition
6713	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)	Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
39989	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
121935	CIP Medium 13	Medium recipe at CIP

@ref	Growth	Type	Temperature (°C)	Range
6713	positive	growth	28	mesophilic
39989	positive	growth	25	mesophilic
121935	positive	growth	5-30
121935	negative	growth	37

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
121935	16947 ChEBI	citrate	-	carbon source
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	+	fermentation	from API 20NE
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68369	16899 ChEBI	D-mannitol	+	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	+	assimilation	from API 20NE
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
68369	27689 ChEBI	decanoate	+	assimilation	from API 20NE
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
121935	4853 ChEBI	esculin	+	hydrolysis
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68369	5291 ChEBI	gelatin	+	hydrolysis	from API 20NE
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
121935	17234 ChEBI	glucose	+	fermentation
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	-	builds acid from	from API 50CH acid
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
121935	17716 ChEBI	lactose	+	fermentation
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68369	59640 ChEBI	N-acetylglucosamine	+	assimilation	from API 20NE
121935	17632 ChEBI	nitrate	+	reduction
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
121935	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	-	builds acid from	from API 50CH acid
121935	132112 ChEBI	sodium thiosulfate	-	builds gas from
68371	17992 ChEBI	sucrose	-	builds acid from	from API 50CH acid
68369	27897 ChEBI	tryptophan	+	energy source	from API 20NE
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
121935	15688 ChEBI	acetoin	-
121935	17234 ChEBI	glucose
68369	35581 ChEBI	indole		from API 20NE

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
121935	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
121935	amylase	+
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68382	beta-galactosidase	-	3.2.1.23	from API zym
121935	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
68382	beta-glucuronidase	-	3.2.1.31	from API zym
121935	caseinase	+	3.4.21.50
121935	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
121935	gamma-glutamyltransferase	+	2.3.2.2
121935	gelatinase	+
68369	gelatinase	+		from API 20NE
121935	lecithinase	+
68382	leucine arylamidase	+	3.4.11.1	from API zym
121935	lipase	+
68382	lipase (C 14)	-		from API zym
121935	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
121935	ornithine decarboxylase	-	4.1.1.17
121935	oxidase	+
121935	protease	+
68382	trypsin	+	3.4.21.4	from API zym
121935	tryptophan deaminase	-
121935	tween esterase	+
121935	urease	-	3.5.1.5
68369	urease	-	3.5.1.5	from API 20NE
68382	valine arylamidase	-		from API zym

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Host	#Invertebrates (Other)	#Mollusca

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
6713	bivalve (Nodipecten nodosus) larvae	Nodipecten nodosus	LCMM Florianópolis	Brazil	BRA	Middle and South America
121935	Animal, Bivalue larvae, Nodipecten nodosus		Florianopolis	Brazil	BRA	Middle and South America

Aquatic Samples	6829
Soil Samples	499
Animal Samples	1668
Plant Samples	1105
Total Samples	10101

@ref	Biosafety level	Biosafety level comment
6713	1	Risk group (German classification) According to TRBA 466
121935	2	Risk group (French classification) According to TRBA 466

@ref	Description	Accession	Length	NCBI tax ID
6713	Vibrio pomeroyi partial 16S rRNA gene, type strain LMG 20537T	AJ491290	1507	198832
124043	Vibrio pomeroyi strain LMG 20537(T) 16S ribosomal RNA gene, partial sequence.	OQ147516	1098	198832
124043	Vibrio pomeroyi strain CAIM 578 16S ribosomal RNA gene, partial sequence.	MT759944	1395	198832
124043	Vibrio pomeroyi strain CAIM 578 16S ribosomal RNA gene, partial sequence.	MT757987	1399	198832
124043	Vibrio pomeroyi strain LMG 20537 16S ribosomal RNA gene, partial sequence.	MW198186	601	198832

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.00	no
125439	motility	BacteriaNetⓘ	yes	72.70	no
125439	gram_stain	BacteriaNetⓘ	negative	97.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.50	no

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	100.00	no
125438	anaerobic	anaerobicⓘ	no	96.43	yes
125438	aerobic	aerobicⓘ	no	66.11	no
125438	spore-forming	spore-formingⓘ	no	89.18	no
125438	thermophilic	thermophileⓘ	no	99.50	yes
125438	flagellated	motile2+ⓘ	yes	87.67	no

Title	Authors	Journal	DOI	Year
Characterization of bacteria in ballast water using MALDI-TOF mass spectrometry.	Emami K, Askari V, Ullrich M, Mohinudeen K, Anil AC, Khandeparker L, Burgess JG, Mesbahi E.	PLoS One	10.1371/journal.pone.0038515	2012
A persistent and diverse airway microbiota present during chronic obstructive pulmonary disease exacerbations.	Huang YJ, Kim E, Cox MJ, Brodie EL, Brown R, Wiener-Kronish JP, Lynch SV.	OMICS	10.1089/omi.2009.0100	2010
Vibrio kanaloae sp. nov., Vibrio pomeroyi sp. nov. and Vibrio chagasii sp. nov., from sea water and marine animals.	Thompson FL, Thompson CC, Li Y, Gomez-Gil B, Vandenberghe J, Hoste B, Swings J	Int J Syst Evol Microbiol	10.1099/ijs.0.02490-0	2003

#6713	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17180
#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 )
#39989	; Curators of the CIP;
#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) .
#68369	Automatically annotated from API 20NE .
#68371	Automatically annotated from API 50CH acid .
#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 .
#121935	Collection of Institut Pasteur ; Curators of the CIP; CIP 108273
#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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Vibrio pomeroyi (DSM 17180, CAIM 578, CIP 108273)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

API zym

API 20NE

API 50CHac

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_024347595

16S sequences

GC content

Genome-based predictions

Predictions

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Literature

References

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