Name: Microbulbifer aggregans CCB-MM1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140780

Type strain:

Species: Microbulbifer aggregans

Strain Designation: CCB-MM1

Culture col. no.: LMG 29920, JCM 31875

Strain history: G. Furusawa; Center for Chem. Biol., Univ. Sains Malaysia, Malaysia; CCB-MM1.

NCBI tax ID(s): 1769779 (species)

Section

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.

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Cellvibrionales*
	Family	*Microbulbiferaceae*
	Genus	*Microbulbifer*
	Species	**Microbulbifer aggregans**
	Full Scientific Name (LPSN)	Microbulbifer aggregans Moh et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #43558]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.966

[Ref.: #43558]	Cell length	1.3-2.5 µm

[Ref.: #43558]	Cell width	0.3 µm

[Ref.: #43558]	Cell shape	rod-shaped

[Ref.: #43558]	Motility	no

[Ref.: #43558]	Colony color	White
[Ref.: #43558]	Colony shape	circular
[Ref.: #43558]	Incubation period	1-5 days
[Ref.: #43558]	Cultivation medium used	MA agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43558]

Culture medium

Marine agar (MA)

[Ref.: #43558]

Culture medium growth

		Temperature
[Ref.: #43558]	growth	15-45 °C
[Ref.: #43558]	optimum	30 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #43558]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #43558]			optimum	7
[Ref.: #43558]			growth	6-9

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43558]

Oxygen tolerance

obligate aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.999

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43558]		NaCl		growth	0.5-8	%(w/v)
[Ref.: #43558]		NaCl		optimum	2-3	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43558]	2-oxoglutarate ChEBI	+	oxidation
[Ref.: #43558]	3-O-methyl-D-glucose ChEBI	+	oxidation
[Ref.: #43558]	alpha-D-glucose ChEBI	-	assimilation
[Ref.: #43558]	carboxymethylcellulose ChEBI	-	degradation
[Ref.: #43558]	casein	-	degradation
[Ref.: #43558]	cellobiose ChEBI	-	assimilation
[Ref.: #43558]	chitin ChEBI	-	degradation
[Ref.: #43558]	D-fructose ChEBI	-	assimilation
[Ref.: #43558]	D-galactonic acid lactone ChEBI	+	oxidation
[Ref.: #43558]	D-galactose ChEBI	+	assimilation
[Ref.: #43558]	D-galactose ChEBI	+	oxidation
[Ref.: #43558]	D-mannitol ChEBI	-	assimilation
[Ref.: #43558]	D-mannose ChEBI	+	assimilation
[Ref.: #43558]	D-mannose ChEBI	+	oxidation
[Ref.: #43558]	D-sorbitol ChEBI	-	assimilation
[Ref.: #43558]	dextrin ChEBI	+	oxidation
[Ref.: #43558]	dna ChEBI	-	degradation
[Ref.: #43558]	gelatin ChEBI	-	assimilation
[Ref.: #43558]	glucuronamide ChEBI	+	oxidation
[Ref.: #43558]	glycerol ChEBI	-	assimilation
[Ref.: #43558]	L-rhamnose ChEBI	+	assimilation
[Ref.: #43558]	L-rhamnose ChEBI	+	oxidation
[Ref.: #43558]	maltose ChEBI	-	assimilation
[Ref.: #43558]	myo-inositol ChEBI	-	assimilation
[Ref.: #43558]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #43558]	starch ChEBI	+	degradation
[Ref.: #43558]	sucrose ChEBI	-	assimilation
[Ref.: #43558]	trehalose ChEBI	-	assimilation
[Ref.: #43558]	xylan ChEBI	-	degradation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #43558]	ampicillin ChEBI	yes	10	µg (disc)
[Ref.: #43558]	carbenicillin ChEBI	yes	100	µg (disc)
[Ref.: #43558]	chloramphenicol ChEBI	yes	35	µg (disc)
[Ref.: #43558]	erythromycin ChEBI	yes	20	µg (disc)
[Ref.: #43558]	kanamycin ChEBI				yes	30	µg (disc)
[Ref.: #43558]	streptomycin ChEBI				yes	50	µg (disc)
[Ref.: #43558]	vancomycin ChEBI	yes	25	µg (disc)

	Enzyme	Enzyme activity	EC number
[Ref.: #43558]	acid phosphatase	+	3.1.3.2
[Ref.: #43558]	alkaline phosphatase	+	3.1.3.1
[Ref.: #43558]	catalase	+	1.11.1.6
[Ref.: #43558]	cytochrome oxidase	+	1.9.3.1
[Ref.: #43558]	esterase (C 4)	+
[Ref.: #43558]	esterase Lipase (C 8)	+
[Ref.: #43558]	leucine arylamidase	+	3.4.11.1
[Ref.: #43558]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #43558]	naphthol-AS-BI-phosphohydrolase	+

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #43558]	Sample type/isolated from	estuarine sediment from Matang Mangrove Forest
[Ref.: #43558]	Geographic location (country and/or sea, region)	Perak, Matang Mangrove Forest
[Ref.: #43558]	Country	Malaysia
[Ref.: #43558]	Country ISO 3 Code	MYS
[Ref.: #43558]	Continent	Asia
[Ref.: #43558]	Geographic location	4.8520°/100.5570°

[Ref.: #67770]	Sample type/isolated from	Estuarine sediment from Matang Mangrove Forest
[Ref.: #67770]	Country	Malaysia
[Ref.: #67770]	Country ISO 3 Code	MYS
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Estuary
#Environmental	#Aquatic	#Mangrove
#Environmental	#Aquatic	#Sediment
#Environmental	#Terrestrial	#Forest

What are isolation sources categories?

[Ref.: #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

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #43558]	16S rRNA gene sequence	KU736842		GenBank

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Microbulbifer aggregans CCB-MM1	GCA_001750105	complete	GenBank	1769779 tax ID	*
[Ref.: #66792]	Microbulbifer aggregans CCB-MM1	2751185758	complete	JGI IMG/M	1769779 tax ID	*

[Ref.: #67770]

GC-content

58.9 mol%

genome sequence analysis

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Microbulbifer aggregans CCB-MM1 NCBI: GCA_001750105.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Microbulbifer aggregans CCB-MM1 NCBI: GCA_001750105.1
[Ref.: #69480]	flagellated	no	92.742	no
[Ref.: #69480]	gram-positive	no	98.699	yes
[Ref.: #69480]	anaerobic	no	97.382	no
[Ref.: #69480]	aerobic	yes	89.139	yes
[Ref.: #69480]	halophile	yes	67.377	no
[Ref.: #69480]	spore-forming	no	96.891	no
[Ref.: #69480]	thermophile	no	98.833	yes
[Ref.: #69480]	glucose-util	yes	77.704	yes
[Ref.: #69480]	motile	no	84.953	no
[Ref.: #69480]	glucose-ferment	no	89.452	no

Availability in culture collections External links

[Ref.: #43558]

Culture collection no.

LMG 29920, JCM 31875

Literature:

Topic	Title	Authors	Journal	DOI	Year
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	*
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	*
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	*
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	*

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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

* These data were automatically processed and therefore are not curated

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