Name: Gulosibacter bifidus S7-7
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 7478

Type strain:

Species: Gulosibacter bifidus

Strain Designation: S7-7

Culture col. no.: CCUG 50209, DSM 17450, IAM 14848, TISTR 1511, JCM 12920, CIP 108567, NBRC 103089

Strain history: CIP <- 2004, IAM <- A. Yokota, Tokyo Univ., Tokyo, Japan: strani S7-7

NCBI tax ID(s): 272239 (species)

SI-ID 134311

IAM 14848, TISTR 1511, CCUG 50209, JCM 12920, DSM 17450, CIP 108567, NBRC 103089

Special Collections

Other strains from Gulosibacter bifidus

Section

Gulosibacter bifidus S7-7 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from soil.

Gram-positive
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	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micrococcales*
	Family	*Microbacteriaceae*
	Genus	*Gulosibacter*
	Species	**Gulosibacter bifidus**
	Full Scientific Name (LPSN)	Gulosibacter bifidus (Lin et al. 2004) Nouioui et al. 2018

	Synonym	"Pseudoclavibacter* bifida"*
	Synonym	Zimmermannella bifida

Information on morphological and physiological properties Morphology

[Ref.: #29956]	Gram stain	positive
[Ref.: #116808]	Gram stain	positive

[Ref.: #29956]	Cell length	2.25 µm

[Ref.: #29956]	Cell width	0.35 µm

[Ref.: #29956]	Cell shape	rod-shaped
[Ref.: #116808]	Cell shape	rod-shaped

[Ref.: #29956]	Motility	no
[Ref.: #116808]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %92

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6991]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #6991]

Culture medium growth

[Ref.: #6991]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6991]

Culture medium composition

expand / minimize

[Ref.: #33252]

Culture medium

MEDIUM 6 - Columbia agar with 10 % horse blood

[Ref.: #33252]

Culture medium growth

[Ref.: #33252]

Culture medium composition

expand / minimize

[Ref.: #116808]

Culture medium

CIP Medium 6

[Ref.: #116808]

Culture medium growth

[Ref.: #116808]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #6991]		growth	28 °C
[Ref.: #29956]		optimum	30 °C
[Ref.: #33252]		growth	30 °C
[Ref.: #58787]		growth	30-42 °C
[Ref.: #67770]		growth	28 °C
[Ref.: #116808]		growth	25-41 °C
[Ref.: #116808]	no	growth	10 °C
[Ref.: #116808]	no	growth	15 °C
[Ref.: #116808]	no	growth	45 °C

	pH	Kind of pH		pH
[Ref.: #29956]			optimum	7

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29956]	Oxygen tolerance	aerobe
[Ref.: #116808]	Oxygen tolerance	obligate aerobe

[Ref.: #29956]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Salt		Salt conc.
[Ref.: #29956]	NaCl	growth	0.2-0.3	%
[Ref.: #29956]	NaCl	optimum	0.25	%
[Ref.: #116808]	NaCl	growth	0-10	%

[Ref.: #67770]

Observation

quinones: MK-8, MK-9

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #116808]	citrate ChEBI	-	carbon source
[Ref.: #116808]	esculin ChEBI	-	hydrolysis
[Ref.: #116808]	hippurate ChEBI	+	hydrolysis
[Ref.: #116808]	nitrate ChEBI	-	reduction
[Ref.: #116808]	nitrate ChEBI	-	respiration
[Ref.: #116808]	nitrite ChEBI	-	reduction

	Antibiotica	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #116808]		0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)	no	yes

	Metabolite production	Metabolite	Production
[Ref.: #116808]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #116808]		acetoin ChEBI	+
[Ref.: #116808]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #116808]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #29956]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #116808]	amylase	+
[Ref.: #116808]	beta-galactosidase	-	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #116808]	caseinase	-	3.4.21.50
[Ref.: #29956]	catalase	+	1.11.1.6
[Ref.: #116808]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	+	3.4.11.3	* from API zym
[Ref.: #116808]	DNase	-
[Ref.: #68382]	esterase (C 4)	-		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #116808]	gamma-glutamyltransferase	-	2.3.2.2
[Ref.: #116808]	gelatinase	-
[Ref.: #116808]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #116808]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #116808]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #116808]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #116808]	oxidase	-
[Ref.: #116808]	phenylalanine ammonia-lyase	-	4.3.1.24
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #116808]	tryptophan deaminase	-
[Ref.: #116808]	tween esterase	-
[Ref.: #116808]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® Biotype100:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
[Ref.: #116808]	2808	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #116808]	11290	-	+	-	-	-	+	+	+	-	-	+	+	-	-	-	-	-	-	-	-

