Photobacterium indicum (DSM 5151, ATCC 19614)

Name: Photobacterium indicum (DSM 5151, ATCC 19614)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17222

Type strain

Culture col. no. DSM 5151 ATCC 19614

NCBI tax ID(s) 81447

Special Collections DSMZ

Links

Photobacterium indicum DSM 5151 is a mesophilic prokaryote that was isolated from marine mud.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 37034

CAIM 1856,ATCC 19614,DSM 5151,NCIMB 2221,IFO 14233,NBRC 14233,KCTC 12355,BCRC 15012,CCRC 15012,LMG 22857

@ref 20215

Last LPSN update 2025-12-16 09:51:02

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order "Vibrionales"

Family Vibrionaceae

Genus Photobacterium

Species Photobacterium indicum

Full scientific name Photobacterium indicum (Johnson and Weisrock 1969) Ivanova et al. 2004

Synonyms (2)

Photobacterium indicum
Hyphomicrobium indicum

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	98.8
125438	negative	98.5

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
1933	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

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
1933	positive	growth	25	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	97.6

Spore formation

@ref	Spore formation	Confidence
125439		96.3

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Terrestrial	#Mud (Sludge)
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location
1933	marine mud	Indian Ocean

Taxonmaps

69479

Global distribution of 16S sequence AB159513 (>99% sequence identity) for Photobacterium from Microbeatlas

Aquatic Samples	426
Soil Samples	122
Animal Samples	704
Plant Samples	11
Total Samples	1263

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
1933	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	ASM302621v1 assembly for Photobacterium indicum ATCC 19614	contig	GCA_003026215	81447.4	2902459631	81447	71.12

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Photobacterium indicum gene for 16S rRNA, partial sequence	AB016982	1408	81447
20218	Photobacterium indicum gene for 16S rRNA, partial sequence	AB159513	1402	81447
20218	Photobacterium indicum gene for 16S rRNA, partial sequence, strain: NBRC 14233	AB680594	1404	81447

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Photobacterium indicum ATCC 19614
NCBI: GCA_003026215

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.30	no
125439	motility	BacteriaNetⓘ	yes	76.60	no
125439	gram_stain	BacteriaNetⓘ	negative	98.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Photobacterium indicum strain ATCC 19614
PATRIC: 81447.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	no
125438	anaerobic	anaerobicⓘ	no	95.58	no
125438	aerobic	aerobicⓘ	no	63.58	no
125438	spore-forming	spore-formingⓘ	no	85.13	no
125438	thermophilic	thermophileⓘ	no	99.00	yes
125438	flagellated	motile2+ⓘ	yes	84.91	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	A Polysaccharide Biosynthesis Locus in Vibrio parahaemolyticus Important for Biofilm Formation Has Homologs Widely Distributed in Aquatic Bacteria Mainly from Gammaproteobacteria.	Liu M, Nie H, Luo X, Yang S, Chen H, Cai P.	mSystems	10.1128/msystems.01226-21	2022
Phylogeny	Transfer of Hyphomicrobium indicum to the genus Photobacterium as Photobacterium indicum comb. nov.	Xie CH, Yokota A	Int J Syst Evol Microbiol	10.1099/ijs.0.63159-0	2004
Phylogeny	Photobacterium lipolyticum sp. nov., a bacterium with lipolytic activity isolated from the Yellow Sea in Korea.	Yoon JH, Lee JK, Kim YO, Oh TK	Int J Syst Evol Microbiol	10.1099/ijs.0.63215-0	2005

References

#1933	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 5151
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#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 .
#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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Photobacterium indicum (DSM 5151, ATCC 19614)

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_003026215

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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