Name: Dubosiella newyorkensis NYU-BL-A4
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140270

Type strain:

Species: Dubosiella newyorkensis

Strain Designation: NYU-BL-A4

Culture col. no.: DSM 103457, ATCC TSD-64

Strain history: <- L. Cox, NYU Langone Medical Center, New York, USA; NYU-BL-A4

NCBI tax ID(s): 1862672 (species)

SI-ID 407552

DSM 103457

Section

Dubosiella newyorkensis NYU-BL-A4 is an anaerobe, thermophilic, Gram-positive bacterium that was isolated from murine intestinal contents.

Gram-positive
rod-shaped
anaerobe
thermophilic
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	*Erysipelotrichia*
	Order	*Erysipelotrichales*
	Family	*Erysipelotrichaceae*
	Genus	*Dubosiella*
	Species	**Dubosiella newyorkensis**
	Full Scientific Name (LPSN)	Dubosiella newyorkensis Cox et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #43179]	Gram stain	positive

[Ref.: #43179]	Cell shape	rod-shaped
[Ref.: #43179]	Cell shape	coccus-shaped

[Ref.: #43179]	Motility	no

[Ref.: #43179]	Colony size	0.5 mm
[Ref.: #43179]	Colony color	grey
[Ref.: #43179]	Incubation period	1 day
[Ref.: #43179]	Cultivation medium used	Brucella agar

[Ref.: #43179]	Colony size	2-3 mm
[Ref.: #43179]	Colony color	grey
[Ref.: #43179]	Incubation period	2-3 days
[Ref.: #43179]	Cultivation medium used	Brucella agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43179]

Culture medium

MTGE broth (Anaerobe Systems, Morgan Hill, CA)

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Culture medium growth

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Culture medium

CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

[Ref.: #43179]

Culture medium

chopped meat broth

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Culture medium growth

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Culture medium

thioglcolate broth

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Culture medium growth

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Culture medium

Brucella broth

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Culture medium growth

	Kind of temperature		Temperature
[Ref.: #42877]		growth	37 °C
[Ref.: #43179]	no	growth	42 °C
[Ref.: #43179]		growth	30 °C
[Ref.: #43179]		optimum	37 °C

[Ref.: #42877]	Temperature range	mesophilic
[Ref.: #43179]	Temperature range	thermophilic
[Ref.: #43179]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43179]

Oxygen tolerance

anaerobe

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Ability of spore formation

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43179]	D-mannose ChEBI	+/-	assimilation
[Ref.: #43179]	nitrate ChEBI	-	reduction
[Ref.: #43179]	raffinose ChEBI	+/-	assimilation

	Metabolite production	Metabolite	Production
[Ref.: #43179]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #43179]	6-phospho-beta-galactosidase	+	3.2.1.85
[Ref.: #43179]	alanine arylamidase	-	3.4.11.2
[Ref.: #43179]	alkaline phosphatase	-	3.1.3.1
[Ref.: #43179]	alpha-arabinosidase	-	3.2.1.55
[Ref.: #43179]	alpha-fucosidase	-	3.2.1.51
[Ref.: #43179]	alpha-glucosidase	+/-	3.2.1.20
[Ref.: #43179]	arginine arylamidase	+/-
[Ref.: #43179]	arginine dihydrolase	-	3.5.3.6
[Ref.: #43179]	beta-glucosidase	+	3.2.1.21
[Ref.: #43179]	beta-glucosidase	-	3.2.1.21
[Ref.: #43179]	beta-glucuronidase	+	3.2.1.31
[Ref.: #43179]	catalase	-	1.11.1.6
[Ref.: #43179]	glutamate decarboxylase	-	4.1.1.15
[Ref.: #43179]	glycin arylamidase	+
[Ref.: #43179]	histidine arylamidase	+
[Ref.: #43179]	leucine aminopeptidase	+	3.4.1.1
[Ref.: #43179]	leucine arylamidase	+	3.4.11.1
[Ref.: #43179]	leucyl glycin arylamidase	+	3.4.11.1
[Ref.: #43179]	lipase	-
[Ref.: #43179]	N-acetyl-beta-glucosaminidase	+/-	3.2.1.52
[Ref.: #43179]	phenylalanine arylamidase	+/-
[Ref.: #43179]	proline-arylamidase	+/-	3.4.11.5
[Ref.: #43179]	pyroglutamic acid arylamidase	+/-
[Ref.: #43179]	serine arylamidase	-
[Ref.: #43179]	tyrosine arylamidase	-
[Ref.: #43179]	urease	-	3.5.1.5
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #43179]

Fatty acid	Percentage
C16:0	31.4
C10:0	19.3
C18:1ω9c	13
C18:0	12
C18:2ω6,9c / anteiso-C18:0	9.8
C14:0	6.1
C12:0	3.6
C9:0	3.3
C16:1ω7c / C16:1ω6c	1.4

