Bacteroides graminisolvens (CCUG 60910, DSM 19988, JCM 15093)

Name: Bacteroides graminisolvens (CCUG 60910, DSM 19988, JCM 15093)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1624

Type strain

Strain Designation XDT-1

Culture col. no. CCUG 60910 DSM 19988 JCM 15093 XDT-1 KCTC 15146

NCBI tax ID(s) 1121097 477666

Special Collections DSMZ CCUG JCM KCTC Literature strains

History DSMZ <- A. Ueki; XDT-1 JCM <-- A. Ueki XDT-1.

Links

Bacteroides graminisolvens XDT-1 is an anaerobe, Gram-negative, rod-shaped bacterium that was isolated from rice straw residue from a methanogenic reactor.

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

Name and taxonomic classification

SI-ID 404109

JCM 15093,DSM 19988,CCUG 60910T

@ref 20215

Last LPSN update 2026-05-29 08:25:18

Domain Bacteria

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Bacteroidaceae

Genus Bacteroides

Species Bacteroides graminisolvens

Full scientific name Bacteroides graminisolvens Nishiyama et al. 2009

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29190	negative	2.85 µm	0.5 µm	rod-shaped
125438	negative				90.359
125439	negative				97.868

Colony morphology

@ref	Incubation period
8354	1-2 days
62493	1 day

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
8354	COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)		Medium recipe at MediaDive	Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
8354	CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)		Medium recipe at MediaDive	Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
8354	positive	growth	35
8354	positive	growth	30-37
29190	positive	growth	05-40
29190	positive	optimum	33
62493	positive	growth	37
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH
29190	positive	optimum	7.2

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
8354	anaerobe
29190	anaerobe
62493	anaerobe
125439	facultative anaerobe	92.077

Spore formation

@ref	Spore formation	Confidence
29190
125439		99.84
125438		93.978

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29190	NaCl	positive	growth	0-4 %

Observation

67770

Observationquinones: MK-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29190	30089 ChEBI	acetate	+	carbon source
29190	22599 ChEBI	arabinose	+	carbon source
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
29190	17057 ChEBI	cellobiose	+	carbon source
68380	16024 ChEBI	D-mannose	+	fermentation	from API rID32A
29190	23652 ChEBI	dextrin	+	carbon source
29190	4853 ChEBI	esculin	+	hydrolysis
29190	28757 ChEBI	fructose	+	carbon source
29190	28260 ChEBI	galactose	+	carbon source
29190	17234 ChEBI	glucose	+	carbon source
29190	28087 ChEBI	glycogen	+	carbon source
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
29190	17716 ChEBI	lactose	+	carbon source
29190	17306 ChEBI	maltose	+	carbon source
29190	37684 ChEBI	mannose	+	carbon source
29190	28053 ChEBI	melibiose	+	carbon source
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
29190	17272 ChEBI	propionate	+	carbon source
29190	16634 ChEBI	raffinose	+	carbon source
68380	16634 ChEBI	raffinose	-	fermentation	from API rID32A
29190	26546 ChEBI	rhamnose	+	carbon source
29190	33942 ChEBI	ribose	+	carbon source
29190	17814 ChEBI	salicin	+	carbon source
29190	17992 ChEBI	sucrose	+	carbon source
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A
29190	18222 ChEBI	xylose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68380	35581 ChEBI	indole		from API rID32A

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68380	35581 ChEBI	indole	-	from API rID32A

Enzymes

@ref	Value	Activity	Ec
68380	alanine arylamidase	+	3.4.11.2	from API rID32A
68380	alkaline phosphatase	+	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	+	3.2.1.55	from API rID32A
68380	alpha-fucosidase	-	3.2.1.51	from API rID32A
68380	alpha-galactosidase	-	3.2.1.22	from API rID32A
68380	alpha-glucosidase	+	3.2.1.20	from API rID32A
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68380	beta-galactosidase	+	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68380	beta-glucosidase	+	3.2.1.21	from API rID32A
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
68380	glutamate decarboxylase	-	4.1.1.15	from API rID32A
68380	glycin arylamidase	-		from API rID32A
68380	histidine arylamidase	-		from API rID32A
68380	L-arginine arylamidase	-		from API rID32A
68380	leucine arylamidase	-	3.4.11.1	from API rID32A
68380	leucyl glycin arylamidase	+	3.4.11.1	from API rID32A
68380	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API rID32A
68380	phenylalanine arylamidase	-		from API rID32A
68380	proline-arylamidase	-	3.4.11.5	from API rID32A
68380	pyrrolidonyl arylamidase	-	3.4.19.3	from API rID32A
68380	serine arylamidase	-		from API rID32A
68380	tryptophan deaminase	-	4.1.99.1	from API rID32A
68380	tyrosine arylamidase	-		from API rID32A
68380	urease	-	3.5.1.5	from API rID32A

