Leadbetterella byssophila (DSM 17132, KACC 11308, 4M15)

Name: Leadbetterella byssophila (DSM 17132, KACC 11308, 4M15)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 3812

Type strain

Strain Designation 4M15

Culture col. no. DSM 17132 KACC 11308 4M15 NBRC 106382 JCM 16389

NCBI tax ID(s) 649349 316068

Special Collections DSMZ JCM Literature strains

History DSMZ <- S.-W. Kwon <- H.-Y. Weon; 4M15 JCM <-- KACC 11308 <-- H.-Y. Weon 4M15.

Links

Leadbetterella byssophila 4M15 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from cotton waste compost.

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

Name and taxonomic classification

SI-ID 281446

DSM 17132,KACC 11308,JCM 16389

@ref 20215

Last LPSN update 2026-05-29 08:25:47

Domain Bacteria

Phylum Bacteroidota

Class Cytophagia

Order Cytophagales

Family Spirosomataceae

Genus Leadbetterella

Species Leadbetterella byssophila

Full scientific name Leadbetterella byssophila Weon et al. 2005

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31525	negative	4.5 µm	0.75 µm	rod-shaped
125438					90.506
125438	negative				96.971
125439	negative				93.517

Colony morphology

@ref	Colony color	Medium used
27819	orange	TSA

Pigmentation

@ref	Production	Name
31525
27819		flexirubin type pigments

Multimedia

@ref:	66793
multimedia content:	EM_DSM_17132_1.jpg
multimedia.multimedia content:	EM_DSM_17132_1.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
6779	TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)		Medium recipe at MediaDive	Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water
27819	Trypticase Soy Agar (TSA)

Culture temp

@ref	Growth	Type	Temperature (°C)
6779	positive	growth	30
31525	positive	growth	15-45
31525	positive	optimum	30
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH
31525	positive	optimum	7
31525	positive	growth	06-08

Physiology and metabolism

Oxygen tolerance

31525

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
125439		98.634
125438		90.481

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31525	NaCl	positive	growth	0-1 %
31525	NaCl	positive	optimum	0.5 %

Observation

67770

Observationquinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31525	28644 ChEBI	2-oxopentanoate	+	carbon source
27819	2509 ChEBI	agar	-	hydrolysis
31525	16449 ChEBI	alanine	+	carbon source
31525	40585 ChEBI	alpha-cyclodextrin	+	carbon source
31525	22599 ChEBI	arabinose	+	carbon source
31525	35391 ChEBI	aspartate	+	carbon source
27819	85146 ChEBI	carboxymethylcellulose	-	hydrolysis
27819		casein	-	degradation
27819		casein	-	hydrolysis
31525	17057 ChEBI	cellobiose	+	carbon source
27819	62968 ChEBI	cellulose	-	degradation
27819	17029 ChEBI	chitin	-	degradation
31525	23652 ChEBI	dextrin	+	carbon source
27819	16991 ChEBI	dna	-	degradation
31525	4853 ChEBI	esculin	+	hydrolysis
27819	4853 ChEBI	esculin	+	degradation
31525	28757 ChEBI	fructose	+	carbon source
31525	33984 ChEBI	fucose	+	carbon source
31525	28260 ChEBI	galactose	+	carbon source
31525	24175 ChEBI	galacturonate	+	carbon source
27819	5291 ChEBI	gelatin	+	degradation
27819	5291 ChEBI	gelatin	+	hydrolysis
31525	17234 ChEBI	glucose	+	carbon source
31525	29987 ChEBI	glutamate	+	carbon source
31525	28087 ChEBI	glycogen	+	carbon source
31525	21217 ChEBI	L-alaninamide	+	carbon source
31525	18403 ChEBI	L-arabitol	+	carbon source
31525	17716 ChEBI	lactose	+	carbon source
31525	17306 ChEBI	maltose	+	carbon source
31525	37684 ChEBI	mannose	+	carbon source
31525	28053 ChEBI	melibiose	+	carbon source
31525	37657 ChEBI	methyl D-glucoside	+	carbon source
31525	51850 ChEBI	methyl pyruvate	+	carbon source
31525	506227 ChEBI	N-acetylglucosamine	+	carbon source
27819	17632 ChEBI	nitrate	-	reduction
31525	18257 ChEBI	ornithine	+	carbon source
31525	16634 ChEBI	raffinose	+	carbon source
31525	26546 ChEBI	rhamnose	+	carbon source
31525	17814 ChEBI	salicin	+	carbon source
31525	17822 ChEBI	serine	+	carbon source
27819	28017 ChEBI	starch	+	degradation
27819	28017 ChEBI	starch	+	hydrolysis
31525	17992 ChEBI	sucrose	+	carbon source
31525	26986 ChEBI	threonine	+	carbon source
31525	17748 ChEBI	thymidine	+	carbon source
31525	27082 ChEBI	trehalose	+	carbon source
31525	53424 ChEBI	tween 20	+	carbon source
27819	53424 ChEBI	tween 20	+	degradation
27819	53423 ChEBI	tween 40	-	degradation
27819	53426 ChEBI	tween 80	-	degradation
27819	18186 ChEBI	tyrosine	+	degradation
31525	16704 ChEBI	uridine	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
31525	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
31525	35581 ChEBI	indole	+