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	peptidoglycan biosynthesis	86.67	13 of 15
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	palmitate biosynthesis	81.82	18 of 22
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	photosynthesis	71.43	10 of 14
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	glutamate and glutamine metabolism	67.86	19 of 28
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	pentose phosphate pathway	63.64	7 of 11
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	methionine metabolism	57.69	15 of 26
[Ref.: #66794]	oxidative phosphorylation	57.14	52 of 91
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	purine metabolism	56.38	53 of 94
[Ref.: #66794]	degradation of sugar acids	56	14 of 25
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	metabolism of disaccharids	54.55	6 of 11
[Ref.: #66794]	non-pathway related	52.63	20 of 38
[Ref.: #66794]	pyrimidine metabolism	51.11	23 of 45
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	50	4 of 8
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	tetrahydrofolate metabolism	50	7 of 14
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	tryptophan metabolism	50	19 of 38
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	isoprenoid biosynthesis	50	13 of 26
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	arginine metabolism	50	12 of 24
[Ref.: #66794]	flavin biosynthesis	46.67	7 of 15
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	leucine metabolism	46.15	6 of 13
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	lipid metabolism	45.16	14 of 31
[Ref.: #66794]	alanine metabolism	44.83	13 of 29
[Ref.: #66794]	CO2 fixation in Crenarchaeota	44.44	4 of 9
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	ubiquinone biosynthesis	42.86	3 of 7
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	urea cycle	38.46	5 of 13
[Ref.: #66794]	carnitine metabolism	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]	lysine metabolism	35.71	15 of 42
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	molybdenum cofactor biosynthesis	33.33	3 of 9
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	degradation of pentoses	32.14	9 of 28
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	vitamin B6 metabolism	27.27	3 of 11
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[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
		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.: #42877]	Sample type/isolated from	murine intestinal contents
[Ref.: #42877]	Geographic location (country and/or sea, region)	New York City (40.7370457 N, -73.9768398 W)
[Ref.: #42877]	Country	USA
[Ref.: #42877]	Country ISO 3 Code	USA
[Ref.: #42877]	Continent	North America
[Ref.: #42877]	Geographic location	40.7371°/-73.9768°

[Ref.: #43179]	Sample type/isolated from	murine intestinal contents
* marker position based on {}

Isolation sources categories

#Host	#Mammals	#Muridae (Mouse/Rat)
#Host Body-Site	#Gastrointestinal tract	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KU744405 (>99% sequence identity) for Dubosiella newyorkensis subclade from Microbeatlas

Aquatic Samples	592
Soil Samples	813
Animal Samples	34769
Plant Samples	184
Total Samples	36358

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

[Ref.: #42877]

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.: #42877]	Dubosiella newyorkensis strain NYU-BL-A4 16S ribosomal RNA gene, partial sequence	KU744405	1460	ENA	1862672 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Dubosiella newyorkensis NYU-BL-A4	GCA_001945605	contig	GenBank	1862672 tax ID	*
[Ref.: #66792]	Dubosiella newyorkensis NYU-BL-A4	2788499991	draft	JGI IMG/M	1862672 tax ID	*

[Ref.: #43179]	GC-content	42.5 mol%	genome sequence analysis
[Ref.: #42877]	GC-content	42.5 mol%	sequence analysis

Availability in culture collections External links

[Ref.: #42877]

Culture collection no.

DSM 103457, ATCC TSD-64

[Ref.: #96576]

SI-ID 407552

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Description of two novel members of the family Erysipelotrichaceae: Ileibacterium valens gen. nov., sp. nov. and Dubosiella newyorkensis, gen. nov., sp. nov., from the murine intestine, and emendation to the description of Faecalibaculum rodentium.	Cox LM, Sohn J, Tyrrell KL, Citron DM, Lawson PA, Patel NB, Iizumi T, Perez-Perez GI, Goldstein EJC, Blaser MJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.001793	2017	*

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 )

#42877

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 103457

#43179

Laura M. Cox, Jiho Sohn, Kerin L. Tyrrell, Diane M. Citron, Paul A. Lawson, Nisha B. Patel, Tadasu Iizumi, Guillermo I. Perez-Perez, Ellie J. C. Goldstein, Martin J. Blaser: Description of two novel members of the family Erysipelotrichaceae: Ileibacterium valens gen. nov., sp. nov. And Dubosiella newyorkensis, gen. nov., sp. nov., from the murine intestine, and emendation to the description of Faecalibacterium rodentium. IJSEM 67: 1247 - 1254 2017 ( DOI 10.1099/ijsem.0.001793 , PubMed 28100298 )

#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 )

#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 .

#96576

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-ID407552.1 )

* These data were automatically processed and therefore are not curated

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