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	gluconeogenesis	100	8 of 8
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	suberin monomers biosynthesis	100	2 of 2
66794	starch degradation	100	10 of 10
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	glycogen metabolism	100	5 of 5
66794	teichoic acid biosynthesis	100	1 of 1
66794	palmitate biosynthesis	100	22 of 22
66794	coenzyme A metabolism	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	methylglyoxal degradation	100	5 of 5
66794	folate polyglutamylation	100	1 of 1
66794	lipid A biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	propanol degradation	85.71	6 of 7
66794	vitamin B1 metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	pyrimidine metabolism	82.22	37 of 45
66794	pentose phosphate pathway	81.82	9 of 11
66794	lipoate biosynthesis	80	4 of 5
66794	vitamin K metabolism	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	threonine metabolism	80	8 of 10
66794	photosynthesis	78.57	11 of 14
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	serine metabolism	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	alanine metabolism	75.86	22 of 29
66794	ppGpp biosynthesis	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	biotin biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	vitamin B6 metabolism	72.73	8 of 11
66794	proline metabolism	72.73	8 of 11
66794	purine metabolism	72.34	68 of 94
66794	glutamate and glutamine metabolism	71.43	20 of 28
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	citric acid cycle	71.43	10 of 14
66794	Entner Doudoroff pathway	70	7 of 10
66794	propionate fermentation	70	7 of 10
66794	phenylalanine metabolism	69.23	9 of 13
66794	vitamin B12 metabolism	67.65	23 of 34
66794	acetoin degradation	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	glycolysis	64.71	11 of 17
66794	metabolism of disaccharids	63.64	7 of 11
66794	d-xylose degradation	63.64	7 of 11
66794	degradation of sugar alcohols	62.5	10 of 16
66794	leucine metabolism	61.54	8 of 13
66794	degradation of hexoses	61.11	11 of 18
66794	myo-inositol biosynthesis	60	6 of 10
66794	hydrogen production	60	3 of 5
66794	non-pathway related	57.89	22 of 38
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	methionine metabolism	57.69	15 of 26
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	lysine metabolism	57.14	24 of 42
66794	degradation of sugar acids	56	14 of 25
66794	lipid metabolism	51.61	16 of 31
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	pantothenate biosynthesis	50	3 of 6
66794	degradation of pentoses	50	14 of 28
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	adipate degradation	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	ketogluconate metabolism	50	4 of 8
66794	glycine metabolism	50	5 of 10
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	histidine metabolism	48.28	14 of 29
66794	polyamine pathway	47.83	11 of 23
66794	tryptophan metabolism	47.37	18 of 38
66794	cysteine metabolism	44.44	8 of 18
66794	CO2 fixation in Crenarchaeota	44.44	4 of 9
66794	oxidative phosphorylation	43.96	40 of 91
66794	heme metabolism	42.86	6 of 14
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	tyrosine metabolism	42.86	6 of 14
66794	ascorbate metabolism	40.91	9 of 22
66794	arachidonate biosynthesis	40	2 of 5
66794	O-antigen biosynthesis	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	sulfate reduction	38.46	5 of 13
66794	arginine metabolism	37.5	9 of 24
66794	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
66794	IAA biosynthesis	33.33	1 of 3
66794	nitrate assimilation	33.33	3 of 9
66794	sphingosine metabolism	33.33	2 of 6
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	urea cycle	30.77	4 of 13
66794	coenzyme M biosynthesis	30	3 of 10
66794	vitamin E metabolism	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	glutathione metabolism	21.43	3 of 14

