Francisella philomiragia (CCUG 19701, ATCC 25017)

Name: Francisella philomiragia (CCUG 19701, ATCC 25017)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 143515

Type strain

Culture col. no. CCUG 19701 ATCC 25017

NCBI tax ID(s) 28110

Special Collections CCUG

Links

Francisella philomiragia CCUG 19701 is a prokaryote that was isolated from Water,river.

genome sequence 16S sequence

Name and taxonomic classification

SI-ID 44702

ATCC 25017,CCUG 19701

@ref 20215

Last LPSN update 2025-12-16 10:04:23

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Beggiatoales

Family Francisellaceae

Genus Francisella

Species Francisella philomiragia

Full scientific name Francisella philomiragia (Jensen et al. 1969) Hollis et al. 1990

Synonyms (1)

Yersinia philomiragia

BacDive ID	Other strains from **Francisella philomiragia** (2)	Type strain
142453	F. philomiragia CCUG 12603
142624	F. philomiragia CCUG 13404

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	94.5
125439	negative	96

Culture and growth conditions

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	93.5

Spore formation

@ref	Spore formation	Confidence
125439		96.1

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
68382	trypsin	-	3.4.21.4	from API zym
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
47052	-	+	+	+	-	+	-	-	-	-	+	+	-	-	-	-	-	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#River (Creek)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
47052	Water,river	Utah,Bear River Refuge	USA	USA	North America

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1928v1 assembly for Francisella philomiragia subsp. philomiragia ATCC 25017	complete	GCA_000019285	484022.8	641522628	484022	24.11

Genome browser: GCA_000019285

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
124043	Francisella philomiragia strain ATCC 25017 16S ribosomal RNA gene, partial sequence.	AY928395	1518	484022
124043	F.philomiragia 16S rRNA	Z21933	1518	28110
124043	Francisella philomiragia strain CCUG 19701 16S ribosomal RNA gene, partial sequence.	EF364047	1414	28110

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Francisella philomiragia subsp. philomiragia ATCC 25017
PATRIC: 484022.8

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.10	no
125439	motility	BacteriaNetⓘ	no	63.60	no
125439	gram_stain	BacteriaNetⓘ	negative	96.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	93.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Francisella philomiragia subsp. philomiragia ATCC 25017
PATRIC: 484022.8

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	94.50	no
125438	anaerobic	anaerobicⓘ	no	88.48	no
125438	spore-forming	spore-formingⓘ	no	89.55	no
125438	aerobic	aerobicⓘ	no	51.40	no
125438	thermophilic	thermophileⓘ	no	92.89	no
125438	flagellated	motile2+ⓘ	no	84.34	no

