Microbulbifer aggregans (LMG 29920, JCM 31875, CCB-MM1)

Name: Microbulbifer aggregans (LMG 29920, JCM 31875, CCB-MM1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 140780

Type strain

Strain Designation CCB-MM1

Culture col. no. LMG 29920 JCM 31875 CCB-MM1

NCBI tax ID(s) 1769779

Special Collections JCM Literature strains

History G. Furusawa; Center for Chem. Biol., Univ. Sains Malaysia, Malaysia; CCB-MM1.

Links

Microbulbifer aggregans CCB-MM1 is an obligate aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from estuarine sediment from Matang Mangrove Forest.

Gram-negative rod-shaped colony-forming obligate aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 273111

LMG 29920,JCM 31875

@ref 20215

Last LPSN update 2026-02-09 11:33:42

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Cellvibrionales

Family Microbulbiferaceae

Genus Microbulbifer

Species Microbulbifer aggregans

Full scientific name Microbulbifer aggregans Moh et al. 2017

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
43558	negative	1.3-2.5 µm	0.3 µm	rod-shaped
125439	negative				99.6
125438	negative				99

Colony morphology

@ref	Colony color	Colony shape	Incubation period	Medium used
43558	White	circular	1-5 days	MA agar

Culture and growth conditions

Culture medium

@ref	Name	Growth
43558	Marine agar (MA)

Culture temp

@ref	Growth	Type	Temperature (°C)
43558	positive	growth	15-45
43558	positive	optimum	30
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
43558	positive	optimum	7
43558	positive	growth	6-9	alkaliphile

Physiology and metabolism

Oxygen tolerance

43558

Oxygen toleranceobligate aerobe

Spore formation

@ref	Spore formation	Confidence
125439		98.7
125438		90.705

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43558	NaCl	positive	growth	0.5-8 %(w/v)
43558	NaCl	positive	optimum	2-3 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43558	30916 ChEBI	2-oxoglutarate	+	oxidation
43558	73918 ChEBI	3-O-methyl-D-glucose	+	oxidation
43558	17925 ChEBI	alpha-D-glucose	-	assimilation
43558	85146 ChEBI	carboxymethylcellulose	-	degradation
43558		casein	-	degradation
43558	17057 ChEBI	cellobiose	-	assimilation
43558	17029 ChEBI	chitin	-	degradation
43558	15824 ChEBI	D-fructose	-	assimilation
43558	15895 ChEBI	D-galactonic acid lactone	+	oxidation
43558	12936 ChEBI	D-galactose	+	assimilation
43558	12936 ChEBI	D-galactose	+	oxidation
43558	16899 ChEBI	D-mannitol	-	assimilation
43558	16024 ChEBI	D-mannose	+	assimilation
43558	16024 ChEBI	D-mannose	+	oxidation
43558	17924 ChEBI	D-sorbitol	-	assimilation
43558	23652 ChEBI	dextrin	+	oxidation
43558	16991 ChEBI	dna	-	degradation
43558	5291 ChEBI	gelatin	-	assimilation
43558	32323 ChEBI	glucuronamide	+	oxidation
43558	17754 ChEBI	glycerol	-	assimilation
43558	62345 ChEBI	L-rhamnose	+	assimilation
43558	62345 ChEBI	L-rhamnose	+	oxidation
43558	17306 ChEBI	maltose	-	assimilation
43558	17268 ChEBI	myo-inositol	-	assimilation
43558	506227 ChEBI	N-acetylglucosamine	-	assimilation
43558	28017 ChEBI	starch	+	degradation
43558	17992 ChEBI	sucrose	-	assimilation
43558	27082 ChEBI	trehalose	-	assimilation
43558	37166 ChEBI	xylan	-	degradation

Antibiotic resistance

@ref	ChEBI	Metabolite	Sensitivity conc.	Resistance conc.
43558	28971	ampicillin	10 µg (disc)
43558	3393	carbenicillin	100 µg (disc)
43558	17698	chloramphenicol	35 µg (disc)
43558	48923	erythromycin	20 µg (disc)
43558	6104	kanamycin		30 µg (disc)
43558	17076	streptomycin		50 µg (disc)
43558	28001	vancomycin	25 µg (disc)

