Name: Cellulosilyticum lentocellum RHM5
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 6375

Type strain:

Species: Cellulosilyticum lentocellum

Strain Designation: RHM5

Culture col. no.: DSM 5427, ATCC 49066, KCTC 15127, NCIMB 11756, NCIB 11756

Strain history: <- DSM <- NCIMB <- RH Madden, RHM5

NCBI tax ID(s): 642492 (strain), 29360 (species)

SI-ID 46088

ATCC 49066, NCIMB 11756, DSM 5427, NCIB 11756

Section

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

motile
rod-shaped
spore-forming
anaerobe
mesophilic
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	*Bacillota*
	Class	*Clostridia*
	Order	*Eubacteriales*
	Family	*Lachnospiraceae*
	Genus	*Cellulosilyticum*
	Species	**Cellulosilyticum lentocellum**
	Full Scientific Name (LPSN)	Cellulosilyticum lentocellum (Murray et al. 1987) Cai and Dong 2010

Synonym

Clostridium lentocellum

Information on morphological and physiological properties Morphology

[Ref.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #67771]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	curved-shaped

[Ref.: #67771]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #2163]

Culture medium

RUMINOCLOSTRIDIUM CELLULOLYTICUM (CM3) MEDIUM (DSMZ Medium 520)

[Ref.: #2163]

Culture medium growth

[Ref.: #2163]

Culture medium link

Medium recipe at MediaDive

[Ref.: #2163]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #2163]			growth	30 °C
[Ref.: #67771]			growth	25 °C

[Ref.: #2163]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #2163]	Oxygen tolerance	anaerobe
[Ref.: #67771]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.596

[Ref.: #67771]	Type of spore	spore
[Ref.: #67771]	Ability of spore formation	yes
[Ref.: #69480]	Ability of spore formation	yes Confidence in %95.634

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	cyanate degradation	100	3 of 3
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	vitamin B1 metabolism	92.31	12 of 13
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	pyrimidine metabolism	84.44	38 of 45
[Ref.: #66794]	glycolysis	82.35	14 of 17
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	purine metabolism	73.4	69 of 94
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	metabolism of disaccharids	72.73	8 of 11
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	non-pathway related	68.42	26 of 38
[Ref.: #66794]	oxidative phosphorylation	68.13	62 of 91
[Ref.: #66794]	glutamate and glutamine metabolism	67.86	19 of 28
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	lysine metabolism	61.9	26 of 42
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	sulfate reduction	61.54	8 of 13
[Ref.: #66794]	polyamine pathway	60.87	14 of 23
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	degradation of sugar acids	60	15 of 25
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	tryptophan metabolism	57.89	22 of 38
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	molybdenum cofactor biosynthesis	55.56	5 of 9
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	pentose phosphate pathway	54.55	6 of 11
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	tetrahydrofolate metabolism	50	7 of 14
[Ref.: #66794]	degradation of hexoses	50	9 of 18
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	degradation of pentoses	50	14 of 28
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	50	4 of 8
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	vitamin B12 metabolism	47.06	16 of 34
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	lipid metabolism	45.16	14 of 31
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	degradation of sugar alcohols	37.5	6 of 16
[Ref.: #66794]	dTDPLrhamnose biosynthesis	37.5	3 of 8
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	3-phenylpropionate degradation	26.67	4 of 15
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	23.53	4 of 17
[Ref.: #66794]	allantoin degradation	22.22	2 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		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.: #2163]	Sample type/isolated from	river sediment with paper mill waste
[Ref.: #2163]	Geographic location (country and/or sea, region)	Scotland, Aberdeen, River Don
[Ref.: #2163]	Country	United Kingdom
[Ref.: #2163]	Country ISO 3 Code	GBR
[Ref.: #2163]	Continent	Europe

[Ref.: #67771]	Sample type/isolated from	From river sediment with paper mill waste
[Ref.: #67771]	Geographic location (country and/or sea, region)	River Don, Aberdeen, Scotland
[Ref.: #67771]	Country	United Kingdom
[Ref.: #67771]	Country ISO 3 Code	GBR
[Ref.: #67771]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered	#Industrial	-
#Engineered	#Waste	-
#Environmental	#Aquatic	#River (Creek)
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

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

[Ref.: #2163]

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.: #20218]	C.lentocellum gene for 16S ribosomal RNA	X71851	1508	ENA	642492 tax ID	*
[Ref.: #20218]	Clostridium lentocellum 16S rRNA gene, strain DSM 5427	X76162	1459	ENA	642492 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Cellulosilyticum lentocellum DSM 5427	GCA_000178835	complete	GenBank	642492 tax ID	*
[Ref.: #66792]	Clostridium lentocellum DSM 5427	642492.3	wgs	PATRIC	642492 tax ID	*
[Ref.: #66792]	Cellulosilyticum lentocellum RHM5, DSM 5427	650716026	complete	JGI IMG/M	642492 tax ID	*

[Ref.: #2163]	GC-content	34.0 mol%	sequence analysis
[Ref.: #67771]	GC-content	36.0 mol%	genome sequence analysis
[Ref.: #67771]	GC-content	34.0 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Cellulosilyticum lentocellum DSM 5427 DSM 5427 NCBI: GCA_000178835.2
[Ref.: #69481]	spore-forming	yes	85	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Cellulosilyticum lentocellum DSM 5427 DSM 5427 NCBI: GCA_000178835.2
[Ref.: #69480]	motile	yes	84.636	yes
[Ref.: #69480]	flagellated	yes	70.51	no
[Ref.: #69480]	gram-positive	yes	53.182	yes
[Ref.: #69480]	anaerobic	yes	97.32	yes
[Ref.: #69480]	aerobic	no	97.257	yes
[Ref.: #69480]	halophile	no	86.989	no
[Ref.: #69480]	spore-forming	yes	96.37	yes
[Ref.: #69480]	thermophile	no	99.313	yes
[Ref.: #69480]	glucose-util	yes	84.208	no
[Ref.: #69480]	glucose-ferment	yes	70.868	no

Availability in culture collections External links

[Ref.: #2163]

Culture collection no.

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

[Ref.: #75848]

SI-ID 46088

Literature:

Topic	Title	Authors	Journal	DOI	Year
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;

#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 )

#75848

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-ID46088.1 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Cellulosilyticum lentocellum in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Cellulosilyticum lentocellum DSM 5427 DSM 5427

Cellulosilyticum lentocellum DSM 5427 DSM 5427

Change proposal

Change proposal