Name: Filifactor alocis CCUG 47790
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 152856

Type strain:

Species: Filifactor alocis

Culture col. no.: CCUG 47790, ATCC 35896

NCBI tax ID(s): 546269 (strain), 143361 (species)

SI-ID 41356

ATCC 35896, CCUG 47790

Special Collections

CCUG

Other strains from Filifactor alocis

Section

When using BacDive for research please cite our paper

Filifactor alocis CCUG 47790 is an anaerobe, mesophilic bacterium that was isolated from Human gingival sulcus.

anaerobe
mesophilic
16S sequence
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	*Bacillota*
	Class	*Clostridia*
	Order	*Eubacteriales*
	Family	*Peptostreptococcaceae*
	Genus	*Filifactor*
	Species	**Filifactor alocis**
	Full Scientific Name (LPSN)	Filifactor alocis (Cato et al. 1985) Jalava and Eerola 1999

Synonym

Fusobacterium alocis

Information on morphological and physiological properties Morphology

[Ref.: #57874]

Incubation period

3 days

Information on culture and growth conditions Culture and growth conditions

	Temperatures	Kind of temperature		Temperature
[Ref.: #57874]			growth	37 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #57874]	Oxygen tolerance	anaerobe
[Ref.: #125438]	Oxygen tolerance	anaerobe Confidence in %94.467
[Ref.: #125439]	Oxygen tolerance	anaerobe Confidence in %97.9

[Ref.: #125439]

Ability of spore formation

yes Confidence in %94.2

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	biotin biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	photosynthesis	71.43	10 of 14
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	alanine metabolism	68.97	20 of 29
[Ref.: #66794]	pyrimidine metabolism	68.89	31 of 45
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	glutamate and glutamine metabolism	64.29	18 of 28
[Ref.: #66794]	gluconeogenesis	62.5	5 of 8
[Ref.: #66794]	phenylalanine metabolism	61.54	8 of 13
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	purine metabolism	59.57	56 of 94
[Ref.: #66794]	glycolysis	58.82	10 of 17
[Ref.: #66794]	lipid metabolism	58.06	18 of 31
[Ref.: #66794]	methionine metabolism	57.69	15 of 26
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	arginine metabolism	50	12 of 24
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	vitamin B1 metabolism	46.15	6 of 13
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	tryptophan metabolism	44.74	17 of 38
[Ref.: #66794]	tetrahydrofolate metabolism	42.86	6 of 14
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	starch degradation	40	4 of 10
[Ref.: #66794]	propionate fermentation	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	methylglyoxal degradation	40	2 of 5
[Ref.: #66794]	non-pathway related	39.47	15 of 38
[Ref.: #66794]	oxidative phosphorylation	38.46	35 of 91
[Ref.: #66794]	histidine metabolism	37.93	11 of 29
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	37.5	3 of 8
[Ref.: #66794]	pentose phosphate pathway	36.36	4 of 11
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	isoprenoid biosynthesis	34.62	9 of 26
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	formaldehyde oxidation	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	lysine metabolism	33.33	14 of 42
[Ref.: #66794]	molybdenum cofactor biosynthesis	33.33	3 of 9
[Ref.: #66794]	chorismate metabolism	33.33	3 of 9
[Ref.: #66794]	d-mannose degradation	33.33	3 of 9
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	leucine metabolism	30.77	4 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	urea cycle	30.77	4 of 13
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	citric acid cycle	28.57	4 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	28.57	2 of 7
[Ref.: #66794]	tyrosine metabolism	28.57	4 of 14
[Ref.: #66794]	glutathione metabolism	28.57	4 of 14
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	degradation of pentoses	28.57	8 of 28
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	isoleucine metabolism	25	2 of 8
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	25	3 of 12
[Ref.: #66794]	degradation of sugar alcohols	25	4 of 16
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	sulfate reduction	23.08	3 of 13
[Ref.: #66794]	ascorbate metabolism	22.73	5 of 22
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
[Ref.: #66794]	lipid A biosynthesis	22.22	2 of 9
[Ref.: #66794]	valine metabolism	22.22	2 of 9
[Ref.: #66794]	heme metabolism	21.43	3 of 14
		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.: #57874]	Sample type/isolated from	Human gingival sulcus
[Ref.: #57874]	Geographic location (country and/or sea, region)	Virginia
[Ref.: #57874]	Country	USA
[Ref.: #57874]	Country ISO 3 Code	USA
[Ref.: #57874]	Continent	North America
* marker position based on {}

Isolation sources categories

#Host	#Human	-
#Host Body-Site	#Oral cavity and airways	#Gingiva
#Infection	#Patient	-
#Host Body-Site	#Other	#Wound

What are isolation sources categories?

