Name: Stomatobaculum longum HM-480
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 23072

Type strain:

Species: Stomatobaculum longum

Strain Designation: HM-480

Culture col. no.: DSM 24645, ACC 2

Strain history: <- M. V. Sizova, Northeastern Univ., Boston, USA; ACC2 <- M. V. Sizova {2010}

NCBI tax ID(s): 796942 (species)

SI-ID 405520

DSM 24645

Section

Stomatobaculum longum HM-480 is an anaerobe, mesophilic, Gram-variable bacterium that was isolated from healthy human dental plague.

Gram-variable
rod-shaped
anaerobe
mesophilic
16S sequence
Bacteria

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	*Stomatobaculum*
	Species	**Stomatobaculum longum**
	Full Scientific Name (LPSN)	Stomatobaculum longum Sizova et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #30713]	Gram stain	variable

[Ref.: #30713]	Cell length	22 µm

[Ref.: #30713]	Cell width	0.65 µm

[Ref.: #30713]	Cell shape	rod-shaped

[Ref.: #30713]	Motility	no

[Ref.: #30713]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #19279]

Culture medium

PY + X MEDIUM (DSMZ Medium 104b)

[Ref.: #19279]

Culture medium growth

[Ref.: #19279]

Culture medium link

Medium recipe at MediaDive

[Ref.: #19279]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #19279]	growth	37 °C
[Ref.: #30713]	growth	30-42 °C
[Ref.: #30713]	optimum	37 °C

[Ref.: #19279]	Temperature range	mesophilic
[Ref.: #30713]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30713]			growth	4.9-7.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #19279]	Oxygen tolerance	anaerobe
[Ref.: #30713]	Oxygen tolerance	anaerobe

[Ref.: #30713]

Ability of spore formation

[Ref.: #30713]

Observation

aggregates in clumps

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30713]	glucose ChEBI	+	carbon source
[Ref.: #30713]	maltose ChEBI	+	carbon source
[Ref.: #30713]	sucrose ChEBI	+	carbon source

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	vitamin B12 metabolism	79.41	27 of 34
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	Entner Doudoroff pathway	70	7 of 10
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	purine metabolism	59.57	56 of 94
[Ref.: #66794]	alanine metabolism	58.62	17 of 29
[Ref.: #66794]	tryptophan metabolism	57.89	22 of 38
[Ref.: #66794]	methionine metabolism	57.69	15 of 26
[Ref.: #66794]	glutamate and glutamine metabolism	57.14	16 of 28
[Ref.: #66794]	reductive acetyl coenzyme A pathway	57.14	4 of 7
[Ref.: #66794]	pyrimidine metabolism	55.56	25 of 45
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	oxidative phosphorylation	51.65	47 of 91
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	coenzyme A metabolism	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	degradation of sugar alcohols	50	8 of 16
[Ref.: #66794]	propionate fermentation	50	5 of 10
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	histidine metabolism	48.28	14 of 29
[Ref.: #66794]	isoprenoid biosynthesis	46.15	12 of 26
[Ref.: #66794]	pentose phosphate pathway	45.45	5 of 11
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	lysine metabolism	42.86	18 of 42
[Ref.: #66794]	heme metabolism	42.86	6 of 14
[Ref.: #66794]	ubiquinone biosynthesis	42.86	3 of 7
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	non-pathway related	42.11	16 of 38
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	polyamine pathway	39.13	9 of 23
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	35.71	5 of 14
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	arginine metabolism	33.33	8 of 24
[Ref.: #66794]	molybdenum cofactor biosynthesis	33.33	3 of 9
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	lipid metabolism	32.26	10 of 31
[Ref.: #66794]	degradation of sugar acids	32	8 of 25
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	glycine metabolism	30	3 of 10
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	glutathione metabolism	28.57	4 of 14
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	degradation of pentoses	25	7 of 28
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	25	2 of 8
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	biotin biosynthesis	25	1 of 4
[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.: #19279]	Sample type/isolated from	healthy human dental plague
[Ref.: #19279]	Geographic location (country and/or sea, region)	MA, Boston
[Ref.: #19279]	Country	USA
[Ref.: #19279]	Country ISO 3 Code	USA
[Ref.: #19279]	Continent	North America
* marker position based on {}

Isolation sources categories

#Host	#Human	-
#Host Body-Site	#Oral cavity and airways	#Tooth
#Host Body Product	#Oral cavity and Airways	#Dental plaque

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence HM120209 (>99% sequence identity) for Stomatobaculum longum subclade from Microbeatlas

Aquatic Samples	688
Soil Samples	541
Animal Samples	51438
Plant Samples	293
Total Samples	52960

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

[Ref.: #19279]

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.: #19279]	Stomatobaculum longum strain ACC2 16S ribosomal RNA gene, partial sequence	HM120209	1377	ENA	796942 tax ID

[Ref.: #19279]	GC-content	55.3 mol%	high performance liquid chromatography (HPLC)
[Ref.: #30713]	GC-content	55.175 mol%

Availability in culture collections External links

[Ref.: #19279]

Culture collection no.

DSM 24645, ACC 2

[Ref.: #87310]

SI-ID 405520

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Stomatobaculum longum gen. nov., sp. nov., an obligately anaerobic bacterium from the human oral cavity.	Sizova MV, Muller P, Panikov N, Mandalakis M, Hohmann T, Hazen A, Fowle W, Prozorov T, Bazylinski DA, Epstein SS	Int J Syst Evol Microbiol	10.1099/ijs.0.042812-0	2012	*

References

#19279

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24645

#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 )

#30713

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 #27044 (see below)

#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 )

#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 .

#87310

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-ID405520.1 )

#27044

IJSEM 1450 2013 ( DOI 10.1099/ijs.0.042812-0 , PubMed 22843721 )

* These data were automatically processed and therefore are not curated

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