Literature

Title	Authors	Journal	DOI	Year
Identification of Francisella tularensis Subspecies in a Clinical Setting Using MALDI-TOF MS: An In-House Francisella Library and Biomarkers.	de Vries MC, Hoeve-Bakker BJA, van den Beld MJC, Hendriks ACA, Harpal ASD, Noomen RCEA, Reubsaet FAG.	Microorganisms	10.3390/microorganisms11040905	2023
Shared features of cryptic plasmids from environmental and pathogenic Francisella species.	Challacombe JF, Pillai S, Kuske CR.	PLoS One	10.1371/journal.pone.0183554	2017
Whole genome sequencing of the fish pathogen Francisella noatunensis subsp. orientalis Toba04 gives novel insights into Francisella evolution and pathogenecity.	Sridhar S, Sharma A, Kongshaug H, Nilsen F, Jonassen I.	BMC Genomics	10.1186/1471-2164-13-598	2012
Rational probe design for efficient rRNA depletion and improved metatranscriptomic analysis of human microbiomes.	Tan A, Murugapiran S, Mikalauskas A, Koble J, Kennedy D, Hyde F, Ruotti V, Law E, Jensen J, Schroth GP, Macklaim JM, Kuersten S, LeFrancois B, Gohl DM.	BMC Microbiol	10.1186/s12866-023-03037-y	2023
A method for assessing efficiency of bacterial cell disruption and DNA release.	de Bruin OM, Birnboim HC.	BMC Microbiol	10.1186/s12866-016-0815-3	2016
Conservation analysis of the CydX protein yields insights into small protein identification and evolution.	Allen RJ, Brenner EP, VanOrsdel CE, Hobson JJ, Hearn DJ, Hemm MR.	BMC Genomics	10.1186/1471-2164-15-946	2014
Class A carbapenemase FPH-1 from Francisella philomiragia.	Toth M, Vakulenko V, Antunes NT, Frase H, Vakulenko SB.	Antimicrob Agents Chemother	10.1128/aac.00223-12	2012
Comparative in silico analysis of ftsZ gene from different bacteria reveals the preference for core set of codons in coding sequence structuring and secondary structural elements determination.	Pal A, Saha BK, Saha J.	PLoS One	10.1371/journal.pone.0219231	2019
Evolutionary switches between two serine codon sets are driven by selection.	Rogozin IB, Belinky F, Pavlenko V, Shabalina SA, Kristensen DM, Koonin EV.	Proc Natl Acad Sci U S A	10.1073/pnas.1615832113	2016
Genomes of model organisms: know thy tools.	Galperin MY.	Environ Microbiol	10.1111/j.1462-2920.2008.01656.x	2008
Preparation of monoclonal antibodies for detection and identification of Francisella tularensis.	Hotta A, Uda A, Fujita O, Tanabayashi K, Yamada A.	Clin Vaccine Immunol	10.1128/cvi.00057-06	2007
Identification of Francisella tularensis by whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry: fast, reliable, robust, and cost-effective differentiation on species and subspecies levels.	Seibold E, Maier T, Kostrzewa M, Zeman E, Splettstoesser W.	J Clin Microbiol	10.1128/jcm.01953-09	2010
Common ancestry and novel genetic traits of Francisella novicida-like isolates from North America and Australia as revealed by comparative genomic analyses.	Siddaramappa S, Challacombe JF, Petersen JM, Pillai S, Hogg G, Kuske CR.	Appl Environ Microbiol	10.1128/aem.00337-11	2011
Self-targeting by CRISPR: gene regulation or autoimmunity?	Stern A, Keren L, Wurtzel O, Amitai G, Sorek R.	Trends Genet	10.1016/j.tig.2010.05.008	2010
A Francisella virulence factor catalyses an essential reaction of biotin synthesis.	Feng Y, Napier BA, Manandhar M, Henke SK, Weiss DS, Cronan JE.	Mol Microbiol	10.1111/mmi.12460	2014
Molecular evolutionary consequences of niche restriction in Francisella tularensis, a facultative intracellular pathogen.	Larsson P, Elfsmark D, Svensson K, Wikstrom P, Forsman M, Brettin T, Keim P, Johansson A.	PLoS Pathog	10.1371/journal.ppat.1000472	2009
The unusual substrate specificity of a virulence associated serine hydrolase from the highly toxic bacterium, Francisella tularensis.	Farberg AM, Hart WK, Johnson RJ.	Biochem Biophys Rep	10.1016/j.bbrep.2016.07.006	2016
Protein tyrosine O-glycosylation--a rather unexplored prokaryotic glycosylation system.	Zarschler K, Janesch B, Pabst M, Altmann F, Messner P, Schaffer C.	Glycobiology	10.1093/glycob/cwq035	2010
Population structure of Francisella tularensis.	Nubel U, Reissbrodt R, Weller A, Grunow R, Porsch-Ozcurumez M, Tomaso H, Hofer E, Splettstoesser W, Finke EJ, Tschape H, Witte W.	J Bacteriol	10.1128/jb.01662-05	2006
Whole-Genome Relationships among Francisella Bacteria of Diverse Origins Define New Species and Provide Specific Regions for Detection.	Challacombe JF, Petersen JM, Gallegos-Graves V, Hodge D, Pillai S, Kuske CR.	Appl Environ Microbiol	10.1128/aem.02589-16	2017
