Algoriphagus machipongonensis (DSM 24695, ATCC BAA-2233, PR1)

Name: Algoriphagus machipongonensis (DSM 24695, ATCC BAA-2233, PR1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 23439

Type strain

Strain Designation PR1

Culture col. no. DSM 24695 ATCC BAA-2233 PR1

NCBI tax ID(s) 388413

Special Collections DSMZ Literature strains

History <- R. Alegado, Univ. of California, Berkeley, USA; PR1 <- R. Zuzow

Links

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

Gram-negative rod-shaped aerobe genome sequence Bacteria

Name and taxonomic classification

SI-ID 404908

ATCC BAA-2233,DSM 24695

@ref 20215

Last LPSN update 2026-02-09 11:23:44

Domain Bacteria

Phylum Bacteroidota

Class Cytophagia

Order Cytophagales

Family Cyclobacteriaceae

Genus Algoriphagus

Species Algoriphagus machipongonensis

Full scientific name Algoriphagus machipongonensis Alegado et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
30556	negative	2.5 µm	0.5 µm	rod-shaped
125439	negative					91.4

Pigmentation

30556

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
19197	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)		Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
19197	positive	growth	28
30556	positive	growth	10-40
30556	positive	optimum	30

Culture pH

@ref	Ability	Type	PH	PH range
30556	positive	optimum	7.5
30556	positive	growth	05-09	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30556	aerobe
125439	obligate aerobe	90.1

Spore formation

30556

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30556	NaCl	positive	growth	0-10 %
30556	NaCl	positive	optimum	3 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30556	4853 ChEBI	esculin	+	hydrolysis
30556	28260 ChEBI	galactose	+	carbon source
30556	17754 ChEBI	glycerol	+	carbon source
30556	29864 ChEBI	mannitol	+	carbon source

Enzymes

@ref	Value	Activity	Ec
30556	acid phosphatase	+	3.1.3.2
30556	alkaline phosphatase	+	3.1.3.1
30556	catalase	+	1.11.1.6
30556	cytochrome oxidase	+	1.9.3.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	palmitate biosynthesis	100	22 of 22
66794	quinate degradation	100	2 of 2
66794	gluconeogenesis	100	8 of 8
66794	vitamin K metabolism	100	5 of 5
66794	kanosamine biosynthesis II	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	coenzyme A metabolism	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	denitrification	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	ppGpp biosynthesis	100	4 of 4
66794	ceramide biosynthesis	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	NAD metabolism	94.44	17 of 18
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	phenylalanine metabolism	92.31	12 of 13
66794	pentose phosphate pathway	90.91	10 of 11
66794	Entner Doudoroff pathway	90	9 of 10
66794	serine metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	flavin biosynthesis	86.67	13 of 15
66794	photosynthesis	85.71	12 of 14
66794	heme metabolism	85.71	12 of 14
66794	proline metabolism	81.82	9 of 11
66794	threonine metabolism	80	8 of 10
66794	3-chlorocatechol degradation	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	starch degradation	80	8 of 10
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	glycogen metabolism	80	4 of 5
66794	alanine metabolism	79.31	23 of 29
66794	valine metabolism	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	leucine metabolism	76.92	10 of 13
66794	purine metabolism	75.53	71 of 94
66794	glutamate and glutamine metabolism	75	21 of 28
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	ketogluconate metabolism	75	6 of 8
66794	propanol degradation	71.43	5 of 7
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	lysine metabolism	71.43	30 of 42
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	pyrimidine metabolism	71.11	32 of 45
66794	tryptophan metabolism	71.05	27 of 38
66794	lipid metabolism	70.97	22 of 31
66794	propionate fermentation	70	7 of 10
66794	urea cycle	69.23	9 of 13
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	arginine metabolism	66.67	16 of 24
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	histidine metabolism	65.52	19 of 29
66794	methionine metabolism	65.38	17 of 26
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	glycolysis	64.71	11 of 17
66794	tyrosine metabolism	64.29	9 of 14
66794	citric acid cycle	64.29	9 of 14
66794	degradation of sugar acids	64	16 of 25
66794	d-xylose degradation	63.64	7 of 11
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	degradation of sugar alcohols	62.5	10 of 16
66794	factor 420 biosynthesis	60	3 of 5
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	arachidonate biosynthesis	60	3 of 5
66794	gallate degradation	60	3 of 5
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	non-pathway related	57.89	22 of 38
66794	glutathione metabolism	57.14	8 of 14
66794	cysteine metabolism	55.56	10 of 18
66794	metabolism of disaccharids	54.55	6 of 11
66794	carotenoid biosynthesis	54.55	12 of 22
66794	degradation of pentoses	53.57	15 of 28
66794	coenzyme M biosynthesis	50	5 of 10
66794	sphingosine metabolism	50	3 of 6
66794	glycine metabolism	50	5 of 10
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	resorcinol degradation	50	1 of 2
66794	ribulose monophosphate pathway	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	degradation of hexoses	50	9 of 18
66794	ethanol fermentation	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	ascorbate metabolism	50	11 of 22
66794	sulfate reduction	46.15	6 of 13
66794	vitamin B1 metabolism	46.15	6 of 13
66794	vitamin B6 metabolism	45.45	5 of 11
66794	nitrate assimilation	44.44	4 of 9
66794	allantoin degradation	44.44	4 of 9
66794	elloramycin biosynthesis	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	4-hydroxyphenylacetate degradation	40	4 of 10
66794	myo-inositol biosynthesis	40	4 of 10
66794	oxidative phosphorylation	39.56	36 of 91
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	pantothenate biosynthesis	33.33	2 of 6
66794	arachidonic acid metabolism	33.33	6 of 18
66794	IAA biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	polyamine pathway	30.43	7 of 23
66794	phenol degradation	30	6 of 20
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	toluene degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	biotin biosynthesis	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	alginate biosynthesis	25	1 of 4
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	4-hydroxymandelate degradation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Mud (Sludge)
#Host	#Other	-

