Cellulosilyticum lentocellum (DSM 5427, ATCC 49066, KCTC 15127)

Name: Cellulosilyticum lentocellum (DSM 5427, ATCC 49066, KCTC 15127)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6375

Type strain

Strain Designation RHM5

Culture col. no. DSM 5427 ATCC 49066 KCTC 15127 NCIMB 11756 RHM5 1 more

NCBI tax ID(s) 642492 29360

Special Collections DSMZ KCTC

History DSMZ <- NCIMB <- R.H. Madden, RHM5 KCTC <- DSM <- NCIMB <- RH Madden, RHM5

Links

Cellulosilyticum lentocellum RHM5 is an anaerobe, spore-forming, motile bacterium that was isolated from river sediment with paper mill waste.

spore-forming motile rod-shaped anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 46088

KCTC 15127,ATCC 49066,NCIMB 11756,DSM 5427,NCIB 11756

@ref 20215

Last LPSN update 2026-05-29 08:26:23

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Lachnospiraceae

Genus Cellulosilyticum

Species Cellulosilyticum lentocellum

Full scientific name Cellulosilyticum lentocellum (Murray et al. 1987) Cai and Dong 2010

Synonyms (1)

Clostridium lentocellum

Morphology

Cell morphology

@ref	Cell shape	Gram stain
67771	rod-shaped
67771	curved-shaped
67771		negative

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
2163	RUMINOCLOSTRIDIUM CELLULOLYTICUM (CM3) MEDIUM (DSMZ Medium 520)		Medium recipe at MediaDive	Name: RUMINOCLOSTRIDIUM CELLULOLYTICUM (CM3) MEDIUM (DSMZ Medium 520) Composition: Cellulose 9.97009 g/l (optional) Cellobiose 5.98205 g/l K2HPO4 x 3 H2O 2.89133 g/l Yeast extract 1.99402 g/l Na2CO3 1.49551 g/l KH2PO4 1.49551 g/l (NH4)2SO4 1.29611 g/l L-Cysteine HCl x H2O 0.498504 g/l MgCl2 x 6 H2O 0.199402 g/l CaCl2 x 2 H2O 0.0747757 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l FeSO4 x 7 H2O 0.00124626 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l MnCl2 x 4 H2O 9.97009e-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 H3BO3 5.98205e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
2163	positive	growth	30
67771	positive	growth	25

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
2163	anaerobe
67771	anaerobe
125439	facultative anaerobe	96.509

Spore formation

@ref	Type of spore	Spore formation
67771	spore

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	palmitate biosynthesis	100	22 of 22
66794	cyanate degradation	100	3 of 3
66794	gluconeogenesis	100	8 of 8
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	cardiolipin biosynthesis	100	7 of 7
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	threonine metabolism	100	10 of 10
66794	ethanol fermentation	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	L-lactaldehyde degradation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	cellulose degradation	100	5 of 5
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	starch degradation	100	10 of 10
66794	folate polyglutamylation	100	1 of 1
66794	vitamin B1 metabolism	92.31	12 of 13
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	chorismate metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	phenylalanine metabolism	84.62	11 of 13
66794	pyrimidine metabolism	84.44	38 of 45
66794	glycolysis	82.35	14 of 17
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	Entner Doudoroff pathway	80	8 of 10
66794	glycogen metabolism	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	photosynthesis	78.57	11 of 14
66794	d-mannose degradation	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	alanine metabolism	75.86	22 of 29
66794	ppGpp biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	purine metabolism	73.4	69 of 94
66794	flavin biosynthesis	73.33	11 of 15
66794	metabolism of disaccharids	72.73	8 of 11
66794	heme metabolism	71.43	10 of 14
66794	methionine metabolism	69.23	18 of 26
66794	non-pathway related	68.42	26 of 38
66794	oxidative phosphorylation	68.13	62 of 91
66794	glutamate and glutamine metabolism	67.86	19 of 28
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	citric acid cycle	64.29	9 of 14
66794	d-xylose degradation	63.64	7 of 11
66794	lysine metabolism	61.9	26 of 42
66794	leucine metabolism	61.54	8 of 13
66794	urea cycle	61.54	8 of 13
66794	sulfate reduction	61.54	8 of 13
66794	polyamine pathway	60.87	14 of 23
66794	factor 420 biosynthesis	60	3 of 5
66794	degradation of sugar acids	60	15 of 25
66794	hydrogen production	60	3 of 5
66794	myo-inositol biosynthesis	60	6 of 10
66794	propionate fermentation	60	6 of 10
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	tryptophan metabolism	57.89	22 of 38
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	propanol degradation	57.14	4 of 7
66794	glutathione metabolism	57.14	8 of 14
66794	cysteine metabolism	55.56	10 of 18
66794	molybdenum cofactor biosynthesis	55.56	5 of 9
66794	histidine metabolism	55.17	16 of 29
66794	pentose phosphate pathway	54.55	6 of 11
66794	proline metabolism	54.55	6 of 11
66794	arginine metabolism	54.17	13 of 24
66794	CMP-KDO biosynthesis	50	2 of 4
66794	tetrahydrofolate metabolism	50	7 of 14
66794	degradation of hexoses	50	9 of 18
66794	kanosamine biosynthesis II	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	degradation of pentoses	50	14 of 28
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	biotin biosynthesis	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	vitamin E metabolism	50	2 of 4
66794	ketogluconate metabolism	50	4 of 8
66794	adipate degradation	50	1 of 2
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	50	4 of 8
66794	butanoate fermentation	50	2 of 4
66794	vitamin B12 metabolism	47.06	16 of 34
66794	vitamin B6 metabolism	45.45	5 of 11
66794	lipid metabolism	45.16	14 of 31
66794	nitrate assimilation	44.44	4 of 9
66794	lipid A biosynthesis	44.44	4 of 9
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	coenzyme M biosynthesis	40	4 of 10
66794	creatinine degradation	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	degradation of sugar alcohols	37.5	6 of 16
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
66794	tyrosine metabolism	35.71	5 of 14
66794	IAA biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	octane oxidation	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	ascorbate metabolism	31.82	7 of 22
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	androgen and estrogen metabolism	25	4 of 16
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17
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	#Industrial	-
#Engineered	#Waste	-
#Environmental	#Aquatic	#River (Creek)
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
2163	river sediment with paper mill waste	Scotland, Aberdeen, River Don	United Kingdom	GBR	Europe
67771	From river sediment with paper mill waste	River Don, Aberdeen, Scotland	United Kingdom	GBR	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
2163	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	ASM17883v2 assembly for Cellulosilyticum lentocellum DSM 5427	complete	GCA_000178835	642492.3	650716026	642492	96.78