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

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #124043]	Fusobacterium alocis 16S ribosomal RNA, partial	AJ006962	1476	GenBank ENA	143361 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Filifactor alocis ATCC 35896	GCA_000163895	complete	GenBank ENA	546269 tax ID	*
[Ref.: #66792]	Filifactor alocis ATCC 35896	546269.5	complete	PATRIC	546269 tax ID	*
[Ref.: #66792]	Filifactor alocis ATCC 35896	2511231077	complete	JGI IMG/M	546269 tax ID	*

Data predicted using genome information as a basis Genome-based predictions

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Filifactor alocis ATCC 35896 ATCC 35896 NCBI: GCA_000163895.2
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	75.174	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	yes	94.467	yes
[Ref.: #125438]	aerobic	aerobicⓘ	no	99.509	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	67.122	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	88.813	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	85.243	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Filifactor alocis ATCC 35896 PATRIC: 546269.5
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	yes	94.2
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	80.1
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	positive	69.2
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	anaerobe	97.9

Availability in culture collections External links

[Ref.: #57874]

Culture collection no.

CCUG 47790, ATCC 35896

[Ref.: #106757]

SI-ID 41356

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Pathogenicity	Proteome analysis of coinfection of epithelial cells with Filifactor alocis and Porphyromonas gingivalis shows modulation of pathogen and host regulatory pathways.	Aruni AW, Zhang K, Dou Y, Fletcher H	Infect Immun	10.1128/IAI.01727-14	2014	*
Metabolism	Proteome variation among Filifactor alocis strains.	Aruni AW, Roy F, Sandberg L, Fletcher HM	Proteomics	10.1002/pmic.201200211	2012	*
Phylogeny	Filifactor alocis has virulence attributes that can enhance its persistence under oxidative stress conditions and mediate invasion of epithelial cells by porphyromonas gingivalis.	Aruni AW, Roy F, Fletcher HM	Infect Immun	10.1128/IAI.05631-11	2011	*
Phylogeny	Phylogenetic analysis of Fusobacterium alocis and Fusobacterium sulci based on 16S rRNA gene sequences: proposal of Filifactor alocis (Cato, Moore and Moore) comb. nov. and Eubacterium sulci (Cato, Moore and Moore) comb. nov.	Jalava J, Eerola E	Int J Syst Bacteriol	10.1099/00207713-49-4-1375	1999	*
Phylogeny	Criibacterium bergeronii gen. nov., sp. nov., a new member of the family Peptostreptococcaceae, isolated from human clinical samples.	Maheux AF, Boudreau DK, Abed JY, Berube E, Brodeur S, Bernard KA, Hashimi A, Ducrey E, Guay EF, Raymond F, Corbeil J, Domingo MC, Roy PH, Boissinot M, Tocheva EI, Omar RF	Int J Syst Evol Microbiol	10.1099/ijsem.0.004691	2021	*
Phylogeny	Phylogenetic Analysis of Filifactor alocis Strains Isolated from Several Oral Infections Identified a Novel RTX Toxin, FtxA.	Oscarsson J, Claesson R, Bao K, Brundin M, Belibasakis GN	Toxins (Basel)	10.3390/toxins12110687	2020	*
Metabolism	Role of Superoxide Reductase FA796 in Oxidative Stress Resistance in Filifactor alocis.	Mishra A, Aja E, Fletcher HM	Sci Rep	10.1038/s41598-020-65806-3	2020	*
Metabolism	Genome sequence and virulence factors of a group G Streptococcus dysgalactiae subsp. equisimilis strain with a new element carrying erm(B).	Wang X, Zhang X, Zong Z	Sci Rep	10.1038/srep20389	2016	*
Proteome	Extracellular Vesicle Subproteome Differences among Filifactor alocis Clinical Isolates.	Bao K, Claesson R, Belibasakis GN, Oscarsson J	Microorganisms	10.3390/microorganisms10091826	2022	*
	Analysis of Chemical Structure and Antibiofilm Properties of Exopolysaccharides from Lactiplantibacillus plantarum EIR/IF-1 Postbiotics.	Karaca B, Haliscelik O, Gursoy M, Kiran F, Loimaranta V, Soderling E, Gursoy UK	Microorganisms	10.3390/microorganisms10112200	2022	*

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 )

#57874 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 47790

#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 )

#106757

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-ID41356.1 )

#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 .

* These data were automatically processed and therefore are not curated

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Filifactor alocis ATCC 35896 ATCC 35896

Filifactor alocis ATCC 35896

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