Name: Lentimicrobium saccharophilum TBC1
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 140821

Type strain:

Species: Lentimicrobium saccharophilum

Strain Designation: TBC1

Culture col. no.: JCM 30898, DSM 100618

Strain history: Y. Sekiguchi; Biomed. Res. Inst., AIST, Japan; TBC1.

NCBI tax ID(s): 1678841 (species)

SI-ID 408372

DSM 100618

Special Collections

Section

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.

colony-forming
Gram-negative
rod-shaped
obligate anaerobe
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	*Bacteroidota*
	Class	*Bacteroidia*
	Order	*Bacteroidales*
	Family	*Lentimicrobiaceae*
	Genus	*Lentimicrobium*
	Species	**Lentimicrobium saccharophilum**
	Full Scientific Name (LPSN)	Lentimicrobium saccharophilum Sun et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #43611]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %94.332

[Ref.: #43611]	Cell length	2-4 µm

[Ref.: #43611]	Cell width	0.4-0.6 µm

[Ref.: #43611]	Cell shape	rod-shaped

[Ref.: #43611]	Motility	no

[Ref.: #43611]	Colony size	0.5 mm
[Ref.: #43611]	Colony color	White
[Ref.: #43611]	Colony shape	circular
[Ref.: #43611]	Incubation period	14 days
[Ref.: #43611]	Cultivation medium used	Basal medium

Information on culture and growth conditions Culture and growth conditions

[Ref.: #66455]

Culture medium

ANAEROBIC FRESHWATER (FWM) MEDIUM (DSMZ Medium 503)

[Ref.: #66455]

Culture medium growth

[Ref.: #66455]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #43611]

Culture medium

Basal medium

[Ref.: #43611]

Culture medium growth

		Temperature
[Ref.: #43611]	growth	20-40 °C
[Ref.: #43611]	optimum	30-37 °C
[Ref.: #66455]	growth	35 °C
[Ref.: #67770]	growth	37 °C

	pH	Kind of pH		pH
[Ref.: #43611]			optimum	7
[Ref.: #43611]			growth	6.5-9

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43611]

Oxygen tolerance

obligate anaerobe

[Ref.: #69481]

Ability of spore formation

no Confidence in %100

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43611]	acetate ChEBI	-	assimilation
[Ref.: #43611]	arabinose ChEBI	-	assimilation
[Ref.: #43611]	benzoate ChEBI	-	assimilation
[Ref.: #43611]	betaine ChEBI	-	assimilation
[Ref.: #43611]	butyrate ChEBI	-	assimilation
[Ref.: #43611]	casamino acids	-	assimilation
[Ref.: #43611]	crotonate ChEBI	-	assimilation
[Ref.: #43611]	elemental sulfur ChEBI	-	electron acceptor
[Ref.: #43611]	ethanol ChEBI	-	assimilation
[Ref.: #43611]	fructose ChEBI	-	assimilation
[Ref.: #43611]	fumarate ChEBI	-	assimilation
[Ref.: #43611]	fumarate ChEBI	-	electron acceptor
[Ref.: #43611]	galactose ChEBI	-	assimilation
[Ref.: #43611]	glycerol ChEBI	-	assimilation
[Ref.: #43611]	lactate ChEBI	-	assimilation
[Ref.: #43611]	methanol ChEBI	-	assimilation
[Ref.: #43611]	nitrate ChEBI	-	electron acceptor
[Ref.: #43611]	pectin ChEBI	-	assimilation
[Ref.: #43611]	peptone	-	assimilation
[Ref.: #43611]	propanol ChEBI	-	assimilation
[Ref.: #43611]	propionate ChEBI	-	assimilation
[Ref.: #43611]	raffinose ChEBI	-	assimilation
[Ref.: #43611]	succinate ChEBI	-	assimilation
[Ref.: #43611]	sulfate ChEBI	-	electron acceptor
[Ref.: #43611]	sulfite ChEBI	-	electron acceptor
[Ref.: #43611]	thiosulfate ChEBI	-	electron acceptor
[Ref.: #43611]	tryptone	-	assimilation
[Ref.: #43611]	xylan ChEBI	-	assimilation
[Ref.: #43611]	yeast extract	+	required for growth
	Only first 10 entries are displayed. Click here to see all.

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

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

[Ref.: #43611]	Sample type/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

[Ref.: #67770]	Sample type/isolated from	Methanogenic granular sludge in a full-scale USAB reactor treating high-strength starch-based organic wastewater
* marker position based on {}

Isolation sources categories

#Condition	#Anoxic (anaerobic)	-
#Engineered	#Bioreactor	-
#Engineered	#Waste	#Wastewater

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #66455]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #43611]	Lentimicrobium saccharophilum gene for 16S ribosomal RNA, partial sequence	LC049960		GenBank ENA

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Lentimicrobium saccharophilum TBC1	GCA_001192835	scaffold	GenBank ENA	1678841 tax ID

[Ref.: #66455]

GC-content

49.2 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: Lentimicrobium saccharophilum TBC1 NCBI: GCA_001192835.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Lentimicrobium saccharophilum TBC1 NCBI: GCA_001192835.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	94.332	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	yes	54.916	yes
[Ref.: #69480]	aerobic	aerobicⓘ	no	67.281	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	88.023	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	95.703	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	87.944	yes

Availability in culture collections External links

[Ref.: #66455]

Culture collection no.

JCM 30898, DSM 100618

[Ref.: #96796]

SI-ID 408372

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 .

#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 )

#96796

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-ID408372.1 )

* These data were automatically processed and therefore are not curated

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