Akkermansia glycaniphila (DSM 100705, CIP 110913, Pyt)

Name: Akkermansia glycaniphila (DSM 100705, CIP 110913, Pyt)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132956

Type strain

Strain Designation Pyt

Culture col. no. DSM 100705 CIP 110913 Pyt

NCBI tax ID(s) 1679444

Special Collections DSMZ CIP Literature strains

History DSMZ <- J. Ouwerkerk, Univ. Wageningen; PytT CIP <- 2015, JP Ouwerkerk, Wageningen Univ., Wageningen, The Netherlands: strain Pyt, Akkermansia pythonifaecis

Links

Akkermansia glycaniphila Pyt is an anaerobe, Gram-negative, oval-shaped bacterium that was isolated from faeces from the reticulated python housed in a zoo.

Gram-negative oval-shaped anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 405563

DSM 100705,CIP 110913

@ref 20215

Last LPSN update 2026-05-29 08:37:58

Domain Bacteria

Phylum Verrucomicrobiota

Class Verrucomicrobiia

Order Verrucomicrobiales

Family Akkermansiaceae

Genus Akkermansia

Species Akkermansia glycaniphila

Full scientific name Akkermansia glycaniphila Ouwerkerk et al. 2016

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell shape	Confidence
25030	negative	0.6-1.0 µm	oval-shaped
125439				95.384
119698	negative		rod-shaped

Colony morphology

@ref	Colony size	Colony color	Medium used
25030	0.7 mm	white	mucin-based medium

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
25030	mucin-based medium
24744	PYG MEDIUM (MODIFIED) (DSMZ Medium 104)	Medium recipe at MediaDive	Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water
24744	FASTIDIOUS ANAEROBE AGAR (DSMZ Medium 1203)	Medium recipe at MediaDive	Name: FASTIDIOUS ANAEROBE AGAR (DSMZ Medium 1203) Composition: Horse blood 100.0 g/l Fastidious Anaerobe Agar 45.7 g/l Distilled water
119698	CIP Medium 187	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
24744	positive	growth	37
25030	positive	growth	15-40
25030	positive	optimum	25-30

Culture pH

@ref	Ability	Type	PH
25030	positive	optimum	6
25030	positive	growth	5.0-7.5

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
25030	anaerobe
125439	facultative anaerobe	99.137

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
25030	17057 ChEBI	cellobiose	-	growth
25030	15824 ChEBI	D-fructose	-	growth
68380	16024 ChEBI	D-mannose	-	fermentation	from API rID32A
25030	4853 ChEBI	esculin	+	hydrolysis
25030	5291 ChEBI	gelatin	+	hydrolysis
25030	18287 ChEBI	L-fucose	-	growth
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
68380	16634 ChEBI	raffinose	-	fermentation	from API rID32A
25030	27897 ChEBI	tryptophan	-	energy source
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A

Metabolite production

@ref	Chebi-ID	Metabolite	Production
25030	35581 ChEBI	indole
68380	35581 ChEBI	indole		from API rID32A

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
25030	35581 ChEBI	indole	-
68380	35581 ChEBI	indole	-	from API rID32A

Enzymes

@ref	Value	Activity	Ec
68380	alanine arylamidase	-	3.4.11.2	from API rID32A
68380	alkaline phosphatase	+	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	-	3.2.1.55	from API rID32A
68380	alpha-fucosidase	-	3.2.1.51	from API rID32A
68380	alpha-galactosidase	-	3.2.1.22	from API rID32A
68380	alpha-glucosidase	+	3.2.1.20	from API rID32A
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68380	beta-galactosidase	+	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	+		from API rID32A
68380	beta-glucosidase	+	3.2.1.21	from API rID32A
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
25030	catalase	+	1.11.1.6
68380	glutamate decarboxylase	-	4.1.1.15	from API rID32A
68380	glutamyl-glutamate arylamidase	-		from API rID32A
68380	glycin arylamidase	-		from API rID32A
68380	histidine arylamidase	-		from API rID32A
68380	L-arginine arylamidase	-		from API rID32A
68380	leucine arylamidase	-	3.4.11.1	from API rID32A
68380	leucyl glycin arylamidase	-	3.4.11.1	from API rID32A
68380	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API rID32A
68380	phenylalanine arylamidase	-		from API rID32A
68380	proline-arylamidase	-	3.4.11.5	from API rID32A
68380	pyrrolidonyl arylamidase	-	3.4.19.3	from API rID32A
68380	serine arylamidase	-		from API rID32A
25030	tryptophan deaminase	-	4.1.99.1
68380	tryptophan deaminase	-	4.1.99.1	from API rID32A
68380	tyrosine arylamidase	-		from API rID32A
25030	urease	-	3.5.1.5
68380	urease	-	3.5.1.5	from API rID32A

