Name: Mucilaginibacter pedocola TBZ30
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 133142

Type strain:

Species: Mucilaginibacter pedocola

Strain Designation: TBZ30

Culture col. no.: KCTC 42833, CCTCC AB 2015301

NCBI tax ID(s): 1792845 (species)

Special Collections

Section

When using BacDive for research please cite our paper

Mucilaginibacter pedocola TBZ30 is an obligate aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from heavy-metal-contaminated paddy field.

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	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Bacteroidota*
	Class	*Sphingobacteriia*
	Order	*Sphingobacteriales*
	Family	*Sphingobacteriaceae*
	Genus	*Mucilaginibacter*
	Species	**Mucilaginibacter pedocola**
	Full Scientific Name (LPSN)	Mucilaginibacter pedocola Tang et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #24910]	Gram stain	negative
[Ref.: #125439]	Gram stain	negative Confidence in %99.5

[Ref.: #24910]	Cell length	1.1-1.3 µm

[Ref.: #24910]	Cell width	0.3-0.4 µm

[Ref.: #24910]	Cell shape	rod-shaped

[Ref.: #24910]	Motility	no

[Ref.: #24910]	Colony size	1.0-1.5 mm
[Ref.: #24910]	Colony color	pink
[Ref.: #24910]	Colony shape	circular
[Ref.: #24910]	Incubation period	2 days
[Ref.: #24910]	Cultivation medium used	R2A agar (Reasoner's 2A agar)

Information on culture and growth conditions Culture and growth conditions

[Ref.: #24910]

Culture medium

Reasoner's 2A agar (R2A)

[Ref.: #24910]

Culture medium growth

	Temperatures	Kind of temperature		Temperature
[Ref.: #24910]			growth	4.0-28.0 °C
[Ref.: #24910]			optimum	25 °C

	pH	Kind of pH		pH
[Ref.: #24910]			optimum	7
[Ref.: #24910]			growth	5.0-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #24910]	Oxygen tolerance	obligate aerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %92.8

[Ref.: #24910]	Ability of spore formation	no
[Ref.: #125439]	Ability of spore formation	no Confidence in %99.2