Enzymes

@ref	Value	Activity	Ec
31525	acid phosphatase	+	3.1.3.2
31525	alkaline phosphatase	+	3.1.3.1
27819	alpha-fucosidase	+	3.2.1.51
31525	alpha-galactosidase	+	3.2.1.22
27819	alpha-galactosidase	+/-	3.2.1.22
27819	alpha-glucosidase	+	3.2.1.20
27819	arginine dihydrolase	-	3.5.3.6
27819	beta-galactosidase	+/-	3.2.1.23
27819	beta-glucosidase	+	3.2.1.21
31525	catalase	+	1.11.1.6
31525	cytochrome oxidase	+	1.9.3.1
27819	leucine arylamidase	+	3.4.11.1
27819	N-acetyl-beta-glucosaminidase	+	3.2.1.52
27819	naphthol-AS-BI-phosphohydrolase	+
27819	valine arylamidase	+

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	ceramide biosynthesis	100	1 of 1
66794	gluconeogenesis	100	8 of 8
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	ppGpp biosynthesis	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	suberin monomers biosynthesis	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	kanosamine biosynthesis II	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	palmitate biosynthesis	100	22 of 22
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	Entner Doudoroff pathway	90	9 of 10
66794	NAD metabolism	88.89	16 of 18
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	d-mannose degradation	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	isoleucine metabolism	87.5	7 of 8
66794	heme metabolism	85.71	12 of 14
66794	photosynthesis	85.71	12 of 14
66794	purine metabolism	85.11	80 of 94
66794	vitamin B1 metabolism	84.62	11 of 13
66794	proline metabolism	81.82	9 of 11
66794	lipoate biosynthesis	80	4 of 5
66794	methylglyoxal degradation	80	4 of 5
66794	vitamin K metabolism	80	4 of 5
66794	threonine metabolism	80	8 of 10
66794	pyrimidine metabolism	80	36 of 45
66794	cellulose degradation	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	valine metabolism	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	ketogluconate metabolism	75	6 of 8
66794	degradation of sugar alcohols	75	12 of 16
66794	CMP-KDO biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	lactate fermentation	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	alanine metabolism	72.41	21 of 29
66794	glutathione metabolism	71.43	10 of 14
66794	tyrosine metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	lysine metabolism	71.43	30 of 42
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	propanol degradation	71.43	5 of 7
66794	citric acid cycle	71.43	10 of 14
66794	glycolysis	70.59	12 of 17
66794	starch degradation	70	7 of 10
66794	propionate fermentation	70	7 of 10
66794	leucine metabolism	69.23	9 of 13
66794	glutamate and glutamine metabolism	67.86	19 of 28
66794	lipid metabolism	67.74	21 of 31
66794	cysteine metabolism	66.67	12 of 18
66794	peptidoglycan biosynthesis	66.67	10 of 15
66794	formaldehyde oxidation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	histidine metabolism	65.52	19 of 29
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	methionine metabolism	65.38	17 of 26
66794	d-xylose degradation	63.64	7 of 11
66794	pentose phosphate pathway	63.64	7 of 11
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	degradation of hexoses	61.11	11 of 18
66794	degradation of pentoses	60.71	17 of 28
66794	myo-inositol biosynthesis	60	6 of 10
66794	arachidonate biosynthesis	60	3 of 5
66794	glycine betaine biosynthesis	60	3 of 5
66794	coenzyme M biosynthesis	60	6 of 10
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	non-pathway related	57.89	22 of 38
66794	degradation of sugar acids	56	14 of 25
66794	tryptophan metabolism	55.26	21 of 38
66794	arginine metabolism	54.17	13 of 24
66794	sulfate reduction	53.85	7 of 13
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	biotin biosynthesis	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	phenylmercury acetate degradation	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	urea cycle	46.15	6 of 13
66794	oxidative phosphorylation	43.96	40 of 91
66794	polyamine pathway	43.48	10 of 23
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	elloramycin biosynthesis	40	2 of 5
66794	phenylacetate degradation (aerobic)	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	gallate degradation	40	2 of 5
66794	4-hydroxyphenylacetate degradation	40	4 of 10
66794	D-cycloserine biosynthesis	40	2 of 5
66794	O-antigen biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	metabolism of disaccharids	36.36	4 of 11
66794	octane oxidation	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	3-phenylpropionate degradation	33.33	5 of 15
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	ascorbate metabolism	31.82	7 of 22
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	phenol degradation	30	6 of 20
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	toluene degradation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	butanoate fermentation	25	1 of 4
66794	allantoin degradation	22.22	2 of 9
66794	4-hydroxymandelate degradation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	-
#Engineered	#Biodegradation	#Composting
#Engineered	#Waste	#Solid plant waste
#Host	#Plants	#Shrub (Scrub)

