Gulosibacter bifidus (CCUG 50209, DSM 17450, IAM 14848)

Name: Gulosibacter bifidus (CCUG 50209, DSM 17450, IAM 14848)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7478

Type strain

Strain Designation S7-7

Culture col. no. CCUG 50209 DSM 17450 IAM 14848 TISTR 1511 S7-7 3 more

NCBI tax ID(s) 272239

Special Collections DSMZ CCUG JCM CIP Literature strains

History <- IAM <- TISTR (Zimmermannella bifida) IAM 14848 <-- A. Yokota S7-7. CIP <- 2004, IAM <- A. Yokota, Tokyo Univ., Tokyo, Japan: strani S7-7

Links

Gulosibacter bifidus S7-7 is an aerobe, mesophilic, Gram-positive prokaryote that was isolated from soil.

Gram-positive rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 134311

LMG 31815,IAM 14848,TISTR 1511,CCUG 50209,JCM 12920,DSM 17450,CIP 108567,NBRC 103089

@ref 20215

Last LPSN update 2025-12-16 09:48:35

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Microbacteriaceae

Genus Gulosibacter

Species Gulosibacter bifidus

Full scientific name Gulosibacter bifidus (Lin et al. 2004) Nouioui et al. 2018

Synonyms (2)

Zimmermannella bifida
"Pseudoclavibacter bifida"

BacDive ID	Other strains from **Gulosibacter bifidus** (2)	Type strain
136047	G. bifidus CIP 102131, IFO 15777, CCUG 50210, IAM 15028, ...
153569	G. bifidus CCUG 50211, IFO 15614, IAM 15029, TISTR 1513, ...

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29956	positive	2.25 µm	0.35 µm	rod-shaped
116808	positive			rod-shaped
125438					92
125439	positive				92.8

Colony morphology

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6991	TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)	Medium recipe at MediaDive	Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
33252	MEDIUM 6 - Columbia agar with 10 % horse blood		Distilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
116808	CIP Medium 6	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
6991	positive	growth	28	mesophilic
29956	positive	optimum	30	mesophilic
33252	positive	growth	30	mesophilic
58787	positive	growth	30-42
67770	positive	growth	28	mesophilic
116808	positive	growth	25-41
116808	negative	growth	10
116808	negative	growth	15
116808	negative	growth	45

Culture pH

@ref	Ability	Type	PH
29956	positive	optimum	7

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29956	aerobe
116808	obligate aerobe
125439	obligate aerobe	95.2

Spore formation

29956

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29956	NaCl	positive	growth	0.2-0.3 %
29956	NaCl	positive	optimum	0.25 %
116808	NaCl	positive	growth	0-10 %

Observation

67770

Observationquinones: MK-8, MK-9

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
116808	16947 ChEBI	citrate	-	carbon source
116808	4853 ChEBI	esculin	-	hydrolysis
116808	606565 ChEBI	hippurate	+	hydrolysis
116808	17632 ChEBI	nitrate	-	reduction
116808	17632 ChEBI	nitrate	-	respiration
116808	16301 ChEBI	nitrite	-	reduction

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
116808	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
116808	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
116808	15688 ChEBI	acetoin	+
116808	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
116808	alcohol dehydrogenase	-	1.1.1.1
29956	alkaline phosphatase	+	3.1.3.1
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
116808	amylase	+
68382	beta-galactosidase	-	3.2.1.23	from API zym
116808	beta-galactosidase	-	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
116808	caseinase	-	3.4.21.50
29956	catalase	+	1.11.1.6
116808	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
116808	DNase	-
68382	esterase (C 4)	-		from API zym
68382	esterase lipase (C 8)	-		from API zym
116808	gamma-glutamyltransferase	-	2.3.2.2
116808	gelatinase	-
116808	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
116808	lipase	-
68382	lipase (C 14)	-		from API zym
116808	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
116808	ornithine decarboxylase	-	4.1.1.17
116808	oxidase	-
116808	phenylalanine ammonia-lyase	-	4.3.1.24
68382	trypsin	-	3.4.21.4	from API zym
116808	tryptophan deaminase	-
116808	tween esterase	-
116808	urease	-	3.5.1.5
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
116808	-	+	-	-	-	+	+	+	-	-	+	+	-	-	-	-	-	-	-	-

API biotype100

@ref	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
116808	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
6991	soil		Thailand	THA	Asia
58787	Soil	Nakhon Ratchasima Province	Thailand	THA	Asia
67770	Soil	Nakhon Ratchasima Province	Thailand	THA	Asia
116808	Environment, Soil	Nakhon, Ratchasima	Thailand	THA	Asia

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
116808	1	Risk group (French 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	ASM4268530v1 assembly for Gulosibacter bifidus TISTR 1511	scaffold	GCA_042685305			272239	72
67770	ASM157092v1 assembly for [Zimmermannella] bifida NBRC 103089	contig	GCA_001570925	1349787.3	2731957611	1349787	70.08

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6991	Zimmermannella bifida gene for 16S rRNA, partial sequence, strain: IAM 14848	AB012595	1487		272239

GC content

@ref	GC-content (mol%)	Method
6991	62
67770	62	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: [Zimmermannella] bifida NBRC 103089
NCBI: GCA_001570925

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	82.80	no
125439	motility	BacteriaNetⓘ	no	88.80	no
125439	gram_stain	BacteriaNetⓘ	positive	92.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	95.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Zimmermannella bifida NBRC 103089
PATRIC: 1349787.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	89.15	no
125438	anaerobic	anaerobicⓘ	no	92.54	yes
125438	spore-forming	spore-formingⓘ	no	89.34	no
125438	aerobic	aerobicⓘ	yes	68.91	yes
125438	thermophilic	thermophileⓘ	no	94.50	yes
125438	flagellated	motile2+ⓘ	no	92.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genome-Based Taxonomic Classification of the Phylum Actinobacteria.	Nouioui I, Carro L, Garcia-Lopez M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Goker M.	Front Microbiol	10.3389/fmicb.2018.02007	2018
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 )
#26325	IJSEM 1669 2004 ( DOI 10.1099/ijs.0.02741-0 , PubMed 15388726 )
#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
#33252	; Curators of the CIP;
#58787	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 50209
#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 .
#116808	Collection of Institut Pasteur ; Curators of the CIP; CIP 108567
#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 )

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Gulosibacter bifidus (CCUG 50209, DSM 17450, IAM 14848)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

API zym

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_042685305

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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