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #24910]		NaCl		growth	0.0-1.0	%(w/v)
[Ref.: #24910]		NaCl		optimum	0	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #24910]	acetate ChEBI	-	assimilation
[Ref.: #24910]	alanine ChEBI	-	assimilation
[Ref.: #24910]	arabinose ChEBI	+	builds acid from
[Ref.: #24910]	butyrate ChEBI	-	assimilation
[Ref.: #24910]	casein	-	hydrolysis
[Ref.: #24910]	cellobiose ChEBI	+	builds acid from
[Ref.: #24910]	D-fructose ChEBI	+	builds acid from
[Ref.: #24910]	D-ribose ChEBI	-	builds acid from
[Ref.: #24910]	esculin ChEBI	+	hydrolysis
[Ref.: #24910]	ethanol ChEBI	-	builds acid from
[Ref.: #24910]	fructose ChEBI	-	assimilation
[Ref.: #24910]	fucose ChEBI	-	assimilation
[Ref.: #24910]	gelatin ChEBI	-	hydrolysis
[Ref.: #24910]	gluconate ChEBI	-	assimilation
[Ref.: #24910]	glucose ChEBI	-	fermentation
[Ref.: #24910]	glucose ChEBI	+	degradation
[Ref.: #24910]	glucose ChEBI	+	assimilation
[Ref.: #24910]	glycerol ChEBI	-	builds acid from
[Ref.: #24910]	glycogen ChEBI	+	assimilation
[Ref.: #24910]	histidine ChEBI	-	assimilation
[Ref.: #24910]	L-arabinose ChEBI	+	assimilation
[Ref.: #24910]	L-serine ChEBI	-	assimilation
[Ref.: #24910]	lactose ChEBI	+	builds acid from
[Ref.: #24910]	malate ChEBI	-	assimilation
[Ref.: #24910]	maltose ChEBI	+	builds acid from
[Ref.: #24910]	maltose ChEBI	+	assimilation
[Ref.: #24910]	mannitol ChEBI	-	builds acid from
[Ref.: #24910]	mannitol ChEBI	-	assimilation
[Ref.: #24910]	mannose ChEBI	+	assimilation
[Ref.: #24910]	melibiose ChEBI	+	assimilation
[Ref.: #24910]	myo-inositol ChEBI	-	assimilation
[Ref.: #24910]	N-acetylglucosamine ChEBI	+	assimilation
[Ref.: #24910]	nitrate ChEBI	-	reduction
[Ref.: #24910]	oxalate ChEBI	-	assimilation
[Ref.: #24910]	pectin ChEBI	+	assimilation
[Ref.: #24910]	phenylacetate ChEBI	-	assimilation
[Ref.: #24910]	rhamnose ChEBI	+	builds acid from
[Ref.: #24910]	rhamnose ChEBI	+	assimilation
[Ref.: #24910]	ribose ChEBI	-	assimilation
[Ref.: #24910]	sodium citrate ChEBI	-	assimilation
[Ref.: #24910]	sorbitol ChEBI	-	assimilation
[Ref.: #24910]	sucrose ChEBI	+	builds acid from
[Ref.: #24910]	tween 20 ChEBI	+	hydrolysis
[Ref.: #24910]	tween 60 ChEBI	-	hydrolysis
[Ref.: #24910]	tween 80 ChEBI	-	hydrolysis
[Ref.: #24910]	tyrosine ChEBI	+	hydrolysis
[Ref.: #24910]	xylose ChEBI	+	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #24910]	acetoin ChEBI	no
[Ref.: #24910]	hydrogen sulfide ChEBI	no
[Ref.: #24910]	indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #24910]	acid phosphatase	+	3.1.3.2
[Ref.: #24910]	alkaline phosphatase	+	3.1.3.1
[Ref.: #24910]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #24910]	alpha-fucosidase	+	3.2.1.51
[Ref.: #24910]	alpha-galactosidase	+	3.2.1.22
[Ref.: #24910]	alpha-glucosidase	+	3.2.1.20
[Ref.: #24910]	alpha-mannosidase	+	3.2.1.24
[Ref.: #24910]	arginine dihydrolase	-	3.5.3.6
[Ref.: #24910]	beta-galactosidase	+	3.2.1.23
[Ref.: #24910]	beta-glucosidase	+	3.2.1.21
[Ref.: #24910]	beta-glucuronidase	-	3.2.1.31
[Ref.: #24910]	catalase	+	1.11.1.6
[Ref.: #24910]	cytochrome oxidase	+	1.9.3.1
[Ref.: #24910]	esterase (C 4)	+
[Ref.: #24910]	leucine arylamidase	+	3.4.11.1
[Ref.: #24910]	lipase (C 14)	-
[Ref.: #24910]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #24910]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #24910]	phenylalanine deaminase	+	4.3.1.5
[Ref.: #24910]	trypsin	+	3.4.21.4
[Ref.: #24910]	urease	-	3.5.1.5
[Ref.: #24910]	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]	cellulose degradation	100	5 of 5
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	quinate degradation	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	acetoin degradation	100	3 of 3
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	purine metabolism	77.66	73 of 94
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	degradation of sugar acids	76	19 of 25
[Ref.: #66794]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	cysteine metabolism	72.22	13 of 18
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	pyrimidine metabolism	71.11	32 of 45
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	degradation of pentoses	67.86	19 of 28
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	tryptophan metabolism	65.79	25 of 38
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	lipid metabolism	64.52	20 of 31
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	carotenoid biosynthesis	63.64	14 of 22
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	degradation of hexoses	61.11	11 of 18
[Ref.: #66794]	phenol degradation	60	12 of 20
[Ref.: #66794]	O-antigen biosynthesis	60	3 of 5
[Ref.: #66794]	arachidonate biosynthesis	60	3 of 5
[Ref.: #66794]	coenzyme M biosynthesis	60	6 of 10
[Ref.: #66794]	lysine metabolism	59.52	25 of 42
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	non-pathway related	55.26	21 of 38
[Ref.: #66794]	ascorbate metabolism	54.55	12 of 22
[Ref.: #66794]	vitamin B1 metabolism	53.85	7 of 13
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	4-hydroxyphenylacetate degradation	50	5 of 10
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	3-phenylpropionate degradation	46.67	7 of 15
[Ref.: #66794]	phenylpropanoid biosynthesis	46.15	6 of 13
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	oxidative phosphorylation	45.05	41 of 91
[Ref.: #66794]	4-hydroxymandelate degradation	44.44	4 of 9
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	polyamine pathway	39.13	9 of 23
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	urea cycle	38.46	5 of 13
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	allantoin degradation	22.22	2 of 9
		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.: #24910]	Sample type/isolated from	heavy-metal-contaminated paddy field
[Ref.: #24910]	Geographic location (country and/or sea, region)	Zhongfang town,Linxiang city,Hunan
[Ref.: #24910]	Country	Republic of China
[Ref.: #24910]	Country ISO 3 Code	CHN
[Ref.: #24910]	Continent	Asia
[Ref.: #24910]	Geographic location	30.0000°/109.0000°
[Ref.: #24910]	Enrichment culture	R2A agar (Reasoner's 2A agar)
[Ref.: #24910]	Enrichment culture composition	containing 100 µM ZnCl2
[Ref.: #24910]	Enrichment culture duration	7 days
[Ref.: #24910]	Enrichment culture temperature	28 ̊C
* marker position based on {}

