Saccharibacter floricola S-877 | Type strain | DSM 15669, AJ 13480, JCM 12116 | BacDiveID:63

Strain identifier

BacDive ID: 63

Type strain:

Species: Saccharibacter floricola

Strain Designation: S-877

Culture col. no.: DSM 15669, AJ 13480, JCM 12116

Strain history: R. Fudou S-877.

NCBI tax ID(s): 1123227 (strain), 231053 (species)

SI-ID 134459

DSM 15669, JCM 12116, LMG 23170

Special Collections

Section

Saccharibacter floricola S-877 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from pollen.

Gram-negative
rod-shaped
aerobe
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Rhodospirillales*
	Family	*Acetobacteraceae*
	Genus	*Saccharibacter*
	Species	**Saccharibacter floricola**
	Full Scientific Name (LPSN)	Saccharibacter floricola Jojima et al. 2004

Information on morphological and physiological properties Morphology

[Ref.: #23247]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.333

[Ref.: #23247]	Cell length	2.5-4.0 µm

[Ref.: #23247]	Cell width	0.8-1.0 µm

[Ref.: #23247]	Cell shape	rod-shaped

[Ref.: #23247]	Motility	no

Multimedia content

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Information on culture and growth conditions Culture and growth conditions

Culture medium

YPG MEDIUM (DSMZ Medium 1017)

Culture medium growth

Culture medium link

Medium recipe at MediaDive

Culture medium composition

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Culture medium

YPG medium

Culture medium growth

Culture medium composition

expand / minimize

Culture medium

YUG medium

Culture medium growth

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #6023]			growth	28 °C
[Ref.: #23247]			growth	28 °C
[Ref.: #67770]			growth	28 °C

	pH	Kind of pH		pH
[Ref.: #23247]			maximum	8
[Ref.: #23247]			minimum	4
[Ref.: #23247]			optimum	5.0-7.0
[Ref.: #23247]			growth	4.0-8.0

Information on physiology and metabolism Physiology and metabolism

Oxygen tolerance

aerobe

[Ref.: #23247]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %92.669
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

Observation

quinones: Q-10

[Ref.: #23247]	Name of tolerated compound	D-Glucose
[Ref.: #23247]	Tolerance percentage	30

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #23247]		acetate ChEBI	-	oxidation
[Ref.: #23247]		D-arabinose ChEBI	-	builds acid from
[Ref.: #23247]		D-fructose ChEBI	+/-	builds acid from
[Ref.: #23247]		D-galactose ChEBI	+	builds acid from
[Ref.: #23247]		D-glucose ChEBI	+	builds acid from
[Ref.: #23247]		D-mannitol ChEBI	+	builds acid from
[Ref.: #23247]		D-mannose ChEBI	+	builds acid from
[Ref.: #23247]		D-sorbitol ChEBI	-	builds acid from
[Ref.: #23247]		D-xylose ChEBI	+	builds acid from
[Ref.: #23247]		ethanol ChEBI	-	builds acid from
[Ref.: #23247]		galactitol ChEBI	-	builds acid from
[Ref.: #23247]		glycerol ChEBI	-	builds acid from
[Ref.: #23247]		L-arabinose ChEBI	+	builds acid from
[Ref.: #23247]		L-rhamnose ChEBI	-	builds acid from
[Ref.: #23247]		L-sorbose ChEBI	-	builds acid from
[Ref.: #23247]		lactate ChEBI	+/-	oxidation
[Ref.: #23247]		melibiose ChEBI	+	builds acid from
[Ref.: #23247]		methanol ChEBI	-	assimilation
[Ref.: #23247]		raffinose ChEBI	-	builds acid from
[Ref.: #23247]		sucrose ChEBI	+	builds acid from
		Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #23247]		2-dehydro-D-gluconate ChEBI	yes
[Ref.: #23247]		5-dehydro-D-gluconate ChEBI	yes
[Ref.: #23247]		acetate ChEBI	yes
[Ref.: #23247]		cellulose ChEBI	no
[Ref.: #23247]		dihydroxyacetone ChEBI	no

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #23247]		catalase	+	1.11.1.6
[Ref.: #23247]		cytochrome oxidase	-	1.9.3.1

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #6023]	Sample type/isolated from	pollen
[Ref.: #6023]	Geographic location (country and/or sea, region)	Kanagawa
[Ref.: #6023]	Country	Japan
[Ref.: #6023]	Country ISO 3 Code	JPN
[Ref.: #6023]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Pollen collected in Kanagawa Pref.
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host Body-Site

#Plant

#Fruit (Seed)

What are isolation sources categories?

Global distribution of 16S sequence AB110421 (>99% sequence identity) for Saccharibacter floricola subclade from Microbeatlas

Aquatic Samples	590
Soil Samples	690
Animal Samples	2893
Plant Samples	257
Total Samples	4430

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

Biosafety level

1

Risk group (German classification)
According to TRBA 466

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.: #6023]	Saccharibacter floricola gene for 16S ribosomal RNA, partial sequence	AB110421	1436	GenBank ENA	231053 tax ID
[Ref.: #20218]	Saccharibacter floricola DNA, 16S-23S rRNA ITS region. strain: JCM 12116	AB210092	680	GenBank ENA	231053 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Saccharibacter floricola DSM 15669	GCA_000378165	scaffold	GenBank ENA	1123227 tax ID
[Ref.: #66792]	Saccharibacter floricola DSM 15669	1123227.4	wgs	PATRIC	1123227 tax ID	*
[Ref.: #66792]	Saccharibacter floricola DSM 15669	2518645607	draft	JGI IMG/M	1123227 tax ID	*

GC-content

52.3 mol%

high performance liquid chromatography (HPLC)

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Saccharibacter floricola DSM 15669 DSM 15669 NCBI: GCA_000378165.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Saccharibacter floricola DSM 15669 PATRIC: 1123227.4
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	99.333	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	92.191	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	92.669	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	69.95	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	93.395	no
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	56.068	no

Availability in culture collections External links

Culture collection no.

DSM 15669, AJ 13480, JCM 12116

SI-ID 134459

*

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Bombella intestini gen. nov., sp. nov., an acetic acid bacterium isolated from bumble bee crop.	Li L, Praet J, Borremans W, Nunes OC, Manaia CM, Cleenwerck I, Meeus I, Smagghe G, De Vuyst L, Vandamme P	Int J Syst Evol Microbiol	10.1099/ijs.0.068049-0	2014	*
Phylogeny	Saccharibacter floricola gen. nov., sp. nov., a novel osmophilic acetic acid bacterium isolated from pollen.	Jojima Y, Mihara Y, Suzuki S, Yokozeki K, Yamanaka S, Fudou R	Int J Syst Evol Microbiol	10.1099/ijs.0.02911-0	2004	*

References

#6023

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15669

#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 )

#23247

Yasuko Jojima, Yasuhiro Mihara, Sonoko Suzuki, Kenzo Yokozeki, Shigeru Yamanaka, Ryosuke Fudou: Saccharibacter floricola gen. nov., sp. nov., a novel osmophilic acetic acid bacterium isolated from pollen. IJSEM 54: 2263 - 2267 2004 ( DOI 10.1099/ijs.0.02911-0 , PubMed 15545468 )

#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 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#69747

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-ID134459.1 )

* These data were automatically processed and therefore are not curated

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