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	acetate fermentation	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	biotin biosynthesis	100	4 of 4
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	palmitate biosynthesis	90.91	20 of 22
66794	propanol degradation	85.71	6 of 7
66794	hydrogen production	80	4 of 5
66794	starch degradation	80	8 of 10
66794	vitamin K metabolism	80	4 of 5
66794	chorismate metabolism	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	lipid A biosynthesis	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	glycogen biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	gluconeogenesis	75	6 of 8
66794	peptidoglycan biosynthesis	73.33	11 of 15
66794	NAD metabolism	72.22	13 of 18
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	citric acid cycle	71.43	10 of 14
66794	propionate fermentation	70	7 of 10
66794	vitamin B12 metabolism	67.65	23 of 34
66794	acetoin degradation	66.67	2 of 3
66794	valine metabolism	66.67	6 of 9
66794	UDP-GlcNAc biosynthesis	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	formaldehyde oxidation	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	glycolysis	64.71	11 of 17
66794	photosynthesis	64.29	9 of 14
66794	heme metabolism	64.29	9 of 14
66794	glutamate and glutamine metabolism	64.29	18 of 28
66794	proline metabolism	63.64	7 of 11
66794	C4 and CAM-carbon fixation	62.5	5 of 8
66794	degradation of sugar alcohols	62.5	10 of 16
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	isoleucine metabolism	62.5	5 of 8
66794	pyrimidine metabolism	62.22	28 of 45
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	phenylalanine metabolism	61.54	8 of 13
66794	methylglyoxal degradation	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	purine metabolism	57.45	54 of 94
66794	degradation of hexoses	55.56	10 of 18
66794	alanine metabolism	55.17	16 of 29
66794	sulfate reduction	53.85	7 of 13
66794	flavin biosynthesis	53.33	8 of 15
66794	non-pathway related	52.63	20 of 38
66794	adipate degradation	50	1 of 2
66794	threonine metabolism	50	5 of 10
66794	glycine metabolism	50	5 of 10
66794	quinate degradation	50	1 of 2
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	ethanol fermentation	50	1 of 2
66794	lysine metabolism	50	21 of 42
66794	cysteine metabolism	50	9 of 18
66794	pantothenate biosynthesis	50	3 of 6
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	Entner Doudoroff pathway	50	5 of 10
66794	methionine metabolism	46.15	12 of 26
66794	leucine metabolism	46.15	6 of 13
66794	pentose phosphate pathway	45.45	5 of 11
66794	CO2 fixation in Crenarchaeota	44.44	4 of 9
66794	cardiolipin biosynthesis	42.86	3 of 7
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	tryptophan metabolism	42.11	16 of 38
66794	lipid metabolism	41.94	13 of 31
66794	arginine metabolism	41.67	10 of 24
66794	histidine metabolism	41.38	12 of 29
66794	arachidonate biosynthesis	40	2 of 5
66794	ketogluconate metabolism	37.5	3 of 8
66794	oxidative phosphorylation	36.26	33 of 91
66794	degradation of sugar acids	36	9 of 25
66794	degradation of pentoses	35.71	10 of 28
66794	L-lactaldehyde degradation	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	octane oxidation	33.33	1 of 3
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	nitrate assimilation	33.33	3 of 9
66794	IAA biosynthesis	33.33	1 of 3
66794	ascorbate metabolism	31.82	7 of 22
66794	urea cycle	30.77	4 of 13
66794	polyamine pathway	30.43	7 of 23
66794	myo-inositol biosynthesis	30	3 of 10
66794	coenzyme M biosynthesis	30	3 of 10
66794	glutathione metabolism	28.57	4 of 14
66794	tyrosine metabolism	28.57	4 of 14
66794	vitamin B6 metabolism	27.27	3 of 11
66794	metabolism of disaccharids	27.27	3 of 11
66794	cholesterol biosynthesis	27.27	3 of 11
66794	toluene degradation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	ppGpp biosynthesis	25	1 of 4
66794	butanoate fermentation	25	1 of 4

