Name: Permianibacter aggregans HW001
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 132184

Type strain:

Species: Permianibacter aggregans

Strain Designation: HW001

Culture col. no.: DSM 103792, CICC 10856, KCTC 32485

Strain history: <- KCTC <- H. Wang and X. Hu, Yantai Institute of Costal Zone Research, Chinese Academy of Sciences, Yantai, China <- H. Wang and R. T. Hill, Institute of Marine and Environmental Technology, University of Maryland, MD, USA

NCBI tax ID(s): 1510150 (species)

SI-ID 407895

DSM 103792

Section

Permianibacter aggregans HW001 is a mesophilic, Gram-negative bacterium that was isolated from microalgae Nannochloropsis oceanica culture grown in 2L-reactors.

Gram-negative
mesophilic
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	*Pseudomonadales*
	Family	*Pseudomonadaceae*
	Genus	*Permianibacter*
	Species	**Permianibacter aggregans**
	Full Scientific Name (LPSN)	Permianibacter aggregans Wang et al. 2014

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.998

Information on culture and growth conditions Culture and growth conditions

[Ref.: #23973]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #23973]

Culture medium growth

[Ref.: #23973]

Culture medium link

Medium recipe at MediaDive

[Ref.: #23973]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #23973]			growth	28 °C

[Ref.: #23973]

Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.995

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	molybdenum cofactor biosynthesis	100	9 of 9
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	aerobactin biosynthesis	100	1 of 1
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	leucine metabolism	92.31	12 of 13
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	alanine metabolism	86.21	25 of 29
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	glutamate and glutamine metabolism	82.14	23 of 28
[Ref.: #66794]	vitamin B6 metabolism	81.82	9 of 11
[Ref.: #66794]	tryptophan metabolism	81.58	31 of 38
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	tyrosine metabolism	78.57	11 of 14
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[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]	histidine metabolism	75.86	22 of 29
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	lactate fermentation	75	3 of 4
[Ref.: #66794]	lysine metabolism	73.81	31 of 42
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	pyrimidine metabolism	68.89	31 of 45
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	pentose phosphate pathway	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	catecholamine biosynthesis	50	2 of 4
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	oxidative phosphorylation	45.05	41 of 91
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	cellulose degradation	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	polyamine pathway	39.13	9 of 23
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	methane metabolism	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of sugar alcohols	31.25	5 of 16
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	degradation of pentoses	28.57	8 of 28
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	3-phenylpropionate degradation	26.67	4 of 15
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	phenol degradation	25	5 of 20
[Ref.: #66794]	ascorbate metabolism	22.73	5 of 22
		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.: #23973]	Sample type/isolated from	microalgae Nannochloropsis oceanica culture grown in 2L-reactors
[Ref.: #23973]	Host species	Nannochloropsis oceanica
[Ref.: #23973]	Country	USA
[Ref.: #23973]	Country ISO 3 Code	USA
[Ref.: #23973]	Continent	North America
[Ref.: #23973]	Geographic location	31.2714°/-102.6800°
* marker position based on {}

Isolation sources categories

#Engineered	#Bioreactor	-
#Engineered	#Laboratory	#Lab enrichment
#Host	#Algae	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KJ721800 (>99% sequence identity) for Permianibacter aggregans subclade from Microbeatlas

Aquatic Samples	1333
Soil Samples	664
Animal Samples	1071
Plant Samples	106
Total Samples	3174

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #23973]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #23973]	Permianibacter aggregans strain HW001 16S ribosomal RNA gene, partial sequence	KJ721800	1423	ENA	1510150 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Permianibacter aggregans DSM 103792	GCA_004363125	scaffold	GenBank	1510150 tax ID	*
[Ref.: #66792]	Permianibacter aggregans HW001	GCA_009756665	complete	GenBank	1510150 tax ID	*
[Ref.: #66792]	Permianibacter aggregans strain DSM 103792	1510150.4	wgs	PATRIC	1510150 tax ID	*
[Ref.: #66792]	Permianibacter aggregans DSM 103792	2795385471	draft	JGI IMG/M	1510150 tax ID	*

[Ref.: #23973]

GC-content

55.4 mol%

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: Permianibacter aggregans HW001 NCBI: GCA_009756665.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Permianibacter aggregans HW001 NCBI: GCA_009756665.1
[Ref.: #69480]	motile	yes	84.768	no
[Ref.: #69480]	flagellated	yes	53.622	no
[Ref.: #69480]	gram-positive	no	99.248	no
[Ref.: #69480]	anaerobic	no	96.816	no
[Ref.: #69480]	aerobic	yes	73.418	no
[Ref.: #69480]	halophile	no	90.223	no
[Ref.: #69480]	spore-forming	no	95.407	no
[Ref.: #69480]	glucose-util	yes	87.707	no
[Ref.: #69480]	thermophile	no	97.456	yes
[Ref.: #69480]	glucose-ferment	no	86.115	no

Availability in culture collections External links

[Ref.: #23973]

Culture collection no.

DSM 103792, CICC 10856, KCTC 32485

[Ref.: #90539]

SI-ID 407895

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Permianibacter fluminis sp. nov., isolated from a freshwater stream.	Park MS, Song J, Chang J, Joung Y, Kang I, Cho JC	Int J Syst Evol Microbiol	10.1099/ijsem.0.004771	2021	*
Phylogeny	Permianibacter aggregans gen. nov., sp. nov., a bacterium of the family Pseudomonadaceae capable of aggregating potential biofuel-producing microalgae.	Wang H, Zheng T, Hill RT, Hu X	Int J Syst Evol Microbiol	10.1099/ijs.0.065003-0	2014	*

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 )

#23973

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 103792

#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 .

#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 )

#90539

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID407895.1 )

* These data were automatically processed and therefore are not curated

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