Name: Peptoniphilus indolicus R13
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 17997

Type strain:

Species: Peptoniphilus indolicus

Strain Designation: R13

Culture col. no.: DSM 20464, ATCC 29427, CCM 5987

Strain history: <- ATCC <- G.H. Sorensen, R13

NCBI tax ID(s): 997350 (strain), 33030 (species)

SI-ID 45858

ATCC 29427, CCM 5987, DSM 20464, CCUG 17639, NCIMB 702666, NCDO2666, NCTC11088, CCUG 46591

Special Collections

DSMZ

Section

Peptoniphilus indolicus R13 is an anaerobe animal pathogen that was isolated from summer mastitis secretion of heifer.

anaerobe
animal pathogen
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	*Peptoniphilaceae*
	Genus	*Peptoniphilus*
	Species	**Peptoniphilus indolicus**
	Full Scientific Name (LPSN)	Peptoniphilus indolicus (Christiansen 1934) Ezaki et al. 2001

	Synonym	"Micrococcus* indolicus"*
	Synonym	"Schleiferella* indolica"*
	Synonym	Peptococcus indolicus
	Synonym	Peptostreptococcus indolicus

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8835]

Culture medium

PYG MEDIUM (MODIFIED) (DSMZ Medium 104)

[Ref.: #8835]

Culture medium growth

[Ref.: #8835]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8835]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #8835]			growth	37 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #8835]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %96.36

[Ref.: #8835]	Murein short key	A21.05
[Ref.: #8835]	Murein types	A4ß L-Orn-D-Glu

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	serine 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]	cellulose degradation	80	4 of 5
[Ref.: #66794]	pyrimidine metabolism	80	36 of 45
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	purine metabolism	76.6	72 of 94
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	NAD metabolism	72.22	13 of 18
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	photosynthesis	71.43	10 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	degradation of sugar alcohols	68.75	11 of 16
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	molybdenum cofactor biosynthesis	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	Entner Doudoroff pathway	60	6 of 10
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	methionine metabolism	57.69	15 of 26
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	oxidative phosphorylation	54.95	50 of 91
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	non-pathway related	52.63	20 of 38
[Ref.: #66794]	histidine metabolism	51.72	15 of 29
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	tryptophan metabolism	50	19 of 38
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	arginine metabolism	50	12 of 24
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	lipid metabolism	48.39	15 of 31
[Ref.: #66794]	lysine metabolism	47.62	20 of 42
[Ref.: #66794]	leucine metabolism	46.15	6 of 13
[Ref.: #66794]	citric acid cycle	42.86	6 of 14
[Ref.: #66794]	ubiquinone biosynthesis	42.86	3 of 7
[Ref.: #66794]	starch degradation	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	propionate fermentation	40	4 of 10
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	40	4 of 10
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	isoprenoid biosynthesis	38.46	10 of 26
[Ref.: #66794]	C4 and CAM-carbon fixation	37.5	3 of 8
[Ref.: #66794]	gluconeogenesis	37.5	3 of 8
[Ref.: #66794]	pentose phosphate pathway	36.36	4 of 11
[Ref.: #66794]	heme metabolism	35.71	5 of 14
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	d-mannose degradation	33.33	3 of 9
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	degradation of pentoses	32.14	9 of 28
[Ref.: #66794]	degradation of sugar acids	32	8 of 25
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	phenol degradation	30	6 of 20
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	polyamine pathway	26.09	6 of 23
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	sulfate reduction	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]	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.: #8835]	Sample type/isolated from	summer mastitis secretion of heifer
* marker position based on {}

Isolation sources categories

#Infection	#Disease	-
#Host	#Mammals	#Bovinae (Cow, Cattle)
#Host Body Product	#Fluids	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence GU993268 (>99% sequence identity) for Peptoniphilus indolicus from Microbeatlas

Aquatic Samples	94
Soil Samples	203
Animal Samples	1754
Plant Samples	32
Total Samples	2083

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

[Ref.: #8835]	Pathogenicity (animal)	yes
[Ref.: #8835]	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.: #8835]	Peptoniphilus indolicus gene for 16S ribosomal RNA, partial sequence	D14147	1372	GenBank ENA	997350 tax ID
[Ref.: #20218]	Peptoniphilus indolicus strain ATCC 29427 16S ribosomal RNA gene, partial sequence	GU993268	1287	GenBank ENA	997350 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Peptoniphilus indolicus ATCC 29427	GCA_000227315	scaffold	GenBank ENA	997350 tax ID	*
[Ref.: #66792]	Peptoniphilus indolicus ATCC 29427	997350.3	wgs	PATRIC	997350 tax ID	*

[Ref.: #8835]

GC-content

34.0 mol%

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Peptoniphilus indolicus ATCC 29427 PATRIC: 997350.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	78	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Peptoniphilus indolicus ATCC 29427 ATCC 29427 NCBI: GCA_000227315.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	85.352	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	yes	96.36	yes
[Ref.: #69480]	aerobic	aerobicⓘ	no	95.291	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	70.894	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	93.344	no
[Ref.: #69480]	flagellated	motile2+ⓘ	no	82.18	no

Availability in culture collections External links

[Ref.: #8835]

Culture collection no.

DSM 20464, ATCC 29427, CCM 5987

[Ref.: #86984]

SI-ID 45858

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Anaerosphaera aminiphila gen. nov., sp. nov., a glutamate-degrading, Gram-positive anaerobic coccus isolated from a methanogenic reactor treating cattle waste.	Ueki A, Abe K, Suzuki D, Kaku N, Watanabe K, Ueki K	Int J Syst Evol Microbiol	10.1099/ijs.0.011858-0	2009	*
Phylogeny	The completely annotated genome and comparative genomics of the Peptoniphilaceae bacterium str. ING2-D1G, a novel acidogenic bacterium isolated from a mesophilic biogas reactor.	Tomazetto G, Hahnke S, Langer T, Wibberg D, Blom J, Maus I, Puhler A, Klocke M, Schluter A	J Biotechnol	10.1016/j.jbiotec.2017.05.027	2017	*

References

#8835

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 20464

#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 )

#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 )

#86984

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-ID45858.1 )

* These data were automatically processed and therefore are not curated

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Peptoniphilus indolicus ATCC 29427

Peptoniphilus indolicus ATCC 29427 ATCC 29427

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