API rID32A

@ref	URE	ADH (Arg)	alpha GAL	beta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha GLU	beta GLU	alpha ARA	beta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	MNE	RAF	GDC	alpha FUC	Reduction of nitrateNIT	IND	PAL	L-arginine arylamidaseArgA	ProA	LGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	PyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
24744	-	-	-	+	+	+	+	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Built environment	-
#Host	#Reptilia	-
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Isolation date
24744	faeces from the reticulated python (Malayopython reticulatus) housed in a zoo	Malayopython reticulatus	Arnhem, Burgers’ Zoo	Netherlands	NLD	Europe	52.0109	5.9009 52.0109/5.9009
119698	Fresh faeces, reticulated python (Malayopython reticulatus)		Burgers' zoo, Arnhem, The Netherlands	Netherlands	NLD	Europe			2012-04-03

Taxonmaps

69479

Global distribution of 16S sequence KT254068 (>99% sequence identity) for Akkermansia glycaniphila subclade from Microbeatlas

Aquatic Samples	1160
Soil Samples	338
Animal Samples	6824
Plant Samples	26
Total Samples	8348

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
24744	1	Risk group (German classification)
119698	1	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	IMG accession	NCBI tax ID	Score
66792	ASM168379v1 assembly for Akkermansia glycaniphila Pyt	scaffold	GCA_001683795	2846452581	1679444	63.66

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24744	Akkermansia glycaniphila strain Pyt 16S ribosomal RNA gene, partial sequence	KT254068	1438		1679444

GC content

@ref	GC-content (mol%)	Method
24744	58.2	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM168379v1 assembly for Akkermansia glycaniphila Pyt
NCBI: GCA_001683795

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	99.14	no
125439	motility	BacteriaNetⓘ	no	95.38	no
125439	gram_stain	BacteriaNetⓘ	negative	84.46	no
125439	spore_formation	BacteriaNetⓘ	no	89.09	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Akkermansia glycaniphila Pyt
NCBI: GCA_001683795.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	88.97	no
125438	anaerobic	anaerobicⓘ	yes	79.35	yes
125438	aerobic	aerobicⓘ	no	86.19	no
125438	spore-forming	spore-formingⓘ	no	88.86	no
125438	thermophilic	thermophileⓘ	no	91.08	no
125438	flagellated	motile2+ⓘ	no	84.99	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Comparative Genomics Guides Elucidation of Vitamin B₁₂ Biosynthesis in Novel Human-Associated Akkermansia Strains.	Kirmiz N, Galindo K, Cross KL, Luna E, Rhoades N, Podar M, Flores GE.	Appl Environ Microbiol	10.1128/aem.02117-19	2020
Phylogeny	Akkermansia glycaniphila sp. nov., an anaerobic mucin-degrading bacterium isolated from reticulated python faeces.	Ouwerkerk JP, Aalvink S, Belzer C, de Vos WM	Int J Syst Evol Microbiol	10.1099/ijsem.0.001399	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 )
#24744	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100705
#25030	J. P. A. Ouwerkerk, S.,Belzer, C.,de Vos, W. M.: Akkermansia glycaniphila sp. nov., an anaerobic mucin-degrading bacterium isolated from reticulated python faeces. IJSEM 66: 4614 - 4620 2016 ( DOI 10.1099/ijsem.0.001399 , PubMed 27499019 )
#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 )
#68380	Automatically annotated from API rID32A .
#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 .
#119698	Collection of Institut Pasteur ; Curators of the CIP; CIP 110913
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#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 )

Content

About us

Akkermansia glycaniphila (DSM 100705, CIP 110913, Pyt)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001683795

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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