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	C.lentocellum gene for 16S ribosomal RNA	X71851	1508		642492
20218	Clostridium lentocellum 16S rRNA gene, strain DSM 5427	X76162	1459		642492

GC content

@ref	GC-content (mol%)	Method
2163	34.0	sequence analysis
67771	36.0	genome sequence analysis
67771	34.0

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM17883v2 assembly for Cellulosilyticum lentocellum DSM 5427
BV-BRC: 642492.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	96.51	no
125439	gram_stain	BacteriaNetⓘ	variable	56.06	no
125439	motility	BacteriaNetⓘ	yes	71.07	no
125439	spore_formation	BacteriaNetⓘ	yes	65.44	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Cellulosilyticum lentocellum DSM 5427 DSM 5427
NCBI: GCA_000178835.2

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	50.85	yes
125438	anaerobic	anaerobicⓘ	yes	79.96	no
125438	aerobic	aerobicⓘ	no	88.64	yes
125438	spore-forming	spore-formingⓘ	yes	77.99	yes
125438	thermophilic	thermophileⓘ	no	86.80	no
125438	flagellated	motile2+ⓘ	yes	81.11	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Deeply branching Bacillota species exhibit atypical Gram-negative staining.	Choi JK, Poudel S, Yee N, Goff JL.	Microbiol Spectr	10.1128/spectrum.00732-24	2024
	The exceptional form and function of the giant bacterium Ca. Epulopiscium viviparus revolves around its sodium motive force.	Sannino DR, Arroyo FA, Pepe-Ranney C, Chen W, Volland JM, Elisabeth NH, Angert ER.	Proc Natl Acad Sci U S A	10.1073/pnas.2306160120	2023
	Establishment and assessment of an amplicon sequencing method targeting the 16S-ITS-23S rRNA operon for analysis of the equine gut microbiome.	Kinoshita Y, Niwa H, Uchida-Fujii E, Nukada T.	Sci Rep	10.1038/s41598-021-91425-7	2021
Metabolism	Pretreatment of Lignocellulosic Biomass with Cattle Rumen Fluid for Methane Production: Fate of Added Rumen Microbes and Indigenous Microbes of Methane Seed Sludge.	Baba Y, Matsuki Y, Takizawa S, Suyama Y, Tada C, Fukuda Y, Saito M, Nakai Y.	Microbes Environ	10.1264/jsme2.me19113	2019
	An efficient system for intestinal on-site butyrate production using novel microbiome-derived esterases.	Jung DH, Yong JH, Hwang W, Yoon MY, Yoon SS.	J Biol Eng	10.1186/s13036-021-00259-4	2021
Genetics	The genomic basis for the evolution of a novel form of cellular reproduction in the bacterium Epulopiscium.	Miller DA, Suen G, Clements KD, Angert ER.	BMC Genomics	10.1186/1471-2164-13-265	2012
Metabolism	Characterization of wheat straw-degrading anaerobic alkali-tolerant mixed cultures from soda lake sediments by molecular and cultivation techniques.	Porsch K, Wirth B, Toth EM, Schattenberg F, Nikolausz M.	Microb Biotechnol	10.1111/1751-7915.12272	2015
Genetics	A phylogenomic view of ecological specialization in the Lachnospiraceae, a family of digestive tract-associated bacteria.	Meehan CJ, Beiko RG.	Genome Biol Evol	10.1093/gbe/evu050	2014
Metabolism	Distribution and preservation of the components of the engulfment. What is beyond representative genomes?	Soto-Avila L, Merce RC, Santos W, Castaneda N, Gutierrez-Rios RM.	PLoS One	10.1371/journal.pone.0246651	2021
Genetics	Complete genome sequence of the cellulose-degrading bacterium Cellulosilyticum lentocellum.	Miller DA, Suen G, Bruce D, Copeland A, Cheng JF, Detter C, Goodwin LA, Han CS, Hauser LJ, Land ML, Lapidus A, Lucas S, Meincke L, Pitluck S, Tapia R, Teshima H, Woyke T, Fox BG, Angert ER, Currie CR	J Bacteriol	10.1128/JB.00239-11	2011
Phylogeny	Cellulosilyticum ruminicola gen. nov., sp. nov., isolated from the rumen of yak, and reclassification of Clostridium lentocellum as Cellulosilyticum lentocellum comb. nov.	Cai S, Dong X	Int J Syst Evol Microbiol	10.1099/ijs.0.014712-0	2009

References

#2163	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 5427
#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 )
#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) .
#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 )
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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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Cellulosilyticum lentocellum (DSM 5427, ATCC 49066, KCTC 15127)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000178835

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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