Treponema saccharophilum (DSM 2985, ATCC 43261, JCM 32279)

Name: Treponema saccharophilum (DSM 2985, ATCC 43261, JCM 32279)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14341

Type strain

Strain Designation PB

Culture col. no. DSM 2985 ATCC 43261 JCM 32279 PB

NCBI tax ID(s) 907348 165

Special Collections DSMZ JCM

History DSMZ <- E. Canale-Parola; PB <- B. J. Paster and E. Canale-Parola {1980} JCM <-- DSM 2985 <-- E. Canale-Parola; PB <-- B. J. Paster and E. Canale-Parola.

Links

Treponema saccharophilum PB is an anaerobe bacterium that was isolated from bovine rumen.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 45122

JCM 32279,ATCC 43261,DSM 2985

@ref 20215

Last LPSN update 2026-05-29 08:28:15

Domain Bacteria

Phylum Spirochaetota

Class Spirochaetia

Order Spirochaetales

Family Treponemataceae

Genus Treponema

Species Treponema saccharophilum

Full scientific name Treponema saccharophilum Paster and Canale-Parola 1986

Morphology

Multimedia

@ref:	66793
multimedia content:	EM_DSM_2985_1.jpg
multimedia.multimedia content:	EM_DSM_2985_1.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_2985_2.jpg
multimedia.multimedia content:	EM_DSM_2985_2.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_2985_3.jpg
multimedia.multimedia content:	EM_DSM_2985_3.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_2985_4.jpg
multimedia.multimedia content:	EM_DSM_2985_4.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_2985_5.jpg
multimedia.multimedia content:	EM_DSM_2985_5.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
1268	TREPONEMA SACCHAROPHILUM MEDIUM (DSMZ Medium 323)		Medium recipe at MediaDive	Name: TREPONEMA SACCHAROPHILUM MEDIUM (DSMZ Medium 323) Composition: Agar 12.0 g/l Na2CO3 2.5 g/l D-Glucose 2.0 g/l Trypticase peptone 2.0 g/l Yeast extract 2.0 g/l L-Cysteine HCl x H2O 1.0 g/l (NH4)2SO4 0.9 g/l NaCl 0.9 g/l KH2PO4 0.45 g/l K2HPO4 0.45 g/l MgSO4 x 7 H2O 0.19 g/l CaCl2 x 2 H2O 0.12 g/l Sodium resazurin 0.0005 g/l n-Butyric acid iso-Butyric acid DL-2-Methylbutyric acid n-Valeric acid iso-Valeric acid Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
1268	positive	growth	37
67770	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
1268	anaerobe
125439	obligate anaerobe	99.777

Spore formation

@ref	Spore formation	Confidence
125439		98.97

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	coenzyme A metabolism	100	4 of 4
66794	ppGpp biosynthesis	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	L-lactaldehyde degradation	100	3 of 3
66794	biotin biosynthesis	100	4 of 4
66794	palmitate biosynthesis	95.45	21 of 22
66794	starch degradation	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	glycogen metabolism	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	threonine metabolism	80	8 of 10
66794	photosynthesis	78.57	11 of 14
66794	d-mannose degradation	77.78	7 of 9
66794	valine metabolism	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	sulfopterin metabolism	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	gluconeogenesis	75	6 of 8
66794	Entner Doudoroff pathway	70	7 of 10
66794	phenylalanine metabolism	69.23	9 of 13
66794	purine metabolism	69.15	65 of 94
66794	pyrimidine metabolism	68.89	31 of 45
66794	vitamin B12 metabolism	67.65	23 of 34
66794	serine metabolism	66.67	6 of 9
66794	formaldehyde oxidation	66.67	2 of 3
66794	flavin biosynthesis	66.67	10 of 15
66794	acetoin degradation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	heme metabolism	64.29	9 of 14
66794	d-xylose degradation	63.64	7 of 11
66794	isoleucine metabolism	62.5	5 of 8
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	C4 and CAM-carbon fixation	62.5	5 of 8
66794	methionine metabolism	61.54	16 of 26
66794	degradation of hexoses	61.11	11 of 18
66794	glutamate and glutamine metabolism	60.71	17 of 28
66794	oxidative phosphorylation	60.44	55 of 91
66794	cellulose degradation	60	3 of 5
66794	glycine betaine biosynthesis	60	3 of 5
66794	glycolysis	58.82	10 of 17
66794	propanol degradation	57.14	4 of 7
66794	CO2 fixation in Crenarchaeota	55.56	5 of 9
66794	metabolism of disaccharids	54.55	6 of 11
66794	leucine metabolism	53.85	7 of 13
66794	degradation of sugar acids	52	13 of 25
66794	alanine metabolism	51.72	15 of 29
66794	butanoate fermentation	50	2 of 4
66794	kanosamine biosynthesis II	50	1 of 2
66794	tetrahydrofolate metabolism	50	7 of 14
66794	pantothenate biosynthesis	50	3 of 6
66794	ethanol fermentation	50	1 of 2
66794	cysteine metabolism	50	9 of 18
66794	arginine metabolism	50	12 of 24
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	ketogluconate metabolism	50	4 of 8
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	non-pathway related	50	19 of 38
66794	CMP-KDO biosynthesis	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	histidine metabolism	48.28	14 of 29
66794	tryptophan metabolism	47.37	18 of 38
66794	degradation of pentoses	46.43	13 of 28
66794	isoprenoid biosynthesis	46.15	12 of 26
66794	proline metabolism	45.45	5 of 11
66794	vitamin B6 metabolism	45.45	5 of 11
66794	degradation of sugar alcohols	43.75	7 of 16
66794	citric acid cycle	42.86	6 of 14
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	cardiolipin biosynthesis	42.86	3 of 7
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	factor 420 biosynthesis	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	methylglyoxal degradation	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	O-antigen biosynthesis	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	lipid metabolism	38.71	12 of 31
66794	urea cycle	38.46	5 of 13
66794	lysine metabolism	38.1	16 of 42
66794	pentose phosphate pathway	36.36	4 of 11
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	octane oxidation	33.33	1 of 3
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	lipid A biosynthesis	33.33	3 of 9
66794	enterobactin biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	ascorbate metabolism	31.82	7 of 22
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	sulfate reduction	30.77	4 of 13
66794	propionate fermentation	30	3 of 10
66794	tyrosine metabolism	28.57	4 of 14
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	degradation of aromatic, nitrogen containing compounds	25	3 of 12
66794	arachidonic acid metabolism	22.22	4 of 18
66794	nitrate assimilation	22.22	2 of 9
66794	glutathione metabolism	21.43	3 of 14

