Name: Notoacmeibacter marinus XMTR2A4
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140696

Type strain:

Species: Notoacmeibacter marinus

Strain Designation: XMTR2A4

Culture col. no.: MCCC 1A01882, KCTC 52427

Strain history: <- Zhaobin Huang, Third institue of Oceanography, State Oceanic Administraion(SOA), China

NCBI tax ID(s): 1876515 (species)

Other strains from Notoacmeibacter marinus

N. marinus JCM 31727, KCCM 90265

Section

Notoacmeibacter marinus XMTR2A4 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from gut of a marine limpet from intertidal rocks located at the coast of Xiamen.

colony-forming
Gram-negative
rod-shaped
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	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Notoacmeibacteraceae*
	Genus	*Notoacmeibacter*
	Species	**Notoacmeibacter marinus**
	Full Scientific Name (LPSN)	Notoacmeibacter marinus Huang et al. 2017

Synonym

Mabikibacter ruber

Information on morphological and physiological properties Morphology

[Ref.: #43465]	Gram stain	negative

[Ref.: #43465]	Cell length	7 µm

[Ref.: #43465]	Cell width	2 µm

[Ref.: #43465]	Cell shape	rod-shaped

[Ref.: #43465]	Colony size	0.5 mm
[Ref.: #43465]	Colony color	light grey
[Ref.: #43465]	Colony shape	circular
[Ref.: #43465]	Incubation period	3 days
[Ref.: #43465]	Cultivation medium used	MS agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43465]

Culture medium

MS agar

[Ref.: #43465]

Culture medium growth

[Ref.: #43465]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #43465]	growth	15-37 °C
[Ref.: #43465]	optimum	28-30 °C
[Ref.: #67771]	growth	25 °C

[Ref.: #43465]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #43465]			optimum	7
[Ref.: #43465]			growth	6-9

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67771]

Oxygen tolerance

aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43465]		NaCl		growth	0.5-9	%
[Ref.: #43465]		NaCl		optimum	1-2	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43465]	adipate ChEBI	-	carbon source
[Ref.: #43465]	amygdalin ChEBI	-	builds acid from
[Ref.: #43465]	arabinose ChEBI	-	builds acid from
[Ref.: #43465]	citrate ChEBI	-	carbon source
[Ref.: #43465]	D-glucose ChEBI	+	carbon source
[Ref.: #43465]	D-glucose ChEBI	+/-	fermentation
[Ref.: #43465]	D-mannitol ChEBI	+	carbon source
[Ref.: #43465]	decanoate ChEBI	-	carbon source
[Ref.: #43465]	esculin ChEBI	-	hydrolysis
[Ref.: #43465]	glucose ChEBI	-	builds acid from
[Ref.: #43465]	L-arabinose ChEBI	-	carbon source
[Ref.: #43465]	malate ChEBI	+	carbon source
[Ref.: #43465]	maltose ChEBI	-	carbon source
[Ref.: #43465]	mannitol ChEBI	-	builds acid from
[Ref.: #43465]	melibiose ChEBI	-	builds acid from
[Ref.: #43465]	myo-inositol ChEBI	-	builds acid from
[Ref.: #43465]	N-acetylglucosamine ChEBI	-	carbon source
[Ref.: #43465]	nitrate ChEBI	+	reduction
[Ref.: #43465]	phenylacetate ChEBI	-	carbon source
[Ref.: #43465]	potassium gluconate ChEBI	-	carbon source
[Ref.: #43465]	rhamnose ChEBI	-	builds acid from
[Ref.: #43465]	sodium citrate ChEBI	-	carbon source
[Ref.: #43465]	sorbitol ChEBI	-	builds acid from
[Ref.: #43465]	sucrose ChEBI	-	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #43465]		hydrogen sulfide ChEBI	no
[Ref.: #43465]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #43465]	2-nitrophenyl beta-D-galactopyranoside	-	3.2.1.52
[Ref.: #43465]	acid phosphatase	+	3.1.3.2
[Ref.: #43465]	alkaline phosphatase	+	3.1.3.1
[Ref.: #43465]	alpha-chymotrypsin	+/-	3.4.21.1
[Ref.: #43465]	alpha-galactosidase	-	3.2.1.22
[Ref.: #43465]	alpha-glucosidase	+	3.2.1.20
[Ref.: #43465]	alpha-mannosidase	-	3.2.1.24
[Ref.: #43465]	arginine dihydrolase	-	3.5.3.6
[Ref.: #43465]	beta-D-fucosidase	-	3.2.1.38
[Ref.: #43465]	beta-galactosidase	-	3.2.1.23
[Ref.: #43465]	beta-glucosidase	-	3.2.1.21
[Ref.: #43465]	beta-glucuronidase	-	3.2.1.31
[Ref.: #43465]	catalase	+	1.11.1.6
[Ref.: #43465]	cystine arylamidase	+/-	3.4.11.3
[Ref.: #43465]	cytochrome oxidase	+	1.9.3.1
[Ref.: #43465]	esterase (C 4)	+
[Ref.: #43465]	esterase Lipase (C 8)	+
[Ref.: #43465]	gelatinase	-
[Ref.: #43465]	leucine arylamidase	+	3.4.11.1
[Ref.: #43465]	lipase (C 14)	-
[Ref.: #43465]	lysine decarboxylase	-	4.1.1.18
[Ref.: #43465]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #43465]	naphthol-AS-BI-phosphohydrolase	+/-
[Ref.: #43465]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #43465]	trypsin	+	3.4.21.4
[Ref.: #43465]	tryptophan deaminase	-	4.1.99.1
[Ref.: #43465]	urease	+/-	3.5.1.5
[Ref.: #43465]	valine arylamidase	+/-
	Only first 10 entries are displayed. Click here to see all.