API rID32A

@ref	URE	ADH (Arg)	alpha GAL	beta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha GLU	beta GLU	alpha ARA	beta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	MNE	RAF	GDC	alpha FUC	Reduction of nitrateNIT	IND	PAL	L-arginine arylamidaseArgA	ProA	LGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	PyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
8354	-	-	-	+	-	+	+	+	-	-	+	-	-	-	-	-	+	-	-	+	-	-	-	-	+	-	-	+/-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Bioreactor	-
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Condition	#Anoxic (anaerobic)	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Sampling date
8354	rice straw residue from a methanogenic reactor	Hokkaido, Betsukai-machi	Japan	JPN	Asia
62493	Rice straw residue from methanogenic reactor		Japan	JPN	Asia	2000
67770	Rice-straw residue in a methanogenic reacter treating waste from cattle farms

Taxonmaps

69479

Global distribution of 16S sequence AB547643 (>99% sequence identity) for Bacteroides graminisolvens subclade from Microbeatlas

Aquatic Samples	21442
Soil Samples	2465
Animal Samples	44247
Plant Samples	705
Total Samples	68859

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8354	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM42812v1 assembly for Bacteroides graminisolvens DSM 19988 = JCM 15093	scaffold	GCA_000428125	1121097.3	2524614553	1121097	70.68
67770	ASM61382v1 assembly for Bacteroides graminisolvens DSM 19988 = JCM 15093	contig	GCA_000613825	1236499.3	2585427863	1121097	54.82

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Bacteroides graminisolvens gene for 16S ribosomal RNA, partial sequence, strain: JCM 15093	AB547643	1486		477666
8354	Bacteroides graminisolvens gene for 16S ribosomal RNA, partial sequence	AB363973	1415		477666

GC content

@ref	GC-content (mol%)	Method
8354	38.0	high performance liquid chromatography (HPLC)
29190	38
8354	41.5	sequence analysis
67770	38	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: ASM42812v1 assembly for Bacteroides graminisolvens DSM 19988 = JCM 15093
BV-BRC: 1121097.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	92.08	no
125439	gram_stain	BacteriaNetⓘ	negative	97.87	no
125439	motility	BacteriaNetⓘ	no	75.80	no
125439	spore_formation	BacteriaNetⓘ	no	99.84	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Bacteroides graminisolvens DSM 19988
PATRIC: 1121097.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	90.36	no
125438	anaerobic	anaerobicⓘ	yes	86.63	yes
125438	spore-forming	spore-formingⓘ	no	93.98	yes
125438	aerobic	aerobicⓘ	no	93.65	yes
125438	thermophilic	thermophileⓘ	no	94.72	yes
125438	flagellated	motile2+ⓘ	no	89.60	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	Identification and cultivation of anaerobic bacterial scavengers of dead cells.	Hirakata Y, Mei R, Morinaga K, Katayama T, Tamaki H, Meng XY, Watari T, Yamaguchi T, Hatamoto M, Nobu MK.	ISME J	10.1038/s41396-023-01538-2	2023
Metabolism	Isolation and characterization of Arthrobacter sp. HY2 capable of degrading a high concentration of p-nitrophenol.	Qiu X, Wu P, Zhang H, Li M, Yan Z.	Bioresour Technol	10.1016/j.biortech.2009.05.056	2009
Genetics	Distribution and evolution of nitrogen fixation genes in the phylum Bacteroidetes.	Inoue J, Oshima K, Suda W, Sakamoto M, Iino T, Noda S, Hongoh Y, Hattori M, Ohkuma M	Microbes Environ	10.1264/jsme2.ME14142	2015
Genetics	'Bacteroides ihuae' sp. nov., a new bacterial species isolated from the human respiratory microbiome.	Fonkou MD, Morand A, Fournier PE, Raoult D, Dubourg G.	New Microbes New Infect	10.1016/j.nmni.2017.01.011	2017
Phylogeny	Bacteroides graminisolvens sp. nov., a xylanolytic anaerobe isolated from a methanogenic reactor treating cattle waste.	Nishiyama T, Ueki A, Kaku N, Watanabe K, Ueki K	Int J Syst Evol Microbiol	10.1099/ijs.0.008268-0	2009

References

#8354	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19988
#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 )
#25614	IJSEM 1901 2009 ( DOI 10.1099/ijs.0.008268-0 , PubMed 19567576 )
#29190	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 #25614
#62493	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 60910
#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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68380	Automatically annotated from API rID32A .
#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 .
#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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Bacteroides graminisolvens (CCUG 60910, DSM 19988, JCM 15093)

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

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000428125

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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