Microbulbifer variabilis (MBIC 01082, ATCC 700307, Ni-2088)

Name: Microbulbifer variabilis (MBIC 01082, ATCC 700307, Ni-2088)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133474

Type strain

Strain Designation Ni-2088

Culture col. no. MBIC 01082 ATCC 700307 Ni-2088

NCBI tax ID(s) 1279017 266805

Special Collections Literature strains

Links

Microbulbifer variabilis Ni-2088 is an aerobe, Gram-negative, ovoid-shaped prokaryote that was isolated from marine algae.

Gram-negative ovoid-shaped aerobe genome sequence 16S sequence

Name and taxonomic classification

SI-ID 285874

ATCC 700307

@ref 20215

Last LPSN update 2026-02-09 11:31:57

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Cellvibrionales

Family Microbulbiferaceae

Genus Microbulbifer

Species Microbulbifer variabilis

Full scientific name Microbulbifer variabilis Nishijima et al. 2009

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29108	negative	0.85 µm	0.6 µm	ovoid-shaped
125438	negative				98.5
125439	negative				99.8

Pigmentation

29108

Productionyes

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
29108	positive	growth	12-42
29108	positive	optimum	30	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
29108	positive	optimum	7.75
29108	positive	growth	6.0-9.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

29108

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
29108
125438		92.642
125439		99.8

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29108	NaCl	positive	growth	0.5-7 %
29108	NaCl	positive	optimum	2 %

Observation

29108

Observationaggregates in chains

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29108	4853 ChEBI	esculin	+	hydrolysis
29108	17306 ChEBI	maltose	+	carbon source
29108	37684 ChEBI	mannose	+	carbon source
29108	17632 ChEBI	nitrate	+	reduction
29108	53426 ChEBI	tween 80	+	carbon source

Enzymes

@ref	Value	Activity	Ec
29108	acid phosphatase	+	3.1.3.2
29108	alkaline phosphatase	+	3.1.3.1
29108	catalase	+	1.11.1.6
29108	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Host	#Algae	-

Isolation

29108

Sample typemarine algae

Taxonmaps

69479

Global distribution of 16S sequence AB167354 (>99% sequence identity) for Microbulbifer from Microbeatlas

Aquatic Samples	389
Soil Samples	25
Animal Samples	19
Plant Samples	1
Total Samples	434

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM38056v1 assembly for Microbulbifer variabilis ATCC 700307	contig	GCA_000380565	1279017.3	2519899636	1279017	73.96

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
29108	Microbulbifer variabilis gene for 16S rRNA, partial sequence	AB167354	1492		266805

GC content

29108

GC-content (mol%)48.75

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Microbulbifer variabilis ATCC 700307
NCBI: GCA_000380565

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.80	no
125439	motility	BacteriaNetⓘ	yes	83.20	no
125439	gram_stain	BacteriaNetⓘ	negative	99.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	70.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Microbulbifer variabilis ATCC 700307
PATRIC: 1279017.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	yes
125438	anaerobic	anaerobicⓘ	no	97.90	no
125438	spore-forming	spore-formingⓘ	no	92.64	no
125438	aerobic	aerobicⓘ	yes	72.67	no
125438	thermophilic	thermophileⓘ	no	97.39	no
125438	flagellated	motile2+ⓘ	no	70.19	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	Phylogenomic Identification of a Highly Conserved Copper-Binding RiPP Biosynthetic Gene Cluster in Marine Microbulbifer Bacteria.	Tang Y, Zhong W, Fu L, Asante E, Kostenko A, Vidya FNU, Mandelare-Ruiz P, Adeogun TT, Anderson GP, Edmonds BE, Fang O, Han M, Hollingsworth AS, Ingham AR, Kirby CR, Landrum A, Mack CR, Nobari NS, Oswald EJ, Polevoy CL, Sharifian Y, So TJ, Stokes JR, Thompson RS, Vuthamaraju R, Wang EC, Yang WH, Onstine AE, Paul VJ, Wu R, Aron AT, Agarwal V.	ACS Chem Biol	10.1021/acschembio.5c00507	2025
Genetics	Complete genome sequence of Microbulbifer sp. CCB-MM1, a halophile isolated from Matang Mangrove Forest, Malaysia.	Moh TH, Lau NS, Furusawa G, Amirul AA.	Stand Genomic Sci	10.1186/s40793-017-0248-0	2017
	Association of germ-free mice with a simplified human intestinal microbiota results in a shortened intestine.	Slezak K, Krupova Z, Rabot S, Loh G, Levenez F, Descamps A, Lepage P, Dore J, Bellier S, Blaut M.	Gut Microbes	10.4161/gmic.28203	2014
Pathogenicity	European collaborative study of reproducibility of quantitative sensitivity testing of anaerobes.	King A, Phillips I.	J Antimicrob Chemother	10.1093/jac/21.4.425	1988
	REGEN: Ancestral Genome Reconstruction for Bacteria.	Yang K, Heath LS, Setubal JC.	Genes (Basel)	10.3390/genes3030423	2012
Enzymology	Stepwise engineering of a Pichia pastoris D-amino acid oxidase whole cell catalyst.	Abad S, Nahalka J, Bergler G, Arnold SA, Speight R, Fotheringham I, Nidetzky B, Glieder A.	Microb Cell Fact	10.1186/1475-2859-9-24	2010
Genetics	An evolutionary network of genes present in the eukaryote common ancestor polls genomes on eukaryotic and mitochondrial origin.	Thiergart T, Landan G, Schenk M, Dagan T, Martin WF.	Genome Biol Evol	10.1093/gbe/evs018	2012
Phylogeny	Microbulbifer discodermiae sp. nov. and Microbulbifer jejuensis sp. nov., isolated from marine sponges.	Moon YL, Park JS.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006980	2025
Genetics	Noncontiguous finished genome sequence and description of Fusobacterium massiliense sp. nov. isolated from human duodenum.	Mailhe M, Ricaboni D, Vitton V, Benezech A, Dubourg G, Michelle C, Andrieu C, Armstrong N, Bittar F, Fournier PE, Raoult D, Million M.	New Microbes New Infect	10.1016/j.nmni.2016.12.003	2017
Phylogeny	Microbulbifer echini sp. nov., isolated from the gastrointestinal tract of a purple sea urchin, Heliocidaris crassispina.	Lee JY, Kim PS, Hyun DW, Kim HS, Shin NR, Jung MJ, Yun JH, Kim MS, Whon TW, Bae JW	Int J Syst Evol Microbiol	10.1099/ijsem.0.001731	2017
Phylogeny	Microbulbifer variabilis sp. nov. and Microbulbifer epialgicus sp. nov., isolated from Pacific marine algae, possess a rod-coccus cell cycle in association with the growth phase.	Nishijima M, Takadera T, Imamura N, Kasai H, An KD, Adachi K, Nagao T, Sano H, Yamasato K	Int J Syst Evol Microbiol	10.1099/ijs.0.006452-0	2009
Phylogeny	Microbulbifer okhotskensis sp. nov., isolated from a deep bottom sediment of the Okhotsk Sea.	Romanenko L, Kurilenko V, Otstavnykh N, Velansky P, Isaeva M, Mikhailov V	Arch Microbiol	10.1007/s00203-022-03161-9	2022

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 )
#25536	IJSEM 1696 2009 ( DOI 10.1099/ijs.0.006452-0 , PubMed 19542114 )
#29108	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 #25536
#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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Microbulbifer variabilis (MBIC 01082, ATCC 700307, Ni-2088)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_000380565

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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