Name: Algoriphagus machipongonensis PR1
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 23439

Type strain:

Species: Algoriphagus machipongonensis

Strain Designation: PR1

Culture col. no.: DSM 24695, ATCC BAA-2233

Strain history: <- R. Alegado, Univ. of California, Berkeley, USA; PR1 <- R. Zuzow

NCBI tax ID(s): 388413 (species)

SI-ID 404908

DSM 24695

Special Collections

Section

When using BacDive for research please cite our paper

Algoriphagus machipongonensis PR1 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from mud, co-isolated with the colonial choanoflagellate Salpingoeca rosetta .

Gram-negative
rod-shaped
aerobe
mesophilic
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	*Cytophagia*
	Order	*Cytophagales*
	Family	*Cyclobacteriaceae*
	Genus	*Algoriphagus*
	Species	**Algoriphagus machipongonensis**
	Full Scientific Name (LPSN)	Algoriphagus machipongonensis Alegado et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #30556]	Gram stain	negative
[Ref.: #125439]	Gram stain	negative Confidence in %91.4

[Ref.: #30556]	Cell length	2.5 µm

[Ref.: #30556]	Cell width	0.5 µm

[Ref.: #30556]	Cell shape	rod-shaped

[Ref.: #30556]	Motility	no

[Ref.: #30556]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #19197]

Culture medium

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

[Ref.: #19197]

Culture medium growth

[Ref.: #19197]

Culture medium link

Medium recipe at MediaDive

[Ref.: #19197]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #19197]	growth	28 °C
[Ref.: #30556]	growth	10-40 °C
[Ref.: #30556]	optimum	30 °C

	pH	Kind of pH		pH
[Ref.: #30556]			optimum	7.5
[Ref.: #30556]			growth	05-09

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30556]	Oxygen tolerance	aerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %90.1

[Ref.: #30556]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30556]		NaCl		growth	0-10	%
[Ref.: #30556]		NaCl		optimum	3	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30556]	esculin ChEBI	+	hydrolysis
[Ref.: #30556]	galactose ChEBI	+	carbon source
[Ref.: #30556]	glycerol ChEBI	+	carbon source
[Ref.: #30556]	mannitol ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #30556]	acid phosphatase	+	3.1.3.2
[Ref.: #30556]	alkaline phosphatase	+	3.1.3.1
[Ref.: #30556]	catalase	+	1.11.1.6
[Ref.: #30556]	cytochrome oxidase	+	1.9.3.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	quinate degradation	100	2 of 2
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	ceramide biosynthesis	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]	NAD metabolism	94.44	17 of 18
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	flavin biosynthesis	86.67	13 of 15
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	3-chlorocatechol degradation	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	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]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	purine metabolism	75.53	71 of 94
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[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]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	lysine metabolism	71.43	30 of 42
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	pyrimidine metabolism	71.11	32 of 45
[Ref.: #66794]	tryptophan metabolism	71.05	27 of 38
[Ref.: #66794]	lipid metabolism	70.97	22 of 31
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	arginine metabolism	66.67	16 of 24
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	degradation of sugar acids	64	16 of 25
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	arachidonate biosynthesis	60	3 of 5
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	metabolism of disaccharids	54.55	6 of 11
[Ref.: #66794]	carotenoid biosynthesis	54.55	12 of 22
[Ref.: #66794]	degradation of pentoses	53.57	15 of 28
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	sphingosine metabolism	50	3 of 6
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	degradation of hexoses	50	9 of 18
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	ascorbate metabolism	50	11 of 22
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	vitamin B1 metabolism	46.15	6 of 13
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	allantoin degradation	44.44	4 of 9
[Ref.: #66794]	elloramycin biosynthesis	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	40	4 of 10
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	oxidative phosphorylation	39.56	36 of 91
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	polyamine pathway	30.43	7 of 23
[Ref.: #66794]	phenol degradation	30	6 of 20
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	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]	lactate fermentation	25	1 of 4
[Ref.: #66794]	biotin biosynthesis	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	4-hydroxymandelate 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.: #19197]	Sample type/isolated from	mud, co-isolated with the colonial choanoflagellate Salpingoeca rosetta (ATCC 50818)
[Ref.: #19197]	Host species	Salpingoeca rosetta
[Ref.: #19197]	Geographic location (country and/or sea, region)	Virginia, Hog Island
[Ref.: #19197]	Country	USA
[Ref.: #19197]	Country ISO 3 Code	USA
[Ref.: #19197]	Continent	North America
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Mud (Sludge)
#Host	#Other	-

What are isolation sources categories?

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

[Ref.: #19197]

Biosafety level

Risk group (German classification)
According to TRBA 466

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

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Algoriphagus machipongonensis PR1	GCA_000166275	complete	GenBank ENA	388413 tax ID	*
[Ref.: #66792]	Algoriphagus machipongonensis PR1	640612202	complete	JGI IMG/M	388413 tax ID	*

[Ref.: #19197]	GC-content	38.7 mol%	sequence analysis
[Ref.: #30556]	GC-content	38.7 mol%

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: Algoriphagus machipongonensis PR1 NCBI: GCA_000166275
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	84.6
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	62.2
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	91.4
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	90.1

Availability in culture collections External links

[Ref.: #19197]

Culture collection no.

DSM 24695, ATCC BAA-2233

[Ref.: #87592]

SI-ID 404908

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Algoriphagus machipongonensis sp. nov., co-isolated with a colonial choanoflagellate.	Alegado RA, Grabenstatter JD, Zuzow R, Morris A, Huang SY, Summons RE, King N	Int J Syst Evol Microbiol	10.1099/ijs.0.038646-0	2012	*

References

#19197

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24695

#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 )

#30556

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26887 (see below)

#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 )

#87592

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-ID404908.1 )

#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 .

#26887

IJSEM 163 2013 ( DOI 10.1099/ijs.0.038646-0 , PubMed 22368173 )

* These data were automatically processed and therefore are not curated

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