Isolation sources categories

#Engineered	#Agriculture	#Field
#Engineered	#Contamination	#Heavy metal
#Host	#Plants	#Herbaceous plants (Grass,Crops)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KU593480 (>99% sequence identity) for Mucilaginibacter pedocola subclade from Microbeatlas

Aquatic Samples	118
Soil Samples	722
Animal Samples	86
Plant Samples	193
Total Samples	1119

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.: #24910]	Mucilaginibacter pedocola strain TBZ30 16S ribosomal RNA gene, partial sequence	KU593480	1445	GenBank ENA	1792845 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Mucilaginibacter pedocola TBZ30	GCA_002013915	contig	GenBank ENA	1792845 tax ID	*
[Ref.: #66792]	Mucilaginibacter pedocola TBZ30	2846139442	draft	JGI IMG/M	1792845 tax ID	*

[Ref.: #24910]

GC-content

49 mol%

high performance liquid chromatography (HPLC)

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

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Mucilaginibacter pedocola TBZ30 NCBI: GCA_002013915
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	99.2
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	72.9
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	99.5
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	92.8

Availability in culture collections External links

[Ref.: #24910]

Culture collection no.

KCTC 42833, CCTCC AB 2015301

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	High-quality-draft genome sequence of the heavy metal resistant and exopolysaccharides producing bacterium Mucilaginibacter pedocola TBZ30(T).	Fan X, Tang J, Nie L, Huang J, Wang G	Stand Genomic Sci	10.1186/s40793-018-0337-8	2018	*
Phylogeny	Mucilaginibacter pedocola sp. nov., isolated from a heavy-metal-contaminated paddy field.	Tang J, Huang J, Qiao Z, Wang R, Wang G	Int J Syst Evol Microbiol	10.1099/ijsem.0.001306	2016	*

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 )

#24910

J. H. Tang, Jing,Qiao, Zixu,Wang, Rui,Wang, Gejiao: Mucilaginibacter pedocola sp. nov., isolated from a heavy-metal-contaminated paddy field. IJSEM 66: 4033 - 4038 2016 ( DOI 10.1099/ijsem.0.001306 , PubMed 27412244 )

#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 )

#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 .

#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 .

* These data were automatically processed and therefore are not curated

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