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
19197	mud, co-isolated with the colonial choanoflagellate Salpingoeca rosetta (ATCC 50818)	Salpingoeca rosetta	Virginia, Hog Island	USA	USA	North America

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
19197	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM16627v1 assembly for Algoriphagus machipongonensis PR1	chromosome	GCA_000166275	388413.5	640612202	388413	89.15

GC content

@ref	GC-content (mol%)	Method
19197	38.7	sequence analysis
30556	38.7

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Algoriphagus machipongonensis PR1
NCBI: GCA_000166275

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	84.60	no
125439	motility	BacteriaNetⓘ	no	62.20	no
125439	gram_stain	BacteriaNetⓘ	negative	91.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	90.10	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Pathogenicity	Synergistic Cues from Diverse Bacteria Enhance Multicellular Development in a Choanoflagellate.	Ireland EV, Woznica A, King N.	Appl Environ Microbiol	10.1128/aem.02920-19	2020
Metabolism	A flagellate-to-amoeboid switch in the closest living relatives of animals.	Brunet T, Albert M, Roman W, Coyle MC, Spitzer DC, King N.	Elife	10.7554/elife.61037	2021
Genetics	Predicted glycosyltransferases promote development and prevent spurious cell clumping in the choanoflagellate S. rosetta.	Wetzel LA, Levin TC, Hulett RE, Chan D, King GA, Aldayafleh R, Booth DS, Sigg MA, King N.	Elife	10.7554/elife.41482	2018
Genetics	The Rosetteless gene controls development in the choanoflagellate S. rosetta.	Levin TC, Greaney AJ, Wetzel L, King N.	Elife	10.7554/elife.04070	2014
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 )
#26887	IJSEM 163 2013 ( DOI 10.1099/ijs.0.038646-0 , PubMed 22368173 )
#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
#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 )
#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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Algoriphagus machipongonensis (DSM 24695, ATCC BAA-2233, PR1)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000166275

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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