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
6779	cotton waste compost	Republic of Korea	KOR	Asia
67770	Cotton-waste composts used as oyster mushroom cultivation	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence AY854022 (>99% sequence identity) for Leadbetterella byssophila subclade from Microbeatlas

Aquatic Samples	1993
Soil Samples	947
Animal Samples	2059
Plant Samples	147
Total Samples	5146

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6779	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
66792	ASM16639v1 assembly for Leadbetterella byssophila DSM 17132	complete	GCA_000166395	649349.3	649633063	649349	99.29

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6779	Leadbetterella byssophila strain 4M15 16S ribosomal RNA gene, partial sequence	AY854022	1457		649349
124043	Leadbetterella byssophila gene for 16S rRNA, partial sequence, strain: NBRC 106382.	AB682398	1426		316068

GC content

@ref	GC-content (mol%)	Method
6779	33.0
31525	33
6779	40.4	sequence analysis
67770	33	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: ASM16639v1 assembly for Leadbetterella byssophila DSM 17132
BV-BRC: 649349.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	81.46	no
125439	gram_stain	BacteriaNetⓘ	negative	93.52	no
125439	motility	BacteriaNetⓘ	no	76.91	no
125439	spore_formation	BacteriaNetⓘ	no	98.63	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Leadbetterella byssophila DSM 17132 DSM 17132
NCBI: GCA_000166395.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.97	yes
125438	anaerobic	anaerobicⓘ	no	95.57	yes
125438	aerobic	aerobicⓘ	yes	85.41	yes
125438	spore-forming	spore-formingⓘ	no	90.48	no
125438	thermophilic	thermophileⓘ	no	95.36	no
125438	flagellated	motile2+ⓘ	no	90.51	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Bacterial endosymbiont Cardinium cSfur genome sequence provides insights for understanding the symbiotic relationship in Sogatella furcifera host.	Zeng Z, Fu Y, Guo D, Wu Y, Ajayi OE, Wu Q.	BMC Genomics	10.1186/s12864-018-5078-y	2018
	Complete genome sequence of Leadbetterella byssophila type strain (4M15).	Abt B, Teshima H, Lucas S, Lapidus A, Del Rio TG, Nolan M, Tice H, Cheng JF, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Goker M, Tindall BJ, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC.	Stand Genomic Sci	10.4056/sigs.1413518	2011
Enzymology	The beta-glucanase ZgLamA from Zobellia galactanivorans evolved a bent active site adapted for efficient degradation of algal laminarin.	Labourel A, Jam M, Jeudy A, Hehemann JH, Czjzek M, Michel G.	J Biol Chem	10.1074/jbc.m113.538843	2014
Phylogeny	Lacihabitans soyangensis gen. nov., sp. nov., a new member of the family Cytophagaceae, isolated from a freshwater reservoir.	Joung Y, Kim H, Kang H, Lee BI, Ahn TS, Joh K.	Int J Syst Evol Microbiol	10.1099/ijs.0.058511-0	2014
Phylogeny	Leadbetterella byssophila gen. nov., sp. nov., isolated from cotton-waste composts for the cultivation of oyster mushroom.	Weon HY, Kim BY, Kwon SW, Park IC, Cha IB, Tindall BJ, Stackebrandt E, Truper HG, Go SJ	Int J Syst Evol Microbiol	10.1099/ijs.0.63741-0	2005

References

#6779	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17132
#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 )
#27819	IJSEM 2297 2005 ( DOI 10.1099/ijs.0.63741-0 , PubMed 16280486 )
#31525	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 #27819
#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 )
#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;
#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 .
#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 )

Content

About us

Leadbetterella byssophila (DSM 17132, KACC 11308, 4M15)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Multimedia

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

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000166395

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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