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Bovinae (Cow, Cattle)
#Host Body-Site	#Organ	#Rumen

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
1268	bovine rumen	Massachusetts, Amherst	USA	USA	North America
67770	Rumen fluid sample obtained from a fistulated cow (Holstein breed) housed at the University of Massachusetts Dairy Facility	South Deerfield, MA	USA	USA	North America

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
1268	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
124043	ASM3625065v1 assembly for Treponema saccharophilum JCM 32279	complete	GCA_036250655	165.5		165	98.91
67770	ASM25555v2 assembly for Treponema saccharophilum DSM 2985	contig	GCA_000255555	907348.7	2509276055	907348	68.35
66792	Treponema saccharophilum DSM 2985	contig		907348.3		907348	30.7

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Treponema saccharophilum strain ATCC 43261 16S ribosomal RNA gene, partial sequence	M71238	1497		165

GC content

@ref	GC-content (mol%)	Method
1268	54.0
67770	53-55	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM3625065v1 assembly for Treponema saccharophilum JCM 32279
NCBI: GCA_036250655

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	negative	71.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	99.78	no
125439	motility	BacteriaNetⓘ	no	79.97	no
125439	spore_formation	BacteriaNetⓘ	no	98.97	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Treponema saccharophilum DSM 2985
PATRIC: 907348.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	85.42	no
125438	anaerobic	anaerobicⓘ	yes	85.70	yes
125438	aerobic	aerobicⓘ	no	95.30	yes
125438	spore-forming	spore-formingⓘ	no	67.73	no
125438	thermophilic	thermophileⓘ	no	85.89	no
125438	flagellated	motile2+ⓘ	yes	59.67	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Identification of fecal microbes as potential biomarkers for early diagnosis of fatty liver disease in cattle.	Sun H, Liu T, Song X, Shah SMS, Zhang Q, Shi K.	Virulence	10.1080/21505594.2025.2530166	2025
Genetics	Discovery of novel treponemes associated with pododermatitis in elk (Cervus canadensis).	Deb S, Wild MA, LeClair T, Shah DH.	Appl Environ Microbiol	10.1128/aem.00105-24	2024
	Winery by-products as a feed source with functional properties: dose-response effect of grape pomace, grape seed meal, and grape seed extract on rumen microbial community and their fermentation activity in RUSITEC.	Khiaosa-Ard R, Mahmood M, Mickdam E, Pacifico C, Meixner J, Traintinger LS.	J Anim Sci Biotechnol	10.1186/s40104-023-00892-7	2023
	Use of milk proteins as biomarkers of changes in the rumen metaproteome of Holstein cows fed low-fiber, high-starch diets.	Mulakala BK, Smith KM, Snider MA, Ayers A, Honan MC, Greenwood SL.	J Dairy Sci	10.3168/jds.2022-22910	2023
Metabolism	Characterization of variations within the rumen metaproteome of Holstein dairy cattle relative to morning feed offering.	Honan MC, Greenwood SL.	Sci Rep	10.1038/s41598-020-59974-5	2020
	Systematic Analysis of Escherichia coli Isolates from Sheep and Cattle Suggests Adaption to the Rumen Niche.	Pang J, Liu Z, Zhang Q, Lu X, Qi Q.	Appl Environ Microbiol	10.1128/aem.01417-20	2020
Metabolism	Prokaryotic viperins produce diverse antiviral molecules.	Bernheim A, Millman A, Ofir G, Meitav G, Avraham C, Avraham C, Shomar H, Rosenberg MM, Tal N, Melamed S, Amitai G, Sorek R.	Nature	10.1038/s41586-020-2762-2	2021
Phylogeny	Phylogenetic analysis of the spirochetes.	Paster BJ, Dewhirst FE, Weisburg WG, Tordoff LA, Fraser GJ, Hespell RB, Stanton TB, Zablen L, Mandelco L, Woese CR.	J Bacteriol	10.1128/jb.173.19.6101-6109.1991	1991
	Compilation of small ribosomal subunit RNA structures.	Neefs JM, Van de Peer Y, De Rijk P, Chapelle S, De Wachter R.	Nucleic Acids Res	10.1093/nar/21.13.3025	1993
Phylogeny	Monitoring the rumen pectinolytic bacteria Treponema saccharophilum using real-time PCR.	Liu J, Wang JK, Zhu W, Pu YY, Guan LL, Liu JX	FEMS Microbiol Ecol	10.1111/1574-6941.12246	2013

References

#1268	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 2985
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#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) .
#66793	Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )
#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;
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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

Treponema saccharophilum (DSM 2985, ATCC 43261, JCM 32279)

Name and taxonomic classification

Morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_036250655

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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