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	aerobactin biosynthesis	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	NAD metabolism	94.44	17 of 18
[Ref.: #66794]	citric acid cycle	92.86	13 of 14
[Ref.: #66794]	proline metabolism	90.91	10 of 11
[Ref.: #66794]	myo-inositol biosynthesis	90	9 of 10
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	allantoin degradation	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	glutamate and glutamine metabolism	85.71	24 of 28
[Ref.: #66794]	vitamin B12 metabolism	85.29	29 of 34
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	alanine metabolism	82.76	24 of 29
[Ref.: #66794]	pyrimidine metabolism	82.22	37 of 45
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	4-hydroxymandelate degradation	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	purine metabolism	76.6	72 of 94
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	tyrosine metabolism	71.43	10 of 14
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	photosynthesis	71.43	10 of 14
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	lipid metabolism	70.97	22 of 31
[Ref.: #66794]	oxidative phosphorylation	67.03	61 of 91
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	arginine metabolism	66.67	16 of 24
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	lysine metabolism	66.67	28 of 42
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	non-pathway related	65.79	25 of 38
[Ref.: #66794]	tryptophan metabolism	65.79	25 of 38
[Ref.: #66794]	pentose phosphate pathway	63.64	7 of 11
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	vitamin K metabolism	60	3 of 5
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	flavin biosynthesis	60	9 of 15
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	methionine metabolism	57.69	15 of 26
[Ref.: #66794]	degradation of pentoses	57.14	16 of 28
[Ref.: #66794]	degradation of sugar alcohols	56.25	9 of 16
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	carnitine metabolism	50	4 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	47.06	8 of 17
[Ref.: #66794]	3-phenylpropionate degradation	46.67	7 of 15
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	ascorbate metabolism	45.45	10 of 22
[Ref.: #66794]	phenol degradation	45	9 of 20
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	polyamine pathway	43.48	10 of 23
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	cholesterol biosynthesis	36.36	4 of 11
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	degradation of sugar acids	36	9 of 25
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #43465]	Sample type/isolated from	gut of a marine limpet (Notoacmea Schrenckii) from intertidal rocks located at the coast of Xiamen
[Ref.: #43465]	Sampling date	2016-03
[Ref.: #43465]	Geographic location (country and/or sea, region)	Coast of Xiamen, Fujian province
[Ref.: #43465]	Country	China
[Ref.: #43465]	Country ISO 3 Code	CHN
[Ref.: #43465]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From the gut of a limpet, Notoacmea schrenckii
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Terrestrial	#Coast
#Host	#Invertebrates (Other)	#Mollusca
#Host Body-Site	#Gastrointestinal tract	#Stomach

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KX530080 (>99% sequence identity) for Hyphomicrobiales from Microbeatlas

Aquatic Samples	243
Soil Samples	78
Animal Samples	57
Plant Samples	40
Total Samples	418

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.: #43465]	16S rRNA gene sequence	KX530080		GenBank

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Notoacmeibacter marinus XMTR2A4	GCA_002238045	contig	GenBank	1876515 tax ID	*
[Ref.: #66792]	Notoacmeibacter marinus XMTR2A4	2786546837	draft	JGI IMG/M	1876515 tax ID	*

[Ref.: #43465]

GC-content

61.5 mol%

genome sequence analysis

Availability in culture collections External links

[Ref.: #43465]

Culture collection no.

MCCC 1A01882, KCTC 52427

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Notoacmeibacter marinus gen. nov., sp. nov., isolated from the gut of a limpet and proposal of Notoacmeibacteraceae fam. nov. in the order Rhizobiales of the class Alphaproteobacteria.	Huang Z, Guo F, Lai Q, Shao Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.001951	2017	*
Phylogeny	Mabikibacter ruber Choi et al. 2017 is a later heterotypic synonym of Notoacmeibacter marinus Huang et al. 2017.	Huang Z, Lai Q	Int J Syst Evol Microbiol	10.1099/ijsem.0.003771	2020	*
Phylogeny	Notoacmeibacter ruber sp. nov., a novel endophytic bacterium isolated from leaf of Rhizophora stylosa.	Yan XR, Tuo L	Antonie Van Leeuwenhoek	10.1007/s10482-019-01225-3	2019	*

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 )

#43465

Zhaobin Huang, Feng Guo, Qiliang Lai, Zongze Shao: Notoacmeibacter marinus gen. nov., sp. nov., isolated from the gut of a limpet and proposal of Notoacmeibacteraceae fam. nov. in the order Rhizobiales of the class Alphaproteobacteria. IJSEM 67: 2527 - 2531 2017 ( DOI 10.1099/ijsem.0.001951 , PubMed 28771124 )

#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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 .

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Notoacmeibacter marinus in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF