Lentimicrobium saccharophilum (JCM 30898, DSM 100618, TBC1)

Name: Lentimicrobium saccharophilum (JCM 30898, DSM 100618, TBC1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 140821

Type strain

Strain Designation TBC1

Culture col. no. JCM 30898 DSM 100618 TBC1

NCBI tax ID(s) 1678841

Special Collections DSMZ JCM Literature strains

History <- Y. Sekiguchi, AIST; TBC1 Y. Sekiguchi; Biomed. Res. Inst., AIST, Japan; TBC1.

Links

Lentimicrobium saccharophilum TBC1 is an obligate anaerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from methanogenic granular sludge in a full-scale mesophilic UASB reactor treating high-strength starch-based organic wastewater discharged from a sweet corn canning plant.

Gram-negative rod-shaped colony-forming obligate anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 408372

JCM 30898,DSM 100618

@ref 20215

Last LPSN update 2026-02-09 11:33:43

Domain Bacteria

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Lentimicrobiaceae

Genus Lentimicrobium

Species Lentimicrobium saccharophilum

Full scientific name Lentimicrobium saccharophilum Sun et al. 2016

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
43611	negative	2-4 µm	0.4-0.6 µm	rod-shaped
125438	negative					94.332

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
43611	0.5 mm	White	circular	14 days	Basal medium

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
66455	ANAEROBIC FRESHWATER (FWM) MEDIUM (DSMZ Medium 503)		Medium recipe at MediaDive	Name: ANAEROBIC FRESHWATER (FWM) MEDIUM (DSMZ Medium 503) Composition: D-Glucose 4.98504 g/l Na2CO3 1.49551 g/l NaCl 0.997008 g/l KCl 0.498505 g/l MgCl2 x 6 H2O 0.398803 g/l Na2S x 9 H2O 0.299103 g/l NH4Cl 0.249252 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149552 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498505 g/l NaOH 0.000498504 g/l Pyridoxine hydrochloride 0.000299103 g/l Nicotinic acid 0.000199402 g/l Thiamine-HCl x 2 H2O 0.000199402 g/l CoCl2 x 6 H2O 0.000189432 g/l Calcium pantothenate 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l Vitamin B12 9.97009e-05 g/l p-Aminobenzoic acid 7.97607e-05 g/l ZnCl2 6.97906e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l D-(+)-biotin 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Distilled water
43611	Basal medium

Culture temp

@ref	Growth	Type	Temperature (°C)
43611	positive	growth	20-40
43611	positive	optimum	30-37
66455	positive	growth	35
67770	positive	growth	37

Culture pH

@ref	Ability	Type	PH	PH range
43611	positive	optimum	7
43611	positive	growth	6.5-9	alkaliphile

Physiology and metabolism

Oxygen tolerance

43611

Oxygen toleranceobligate anaerobe

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43611	30089 ChEBI	acetate	-	assimilation
43611	22599 ChEBI	arabinose	-	assimilation
43611	16150 ChEBI	benzoate	-	assimilation
43611	17750 ChEBI	betaine	-	assimilation
43611	17968 ChEBI	butyrate	-	assimilation
43611		casamino acids	-	assimilation
43611	35899 ChEBI	crotonate	-	assimilation
43611	33403 ChEBI	elemental sulfur	-	electron acceptor
43611	16236 ChEBI	ethanol	-	assimilation
43611	28757 ChEBI	fructose	-	assimilation
43611	29806 ChEBI	fumarate	-	assimilation
43611	29806 ChEBI	fumarate	-	electron acceptor
43611	28260 ChEBI	galactose	-	assimilation
43611	17754 ChEBI	glycerol	-	assimilation
43611	24996 ChEBI	lactate	-	assimilation
43611	17790 ChEBI	methanol	-	assimilation
43611	17632 ChEBI	nitrate	-	electron acceptor
43611	17309 ChEBI	pectin	-	assimilation
43611		peptone	-	assimilation
43611	28831 ChEBI	propanol	-	assimilation
43611	17272 ChEBI	propionate	-	assimilation
43611	16634 ChEBI	raffinose	-	assimilation
43611	30031 ChEBI	succinate	-	assimilation
43611	16189 ChEBI	sulfate	-	electron acceptor
43611	17359 ChEBI	sulfite	-	electron acceptor
43611	16094 ChEBI	thiosulfate	-	electron acceptor
43611		tryptone	-	assimilation
43611	37166 ChEBI	xylan	-	assimilation
43611		yeast extract	+	required for growth

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	L-lactaldehyde degradation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	glycogen metabolism	100	5 of 5
66794	palmitate biosynthesis	100	22 of 22
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	kanosamine biosynthesis II	100	2 of 2
66794	vitamin K metabolism	100	5 of 5
66794	coenzyme A metabolism	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	denitrification	100	2 of 2
66794	suberin monomers biosynthesis	100	2 of 2
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	serine metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	gluconeogenesis	87.5	7 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	87.5	7 of 8
66794	citric acid cycle	85.71	12 of 14
66794	propanol degradation	85.71	6 of 7
66794	leucine metabolism	84.62	11 of 13
66794	alanine metabolism	82.76	24 of 29
66794	hydrogen production	80	4 of 5
66794	starch degradation	80	8 of 10
66794	methylglyoxal degradation	80	4 of 5
66794	threonine metabolism	80	8 of 10
66794	propionate fermentation	80	8 of 10
66794	glycine betaine biosynthesis	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	photosynthesis	78.57	11 of 14
66794	NAD metabolism	77.78	14 of 18
66794	d-mannose degradation	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	pyrimidine metabolism	75.56	34 of 45
66794	purine metabolism	75.53	71 of 94
66794	CMP-KDO biosynthesis	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	glutamate and glutamine metabolism	75	21 of 28
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	lysine metabolism	71.43	30 of 42
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	phenylalanine metabolism	69.23	9 of 13
66794	methionine metabolism	69.23	18 of 26
66794	formaldehyde oxidation	66.67	2 of 3
66794	cysteine metabolism	66.67	12 of 18
66794	chorismate metabolism	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	tyrosine metabolism	64.29	9 of 14
66794	sulfate reduction	61.54	8 of 13
66794	coenzyme M biosynthesis	60	6 of 10
66794	lipoate biosynthesis	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	myo-inositol biosynthesis	60	6 of 10
66794	lipid metabolism	58.06	18 of 31
66794	non-pathway related	57.89	22 of 38
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	reductive acetyl coenzyme A pathway	57.14	4 of 7
66794	vitamin B6 metabolism	54.55	6 of 11
66794	d-xylose degradation	54.55	6 of 11
66794	polyamine pathway	52.17	12 of 23
66794	ethanol fermentation	50	1 of 2
66794	isoleucine metabolism	50	4 of 8
66794	tryptophan metabolism	50	19 of 38
66794	Entner Doudoroff pathway	50	5 of 10
66794	biotin biosynthesis	50	2 of 4
66794	selenocysteine biosynthesis	50	3 of 6
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	toluene degradation	50	2 of 4
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	catecholamine biosynthesis	50	2 of 4
66794	butanoate fermentation	50	2 of 4
66794	urea cycle	46.15	6 of 13
66794	arginine metabolism	45.83	11 of 24
66794	carotenoid biosynthesis	45.45	10 of 22
66794	cholesterol biosynthesis	45.45	5 of 11
66794	histidine metabolism	44.83	13 of 29
66794	degradation of hexoses	44.44	8 of 18
66794	mevalonate metabolism	42.86	3 of 7
66794	3-chlorocatechol degradation	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	flavin biosynthesis	40	6 of 15
66794	factor 420 biosynthesis	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	oxidative phosphorylation	38.46	35 of 91
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	vitamin B1 metabolism	38.46	5 of 13
66794	degradation of sugar alcohols	37.5	6 of 16
66794	ketogluconate metabolism	37.5	3 of 8
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
66794	pentose phosphate pathway	36.36	4 of 11
66794	proline metabolism	36.36	4 of 11
66794	degradation of pentoses	35.71	10 of 28
66794	glutathione metabolism	35.71	5 of 14
66794	cyanate degradation	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	sphingosine metabolism	33.33	2 of 6
66794	nitrate assimilation	33.33	3 of 9
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	octane oxidation	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	valine metabolism	33.33	3 of 9
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	degradation of sugar acids	32	8 of 25
66794	ascorbate metabolism	31.82	7 of 22
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	heme metabolism	28.57	4 of 14
66794	metabolism of disaccharids	27.27	3 of 11
66794	carnitine metabolism	25	2 of 8
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	chlorophyll metabolism	22.22	4 of 18

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Condition	#Anoxic (anaerobic)	-
#Engineered	#Bioreactor	-
#Engineered	#Waste	#Wastewater

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
43611	methanogenic granular sludge in a full-scale mesophilic UASB reactor treating high-strength starch-based organic wastewater discharged from a sweet corn canning plant
67770	Methanogenic granular sludge in a full-scale USAB reactor treating high-strength starch-based organic wastewater
66455	methanogenic granular sludge in a full-scale mesophilic anaerobic sludge blanket reactor treating high-strength starch-based organic wastewater	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence LC049960 (>99% sequence identity) for Lentimicrobium saccharophilum subclade from Microbeatlas

Aquatic Samples	3695
Soil Samples	706
Animal Samples	808
Plant Samples	117
Total Samples	5326

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
66455	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM119283v1 assembly for Lentimicrobium saccharophilum TBC1	scaffold	GCA_001192835	1678841.5	2645728068	1678841	72.62

16S sequences

@ref	Description	Accession	Database
43611	Lentimicrobium saccharophilum gene for 16S ribosomal RNA, partial sequence	LC049960

GC content

@ref	GC-content (mol%)	Method
66455	49.2	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Lentimicrobium saccharophilum TBC1
NCBI: GCA_001192835.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	94.33	yes
125438	anaerobic	anaerobicⓘ	yes	54.92	yes
125438	aerobic	aerobicⓘ	no	67.28	yes
125438	spore-forming	spore-formingⓘ	no	88.02	no
125438	thermophilic	thermophileⓘ	no	95.70	yes
125438	flagellated	motile2+ⓘ	no	87.94	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Lentimicrobium saccharophilum gen. nov., sp. nov., a strictly anaerobic bacterium representing a new family in the phylum Bacteroidetes, and proposal of Lentimicrobiaceae fam. nov.	Sun L, Toyonaga M, Ohashi A, Tourlousse DM, Matsuura N, Meng XY, Tamaki H, Hanada S, Cruz R, Yamaguchi T, Sekiguchi Y	Int J Syst Evol Microbiol	10.1099/ijsem.0.001103	2016

References

#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 )
#43611	Liwei Sun, Mayu Toyonaga, Akiko Ohashi, Dieter M. Tourlousse, Norihisa Matsuura, Xian-Ying Meng, Hideyuki Tamaki, Satoshi Hanada, Rodrigo Cruz, Takashi Yamaguchi, Yuji Sekiguchi: Lentimicrobium saccharophilum gen. nov., sp. nov., a strictly anaerobic bacterium representing a new family in the phylum Bacteroidetes, and proposal of Lentimicrobiaceae fam. nov.. IJSEM 66: 2635 - 2642 2016 ( DOI 10.1099/ijsem.0.001103 , PubMed 27098854 )
#66455	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100618
#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 .
#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 )
#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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Lentimicrobium saccharophilum (JCM 30898, DSM 100618, TBC1)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Metabolite utilization

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001192835

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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