Bifidobacterium psychraerophilum (DSM 22366, LMG 21775, NCIMB 13940)

Name: Bifidobacterium psychraerophilum (DSM 22366, LMG 21775, NCIMB 13940)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1738

Type strain

Strain Designation T16

Culture col. no. DSM 22366 LMG 21775 NCIMB 13940 T16 JCM 15958

NCBI tax ID(s) 1435464 218140

Special Collections DSMZ JCM Literature strains Pig DSMZ

Links

Bifidobacterium psychraerophilum T16 is an anaerobe, mesophilic, Gram-positive prokaryote that was isolated from pig caecum.

Gram-positive rod-shaped anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 94702

LMG 21775,NCIMB 13940,JCM 15958,DSM 22366

@ref 20215

Last LPSN update 2025-12-16 09:47:10

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Bifidobacteriales

Family Bifidobacteriaceae

Genus Bifidobacterium

Species Bifidobacterium psychraerophilum

Full scientific name Bifidobacterium psychraerophilum Simpson et al. 2004

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
29919	positive	1.1 µm	0.85 µm	rod-shaped
125438						91.5

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
16188	BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58)		Medium recipe at MediaDive	Name: BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58) Composition: Glucose 10.0 g/l Casein peptone 10.0 g/l Bacto Soytone 5.0 g/l Meat extract 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l MnSO4 x H2O 0.05 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Tween 80 Resazurin Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
16188	positive	growth	37	mesophilic
29919	positive	growth	04-42
29919	positive	optimum	37	mesophilic
67770	positive	growth	37	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
29919	positive	growth	4.0-4.5	acidophile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
16188	anaerobe
29919	facultative aerobe

Spore formation

@ref	Spore formation	Confidence
29919
125439		91.7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	+	builds acid from	from API 50CH acid
29919	22599 ChEBI	arabinose	+	carbon source
68371	18305 ChEBI	arbutin	+	builds acid from	from API 50CH acid
68371	17057 ChEBI	cellobiose	-	builds acid from	from API 50CH acid
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	+	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	+	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	-	builds acid from	from API 50CH acid
68371	16988 ChEBI	D-ribose	+	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	+	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68371	28066 ChEBI	gentiobiose	+	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	+	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
29919	17306 ChEBI	maltose	+	carbon source
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
29919	37684 ChEBI	mannose	+	carbon source
68371	6731 ChEBI	melezitose	+	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	+	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	+	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	-	builds acid from	from API 50CH acid
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
29919	16634 ChEBI	raffinose	+	carbon source
68371	16634 ChEBI	raffinose	+	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
29919	17814 ChEBI	salicin	+	carbon source
68371	17814 ChEBI	salicin	+	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
29919	17992 ChEBI	sucrose	+	carbon source
68371	17992 ChEBI	sucrose	+	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	-	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid
29919	18222 ChEBI	xylose	+	carbon source

