Name: Peptoniphilus coxii CCUG 59622
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 155907

Type strain:

Species: Peptoniphilus coxii

Culture col. no.: CCUG 59622, JCM 16892, ATCC BAA-2106, KCTC 15410

Strain history: K. L. Tyrrell RMA 16757.

NCBI tax ID(s): 755172 (species)

SI-ID 411307

CCUG 59622

Special Collections

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When using BacDive for research please cite our paper

Peptoniphilus coxii CCUG 59622 is an anaerobe, mesophilic bacterium that was isolated from Human wound,leg.

anaerobe
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Bacillota*
	Class	*Clostridia*
	Order	*Eubacteriales*
	Family	*Peptoniphilaceae*
	Genus	*Peptoniphilus*
	Species	**Peptoniphilus coxii**
	Full Scientific Name (LPSN)	Peptoniphilus coxii Citron et al. 2013

Synonym

Aedoeadaptatus coxii

Information on morphological and physiological properties Morphology

[Ref.: #62039]

Incubation period

1 day

Information on culture and growth conditions Culture and growth conditions

	Temperatures	Kind of temperature		Temperature
[Ref.: #62039]			growth	37 °C
[Ref.: #67770]			growth	37 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #62039]	Oxygen tolerance	anaerobe
[Ref.: #125438]	Oxygen tolerance	anaerobe Confidence in %92.303
[Ref.: #125439]	Oxygen tolerance	anaerobe Confidence in %98.2

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	palmitate biosynthesis	86.36	19 of 22
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	photosynthesis	71.43	10 of 14
[Ref.: #66794]	vitamin B12 metabolism	70.59	24 of 34
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	pyrimidine metabolism	64.44	29 of 45
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	purine metabolism	59.57	56 of 94
[Ref.: #66794]	glycolysis	58.82	10 of 17
[Ref.: #66794]	heme metabolism	57.14	8 of 14
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	serine metabolism	55.56	5 of 9
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	glutamate and glutamine metabolism	53.57	15 of 28
[Ref.: #66794]	alanine metabolism	51.72	15 of 29
[Ref.: #66794]	oxidative phosphorylation	50.55	46 of 91
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	acetate fermentation	50	2 of 4
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	isoleucine metabolism	50	4 of 8
[Ref.: #66794]	citric acid cycle	50	7 of 14
[Ref.: #66794]	methionine metabolism	46.15	12 of 26
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	chorismate metabolism	44.44	4 of 9
[Ref.: #66794]	tetrahydrofolate metabolism	42.86	6 of 14
[Ref.: #66794]	methylglyoxal degradation	40	2 of 5
[Ref.: #66794]	propionate fermentation	40	4 of 10
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	starch degradation	40	4 of 10
[Ref.: #66794]	non-pathway related	39.47	15 of 38
[Ref.: #66794]	isoprenoid biosynthesis	38.46	10 of 26
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	37.5	3 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	37.5	3 of 8
[Ref.: #66794]	tryptophan metabolism	36.84	14 of 38
[Ref.: #66794]	proline metabolism	36.36	4 of 11
[Ref.: #66794]	pentose phosphate pathway	36.36	4 of 11
[Ref.: #66794]	glutathione metabolism	35.71	5 of 14
[Ref.: #66794]	lipid metabolism	35.48	11 of 31
[Ref.: #66794]	histidine metabolism	34.48	10 of 29
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	L-lactaldehyde degradation	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	molybdenum cofactor biosynthesis	33.33	3 of 9
[Ref.: #66794]	lysine metabolism	30.95	13 of 42
[Ref.: #66794]	leucine metabolism	30.77	4 of 13
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	glycine metabolism	30	3 of 10
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	degradation of sugar alcohols	25	4 of 16
[Ref.: #66794]	urea cycle	23.08	3 of 13
[Ref.: #66794]	ascorbate metabolism	22.73	5 of 22
[Ref.: #66794]	lipid A biosynthesis	22.22	2 of 9
[Ref.: #66794]	d-mannose degradation	22.22	2 of 9
[Ref.: #66794]	polyamine pathway	21.74	5 of 23
[Ref.: #66794]	degradation of pentoses	21.43	6 of 28
[Ref.: #66794]	tyrosine metabolism	21.43	3 of 14
		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.: #62039]	Sample type/isolated from	Human wound,leg
[Ref.: #62039]	Sampling date	2007-08-01
[Ref.: #62039]	Geographic location (country and/or sea, region)	CA,Santa Monica
[Ref.: #62039]	Country	USA
[Ref.: #62039]	Country ISO 3 Code	USA
[Ref.: #62039]	Continent	North America

[Ref.: #67770]	Sample type/isolated from	Human clinical specimen
* marker position based on {}

Isolation sources categories

#Host	#Human	-
#Host Body-Site	#Other	#Wound
#Host Body-Site	#Limb	#Leg
#Infection	#Patient	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence GU938836 (>99% sequence identity) for Peptoniphilus coxii subclade from Microbeatlas

Aquatic Samples	1113
Soil Samples	819
Animal Samples	67578
Plant Samples	247
Total Samples	69757

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.: #67770]	Peptoniphilus coxii strain RMA 16757 16S ribosomal RNA gene, partial sequence	GU938836	1465	GenBank ENA	755172 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Peptoniphilus sp. 1804121828	2582829.3	wgs	PATRIC	2582829 tax ID	*
[Ref.: #66792]	Peptoniphilus tyrrelliae strain 261-21	755171.3	wgs	PATRIC	755171 tax ID	*

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Peptoniphilus sp. 1804121828 PATRIC: 2582829.3
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	81.773	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	yes	92.303	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	68.794	no
[Ref.: #125438]	aerobic	aerobicⓘ	no	96.9	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	89.677	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	84.28	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Peptoniphilus sp. 1804121828 PATRIC: 2582829.3
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	77.4
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	78.5
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	variable	78.6
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	anaerobe	98.2

Availability in culture collections External links

[Ref.: #62039]

Culture collection no.

CCUG 59622, JCM 16892, ATCC BAA-2106, KCTC 15410

[Ref.: #109266]

SI-ID 411307

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Peptoniphilus coxii sp. nov. and Peptoniphilus tyrrelliae sp. nov. isolated from human clinical infections.	Citron DM, Tyrrell KL, Goldstein EJ	Anaerobe	10.1016/j.anaerobe.2011.11.008	2011	*

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 )

#62039 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 59622

#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 )

#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 .

#109266

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-ID411307.1 )

#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 .

* These data were automatically processed and therefore are not curated

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Peptoniphilus sp. 1804121828

Peptoniphilus sp. 1804121828

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