Francisella philomiragia comb. nov. (formerly Yersinia philomiragia) and Francisella tularensis biogroup novicida (formerly Francisella novicida) associated with human disease.	Hollis DG, Weaver RE, Steigerwalt AG, Wenger JD, Moss CW, Brenner DJ.	J Clin Microbiol	10.1128/jcm.27.7.1601-1608.1989	1989
A high-throughput pipeline for designing microarray-based pathogen diagnostic assays.	Vijaya Satya R, Zavaljevski N, Kumar K, Reifman J.	BMC Bioinformatics	10.1186/1471-2105-9-185	2008
Novel genomic tools for specific and real-time detection of biothreat and frequently encountered foodborne pathogens.	Woubit A, Yehualaeshet T, Habtemariam T, Samuel T.	J Food Prot	10.4315/0362-028x.jfp-11-480	2012
Dissection of Francisella-Host Cell Interactions in Dictyostelium discoideum.	Lampe EO, Brenz Y, Herrmann L, Repnik U, Griffiths G, Zingmark C, Sjostedt A, Winther-Larsen HC, Hagedorn M.	Appl Environ Microbiol	10.1128/aem.02950-15	2015
Evolution and diversity of periplasmic proteins involved in copper homeostasis in gamma proteobacteria.	Hernandez-Montes G, Arguello JM, Valderrama B.	BMC Microbiol	10.1186/1471-2180-12-249	2012
Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms.	Nasir A, Naeem A, Khan MJ, Nicora HD, Caetano-Anolles G.	Genes (Basel)	10.3390/genes2040869	2011
Phylogenetic distribution and evolutionary history of bacterial DEAD-Box proteins.	Lopez-Ramirez V, Alcaraz LD, Moreno-Hagelsieb G, Olmedo-Alvarez G.	J Mol Evol	10.1007/s00239-011-9441-8	2011
Comprehensive biothreat cluster identification by PCR/electrospray-ionization mass spectrometry.	Sampath R, Mulholland N, Blyn LB, Massire C, Whitehouse CA, Waybright N, Harter C, Bogan J, Miranda MS, Smith D, Baldwin C, Wolcott M, Norwood D, Kreft R, Frinder M, Lovari R, Yasuda I, Matthews H, Toleno D, Housley R, Duncan D, Li F, Warren R, Eshoo MW, Hall TA, Hofstadler SA, Ecker DJ.	PLoS One	10.1371/journal.pone.0036528	2012
Cohesion group approach for evolutionary analysis of aspartokinase, an enzyme that feeds a branched network of many biochemical pathways.	Lo CC, Bonner CA, Xie G, D'Souza M, Jensen RA.	Microbiol Mol Biol Rev	10.1128/mmbr.00024-09	2009
Genetic diversity within the genus Francisella as revealed by comparative analyses of the genomes of two North American isolates from environmental sources.	Siddaramappa S, Challacombe JF, Petersen JM, Pillai S, Kuske CR	BMC Genomics	10.1186/1471-2164-13-422	2012
Complete genome sequence of Francisella philomiragia ATCC 25017.	Zeytun A, Malfatti SA, Vergez LM, Shin M, Garcia E, Chain PS	J Bacteriol	10.1128/JB.00413-12	2012
Description of two new plasmids isolated from Francisella philomiragia strains and construction of shuttle vectors for the study of Francisella tularensis.	Le Pihive E, Blaha D, Chenavas S, Thibault F, Vidal D, Valade E	Plasmid	10.1016/j.plasmid.2009.07.001	2009
Francisella marina sp. nov., Etiologic Agent of Systemic Disease in Cultured Spotted Rose Snapper (Lutjanus guttatus) in Central America.	Soto E, Griffin MJ, Morales JA, Calvo EB, de Alexandre Sebastiao F, Porras AL, Viquez-Rodriguez X, Reichley SR, Rosser TG, Ware C, Byrne BA, Garcia JC, LaFrentz BR, Camus AC.	Appl Environ Microbiol	10.1128/aem.00144-18	2018
Description of Francisella hispaniensis sp. nov., isolated from human blood, reclassification of Francisella novicida (Larson et al. 1955) Olsufiev et al. 1959 as Francisella tularensis subsp. novicida comb. nov. and emended description of the genus Francisella.	Huber B, Escudero R, Busse HJ, Seibold E, Scholz HC, Anda P, Kampfer P, Splettstoesser WD	Int J Syst Evol Microbiol	10.1099/ijs.0.015941-0	2009

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 )
#47052	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 19701
#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) .
#68382	Automatically annotated from API zym .
#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 )

Rate our new design

Content

About us

Francisella philomiragia (CCUG 19701, ATCC 25017)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Physiology and metabolism

Oxygen tolerance

Spore formation

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_000019285

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media