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cellulose degradation	100	5 of 5
66794	cardiolipin biosynthesis	100	7 of 7
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	acetate fermentation	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	ppGpp biosynthesis	100	4 of 4
66794	vitamin B1 metabolism	92.31	12 of 13
66794	palmitate biosynthesis	90.91	20 of 22
66794	threonine metabolism	90	9 of 10
66794	starch degradation	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	photosynthesis	85.71	12 of 14
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	pentose phosphate pathway	81.82	9 of 11
66794	methylglyoxal degradation	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	NAD metabolism	77.78	14 of 18
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	isoleucine metabolism	75	6 of 8
66794	phenylalanine metabolism	69.23	9 of 13
66794	degradation of sugar alcohols	68.75	11 of 16
66794	glutamate and glutamine metabolism	67.86	19 of 28
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	purine metabolism	65.96	62 of 94
66794	oxidative phosphorylation	64.84	59 of 91
66794	glycolysis	64.71	11 of 17
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	metabolism of disaccharids	63.64	7 of 11
66794	d-xylose degradation	63.64	7 of 11
66794	gluconeogenesis	62.5	5 of 8
66794	ketogluconate metabolism	62.5	5 of 8
66794	methionine metabolism	61.54	16 of 26
66794	degradation of pentoses	60.71	17 of 28
66794	lipoate biosynthesis	60	3 of 5
66794	Entner Doudoroff pathway	60	6 of 10
66794	cysteine metabolism	55.56	10 of 18
66794	d-mannose degradation	55.56	5 of 9
66794	pyrimidine metabolism	55.56	25 of 45
66794	non-pathway related	55.26	21 of 38
66794	alanine metabolism	55.17	16 of 29
66794	histidine metabolism	55.17	16 of 29
66794	proline metabolism	54.55	6 of 11
66794	arginine metabolism	54.17	13 of 24
66794	isoprenoid biosynthesis	53.85	14 of 26
66794	leucine metabolism	53.85	7 of 13
66794	ethanol fermentation	50	1 of 2
66794	citric acid cycle	50	7 of 14
66794	adipate degradation	50	1 of 2
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	50	4 of 8
66794	coenzyme A metabolism	50	2 of 4
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	suberin monomers biosynthesis	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	lysine metabolism	47.62	20 of 42
66794	tryptophan metabolism	47.37	18 of 38
66794	vitamin B6 metabolism	45.45	5 of 11
66794	CO2 fixation in Crenarchaeota	44.44	4 of 9
66794	degradation of hexoses	44.44	8 of 18
66794	tyrosine metabolism	42.86	6 of 14
66794	propanol degradation	42.86	3 of 7
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	propionate fermentation	40	4 of 10
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	lipid metabolism	38.71	12 of 31
66794	urea cycle	38.46	5 of 13
66794	ascorbate metabolism	36.36	8 of 22
66794	glutathione metabolism	35.71	5 of 14
66794	cyanate degradation	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	enterobactin biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	flavin biosynthesis	33.33	5 of 15
66794	sulfate reduction	30.77	4 of 13
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	polyamine pathway	30.43	7 of 23
66794	myo-inositol biosynthesis	30	3 of 10
66794	mevalonate metabolism	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	androgen and estrogen metabolism	25	4 of 16
66794	carnitine metabolism	25	2 of 8
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	CMP-KDO biosynthesis	25	1 of 4
66794	nitrate assimilation	22.22	2 of 9
66794	arachidonic acid metabolism	22.22	4 of 18
66794	4-hydroxymandelate degradation	22.22	2 of 9
66794	heme metabolism	21.43	3 of 14

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
16188	-	-	-	-	+	+	+	-	-	-	+	+	+	-	-	-	-	-	-	-	-	+	-	+	+	+	+	-	+	-	+	+	-	-	+	+	-	-	-	+	+/-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Suidae (Pig,Swine)
#Host Body-Site	#Gastrointestinal tract	#Large intestine

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
16188	pig caecum	Fermoy	Ireland	IRL	Europe
67770	Porcine caecum

Taxonmaps

69479

Global distribution of 16S sequence LC483555 (>99% sequence identity) for Bifidobacterium from Microbeatlas

Aquatic Samples	1083
Soil Samples	361
Animal Samples	10871
Plant Samples	162
Total Samples	12477

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16188	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
67770	ASM281320v1 assembly for Bifidobacterium psychraerophilum DSM 22366	contig	GCA_002813205	1435464.5	2627853606	1435464	78.35
67770	Bifpsy assembly for Bifidobacterium psychraerophilum LMG 21775	contig	GCA_000741705	218140.3	2597490219	218140	76.34
67770	DSM-22366 assembly for Bifidobacterium psychraerophilum DSM 22366	contig	GCA_000771565	1435464.3	8119566969	1435464	64.54