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

[Ref.: #6991]	Sample type/isolated from	soil
[Ref.: #6991]	Country	Thailand
[Ref.: #6991]	Country ISO 3 Code	THA
[Ref.: #6991]	Continent	Asia

[Ref.: #58787]	Sample type/isolated from	Soil
[Ref.: #58787]	Geographic location (country and/or sea, region)	Nakhon Ratchasima Province
[Ref.: #58787]	Country	Thailand
[Ref.: #58787]	Country ISO 3 Code	THA
[Ref.: #58787]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Soil
[Ref.: #67770]	Geographic location (country and/or sea, region)	Nakhon Ratchasima Province
[Ref.: #67770]	Country	Thailand
[Ref.: #67770]	Country ISO 3 Code	THA
[Ref.: #67770]	Continent	Asia

[Ref.: #116808]	Sample type/isolated from	Environment, Soil
[Ref.: #116808]	Geographic location (country and/or sea, region)	Nakhon, Ratchasima
[Ref.: #116808]	Country	Thailand
[Ref.: #116808]	Country ISO 3 Code	THA
[Ref.: #116808]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB012595 (>99% sequence identity) for Gulosibacter bifidus subclade from Microbeatlas

Aquatic Samples	379
Soil Samples	119
Animal Samples	5198
Plant Samples	89
Total Samples	5785

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

[Ref.: #116808]

Biosafety level

Risk group (French classification)

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.: #6991]	Zimmermannella bifida gene for 16S rRNA, partial sequence, strain: IAM 14848	AB012595	1487	GenBank ENA	272239 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	[Zimmermannella] bifida NBRC 103089	GCA_001570925	contig	GenBank ENA	1349787 tax ID
[Ref.: #66792]	Zimmermannella bifida NBRC 103089	1349787.3	wgs	PATRIC	1349787 tax ID	*
[Ref.: #66792]	Pseudoclavibacter bifida NBRC 103089	2731957611	draft	JGI IMG/M	1349787 tax ID	*

[Ref.: #6991]	GC-content	62 mol%
[Ref.: #67770]	GC-content	62 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: Zimmermannella bifida NBRC 103089 PATRIC: 1349787.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Zimmermannella bifida NBRC 103089 PATRIC: 1349787.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	89.15	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	92.543	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	89.335	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	68.913	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	94.5	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	92	yes

Availability in culture collections External links

[Ref.: #6991]

Culture collection no.

CCUG 50209, DSM 17450, IAM 14848, TISTR 1511, JCM 12920, CIP 108567, NBRC 103089

[Ref.: #76923]

SI-ID 134311

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Gulosibacter macacae sp. nov., a novel actinobacterium isolated from Macaca mulatta faeces.	Li G, Li Q, Chen X, Jiang L, Zhang K, An D, Lang L, Jiang Y, Han L, Huang X, Jiang C	Int J Syst Evol Microbiol	10.1099/ijsem.0.004389	2020	*
Phylogeny	Zimmermannella helvola gen. nov., sp. nov., Zimmermannella alba sp. nov., Zimmermannella bifida sp. nov., Zimmermannella faecalis sp. nov. and Leucobacter albus sp. nov., novel members of the family Microbacteriaceae.	Lin YC, Uemori K, de Briel DA, Arunpairojana V, Yokota A	Int J Syst Evol Microbiol	10.1099/ijs.0.02741-0	2004	*
Phylogeny	Pseudoclavibacter soli sp. nov., a {beta}-glucosidase-producing bacterium.	Kim MK, Jung HY	Int J Syst Evol Microbiol	10.1099/ijs.0.65627-0	2009	*

References

#6991

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17450

#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 )

#29956

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 #26325 (see below)

#33252 ; Curators of the CIP;
#58787 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 50209

#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) .

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

#68382

Automatically annotated from API zym .

#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 )

#76923

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-ID134311.1 )

#116808 Collection of Institut Pasteur ; Curators of the CIP; CIP 108567

#26325

IJSEM 1669 2004 ( DOI 10.1099/ijs.0.02741-0 , PubMed 15388726 )

* These data were automatically processed and therefore are not curated

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Search for species Gulosibacter bifidus in external resources:
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Zimmermannella bifida NBRC 103089

Zimmermannella bifida NBRC 103089

Change proposal

Change proposal