Name: Peptococcus niger DSM 20475
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 11782

Type strain:

Species: Peptococcus niger

Culture col. no.: DSM 20475, ATCC 27731, VPI 7953, JCM 6506, CCM 6019, CIP 105947, NCTC 11805

Strain history: Y. Benno <-- T. Mitsuoka <-- ATCC 27731 <-- VPI 7953.

NCBI tax ID(s): 2741 (species)

SI-ID 44778

ATCC 27731, CIP 105947, DSM 20475, CCM 6019, NCTC 11805, JCM 6506

Section

Peptococcus niger DSM 20475 is an anaerobe, mesophilic, Gram-positive human pathogen that was isolated from umbilicus.

Gram-positive
anaerobe
human pathogen
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	*Peptococcaceae*
	Genus	*Peptococcus*
	Species	**Peptococcus niger**
	Full Scientific Name (LPSN)	Peptococcus niger (Hall 1930) Kluyver and van Niel 1936 (Approved Lists 1980)

Synonym

"Micrococcus niger"

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	positive Confidence in %97.781

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8844]

Culture medium

RCM MEDIUM (DSMZ Medium 634)

[Ref.: #8844]

Culture medium growth

[Ref.: #8844]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8844]

Culture medium composition

expand / minimize

[Ref.: #8844]

Culture medium

CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)

[Ref.: #8844]

Culture medium growth

[Ref.: #8844]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8844]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #8844]			growth	37 °C
[Ref.: #67770]			growth	37 °C

[Ref.: #8844]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #8844]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.491

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.826

[Ref.: #8844]	Murein short key	A11.31
[Ref.: #8844]	Murein types	A4alpha L-Lys-D-Asp

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	vitamin B1 metabolism	100	13 of 13
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[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]	adipate degradation	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	palmitate biosynthesis	86.36	19 of 22
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[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]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	cysteine metabolism	72.22	13 of 18
[Ref.: #66794]	photosynthesis	71.43	10 of 14
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	pyrimidine metabolism	68.89	31 of 45
[Ref.: #66794]	glutamate and glutamine metabolism	67.86	19 of 28
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[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]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	purine metabolism	63.83	60 of 94
[Ref.: #66794]	arginine metabolism	62.5	15 of 24
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	alanine metabolism	62.07	18 of 29
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	lysine metabolism	54.76	23 of 42
[Ref.: #66794]	pentose phosphate pathway	54.55	6 of 11
[Ref.: #66794]	isoprenoid biosynthesis	53.85	14 of 26
[Ref.: #66794]	glycolysis	52.94	9 of 17
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	isoleucine metabolism	50	4 of 8
[Ref.: #66794]	non-pathway related	50	19 of 38
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	C4 and CAM-carbon fixation	50	4 of 8
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	Entner Doudoroff pathway	50	5 of 10
[Ref.: #66794]	methionine metabolism	50	13 of 26
[Ref.: #66794]	polyamine pathway	47.83	11 of 23
[Ref.: #66794]	oxidative phosphorylation	47.25	43 of 91
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	tryptophan metabolism	44.74	17 of 38
[Ref.: #66794]	tetrahydrofolate metabolism	42.86	6 of 14
[Ref.: #66794]	ubiquinone biosynthesis	42.86	3 of 7
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	starch degradation	40	4 of 10
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	propionate fermentation	40	4 of 10
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	glutathione metabolism	35.71	5 of 14
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	molybdenum cofactor biosynthesis	33.33	3 of 9
[Ref.: #66794]	d-mannose degradation	33.33	3 of 9
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	lipid metabolism	32.26	10 of 31
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	leucine metabolism	30.77	4 of 13
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	chlorophyll metabolism	27.78	5 of 18
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	gluconeogenesis	25	2 of 8
[Ref.: #66794]	degradation of sugar alcohols	25	4 of 16
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	degradation of pentoses	25	7 of 28
[Ref.: #66794]	biotin biosynthesis	25	1 of 4
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
[Ref.: #66794]	degradation of hexoses	22.22	4 of 18
[Ref.: #66794]	lipid A biosynthesis	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.: #8844]	Sample type/isolated from	umbilicus

[Ref.: #67770]	Sample type/isolated from	Navel swab
* marker position based on {}

Isolation sources categories

#Host

#Plants

#Herbaceous plants (Grass,Crops)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB644260 (>99% sequence identity) for Peptococcus niger subclade from Microbeatlas

Aquatic Samples	185
Soil Samples	79
Animal Samples	10638
Plant Samples	23
Total Samples	10925

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

[Ref.: #8844]	Pathogenicity (human)	yes
[Ref.: #8844]	Pathogenicity (animal)	yes
[Ref.: #8844]	Biosafety level	2	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]	Peptococcus niger DNA for 16S ribosomal RNA	X55797	1410	ENA	2741 tax ID	*
[Ref.: #20218]	Peptococcus niger gene for 16S ribosomal RNA, partial sequence, strain: JCM 6506	AB644260	1528	ENA	2741 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Peptococcus niger DSM 20475	GCA_900101835	scaffold	GenBank	2741 tax ID
[Ref.: #66792]	Peptococcus niger strain DSM 20475	2741.7	wgs	PATRIC	2741 tax ID	*
[Ref.: #66792]	Peptococcus niger DSM 20475	2634166305	draft	JGI IMG/M	2741 tax ID	*

[Ref.: #8844]	GC-content	51.0 mol%
[Ref.: #67770]	GC-content	50 mol%	thermal denaturation, midpoint method (Tm)

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: Peptococcus niger DSM 20475 NCBI: GCA_900101835.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Peptococcus niger strain DSM 20475 PATRIC: 2741.7
[Ref.: #69480]	motile	no	93.945	no
[Ref.: #69480]	gram-positive	yes	77.458	no
[Ref.: #69480]	anaerobic	yes	98.057	yes
[Ref.: #69480]	halophile	no	80.425	no
[Ref.: #69480]	spore-forming	no	68.999	no
[Ref.: #69480]	glucose-util	yes	57.18	no
[Ref.: #69480]	aerobic	no	94.628	yes
[Ref.: #69480]	flagellated	no	98.563	no
[Ref.: #69480]	thermophile	no	98.374	yes
[Ref.: #69480]	glucose-ferment	no	68.307	no

Availability in culture collections External links

[Ref.: #8844]

Culture collection no.

DSM 20475, ATCC 27731, VPI 7953, JCM 6506, CCM 6019, CIP 105947, NCTC 11805

[Ref.: #81000]

SI-ID 44778

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	16S ribosomal DNA sequences of anaerobic cocci and proposal of Ruminococcus hansenii comb. nov. and Ruminococcus productus comb. nov.	Ezaki T, Li N, Hashimoto Y, Miura H, Yamamoto H	Int J Syst Bacteriol	10.1099/00207713-44-1-130	1994	*

References

#8844

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 20475

#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 )

#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 .

#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 )

#81000

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-ID44778.1 )

* 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 Peptococcus niger in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Peptococcus niger DSM 20475

Peptococcus niger strain DSM 20475

Change proposal

Change proposal