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
67770	Bifidobacterium psychraerophilum gene for 16S ribosomal RNA, partial sequence, strain: YIT 11814	AB437351	1499	218140
67770	Bifidobacterium psychroaerophilum 16S ribosomal RNA gene, partial sequence	AY174108	1428	218140
67770	Bifidobacterium psychraerophilum gene for 16S ribosomal RNA, partial sequence	LC483555	1464	218140

GC content

@ref	GC-content (mol%)	Method
16188	59.2
67770	59.2	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: Bifidobacterium psychraerophilum DSM 22366
NCBI: GCA_000771565

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	91.70	no
125439	motility	BacteriaNetⓘ	no	65.30	no
125439	gram_stain	BacteriaNetⓘ	positive	79.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	75.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Bifidobacterium psychraerophilum DSM 22366
PATRIC: 1435464.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	86.47	no
125438	anaerobic	anaerobicⓘ	yes	64.71	no
125438	spore-forming	spore-formingⓘ	no	86.52	yes
125438	aerobic	aerobicⓘ	no	88.84	yes
125438	thermophilic	thermophileⓘ	no	93.00	yes
125438	flagellated	motile2+ⓘ	no	91.50	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Pathogenicity	Exploring the Ecology of Bifidobacteria and Their Genetic Adaptation to the Mammalian Gut.	Duranti S, Longhi G, Ventura M, van Sinderen D, Turroni F.	Microorganisms	10.3390/microorganisms9010008	2020
Phylogeny	Investigation of the evolutionary development of the genus Bifidobacterium by comparative genomics.	Lugli GA, Milani C, Turroni F, Duranti S, Ferrario C, Viappiani A, Mancabelli L, Mangifesta M, Taminiau B, Delcenserie V, van Sinderen D, Ventura M.	Appl Environ Microbiol	10.1128/aem.02004-14	2014
Phylogeny	Phylogenetic Analysis of the Bifidobacterium Genus Using Glycolysis Enzyme Sequences.	Brandt K, Barrangou R.	Front Microbiol	10.3389/fmicb.2016.00657	2016
Enzymology	Detection and characterization of Bifidobacterium crudilactis and B. mongoliense able to grow during the manufacturing process of French raw milk cheeses.	Delcenserie V, Taminiau B, Gavini F, de Schaetzen MA, Cleenwerck I, Theves M, Mahieu M, Daube G.	BMC Microbiol	10.1186/1471-2180-13-239	2013
Phylogeny	Genomic encyclopedia of type strains of the genus Bifidobacterium.	Milani C, Lugli GA, Duranti S, Turroni F, Bottacini F, Mangifesta M, Sanchez B, Viappiani A, Mancabelli L, Taminiau B, Delcenserie V, Barrangou R, Margolles A, van Sinderen D, Ventura M.	Appl Environ Microbiol	10.1128/aem.02308-14	2014
Metabolism	Diversity, ecology and intestinal function of bifidobacteria.	Bottacini F, Ventura M, van Sinderen D, O'Connell Motherway M.	Microb Cell Fact	10.1186/1475-2859-13-s1-s4	2014
Phylogeny	Description of a new species, Bifidobacterium crudilactis sp. nov., isolated from raw milk and raw milk cheeses.	Delcenserie V, Gavini F, Beerens H, Tresse O, Franssen C, Daube G	Syst Appl Microbiol	10.1016/j.syapm.2007.01.004	2007
Phylogeny	Bifidobacterium psychraerophilum sp. nov. and Aeriscardovia aeriphila gen. nov., sp. nov., isolated from a porcine caecum.	Simpson PJ, Ross RP, Fitzgerald GF, Stanton C	Int J Syst Evol Microbiol	10.1099/ijs.0.02667-0	2004

References

#16188	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22366
#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 )
#29919	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 #26290 (see below)
#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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68371	Automatically annotated from API 50CH acid .
#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 .
#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 )

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Bifidobacterium psychraerophilum (DSM 22366, LMG 21775, NCIMB 13940)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Pathway annotation

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002813205

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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