Enzymes

@ref	Value	Activity	Ec
43558	acid phosphatase	+	3.1.3.2
43558	alkaline phosphatase	+	3.1.3.1
43558	catalase	+	1.11.1.6
43558	cytochrome oxidase	+	1.9.3.1
43558	esterase (C 4)	+
43558	esterase Lipase (C 8)	+
43558	leucine arylamidase	+	3.4.11.1
43558	N-acetyl-beta-glucosaminidase	+	3.2.1.52
43558	naphthol-AS-BI-phosphohydrolase	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Estuary
#Environmental	#Aquatic	#Mangrove
#Environmental	#Aquatic	#Sediment
#Environmental	#Terrestrial	#Forest

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
43558	estuarine sediment from Matang Mangrove Forest	Perak, Matang Mangrove Forest	Malaysia	MYS	Asia	4.852	100.557 4.852/100.557
67770	Estuarine sediment from Matang Mangrove Forest		Malaysia	MYS	Asia

Taxonmaps

69479

Global distribution of 16S sequence KU736842 (>99% sequence identity) for Microbulbifer aggregans from Microbeatlas

Aquatic Samples	36
Soil Samples	5
Animal Samples
Plant Samples
Total Samples	41

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	IMG accession	NCBI tax ID	Score
66792	ASM175010v1 assembly for Microbulbifer aggregans CCB-MM1	complete	GCA_001750105	2751185758	1769779	98.72

16S sequences

@ref	Description	Accession	Database
43558	Microbulbifer aggregans strain CCB-MM1 16S ribosomal RNA gene, complete sequence	KU736842

GC content

@ref	GC-content (mol%)	Method
67770	58.9	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Microbulbifer aggregans CCB-MM1
NCBI: GCA_001750105

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.70	no
125439	motility	BacteriaNetⓘ	yes	89.80	no
125439	gram_stain	BacteriaNetⓘ	negative	99.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	87.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Microbulbifer aggregans CCB-MM1
NCBI: GCA_001750105.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.00	yes
125438	anaerobic	anaerobicⓘ	no	95.30	yes
125438	aerobic	aerobicⓘ	yes	75.89	yes
125438	spore-forming	spore-formingⓘ	no	90.71	no
125438	thermophilic	thermophileⓘ	no	96.91	no
125438	flagellated	motile2+ⓘ	no	70.75	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Enzymology	An assimilatory sulfite reductase, CysI, negatively regulates the dormancy of Microbulbifer aggregans CCB-MM1(T).	Diyana T, Furusawa G	J Basic Microbiol	10.1002/jobm.202100198	2021
Phylogeny	Metabolic strategies of dormancy of a marine bacterium Microbulbifer aggregans CCB-MM1: Its alternative electron transfer chain and sulfate-reducing pathway.	Furusawa G, Diyana T, Lau NS	Genomics	10.1016/j.ygeno.2021.02.024	2021
Metabolism	Characterisation of marine bacterium Microbulbifer sp. ALW1 with Laminaria japonica degradation capability.	Li Z, Du Z, Li H, Chen Y, Zheng M, Jiang Z, Du X, Ni H, Zhu Y	AMB Express	10.1186/s13568-022-01482-y	2022
Phylogeny	Microbulbifer hainanensis sp. nov., a moderately halopilic bacterium isolated from mangrove sediment.	Cheng Y, Zhu S, Guo C, Xie F, Jung D, Li S, Zhang W, He S	Antonie Van Leeuwenhoek	10.1007/s10482-021-01574-y	2021
Phylogeny	Microbulbifer aggregans sp. nov., isolated from estuarine sediment from a mangrove forest.	Moh TH, Furusawa G, Amirul AA	Int J Syst Evol Microbiol	10.1099/ijsem.0.002258	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 )
#43558	Tsu Horng Moh, Go Furusawa, Abdullah Al-Ashraf Amirul: Microbulbifer aggregans sp. nov., isolated from estuarine sediment from a mangrove forest. IJSEM 67: 4089 - 4094 2017 ( DOI 10.1099/ijsem.0.002258 , PubMed 28905698 )
#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;
#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 aggregans (LMG 29920, JCM 31875, CCB-MM1)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Antibiotic resistance

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_001750105

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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