Prevotella rara (DSM 105141, VKM B-2992, 109)

Name: Prevotella rara (DSM 105141, VKM B-2992, 109)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 158435

Type strain

Strain Designation 109

Culture col. no. DSM 105141 VKM B-2992 109

NCBI tax ID(s) 1676614

Special Collections DSMZ Literature strains

History DSMZ <- V. Shcherbakova, Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Science, Pushchino, Russia; 109

Links

Prevotella rara 109 is an obligate anaerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from feces adult human female, 43 years old.

Gram-negative rod-shaped colony-forming obligate anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 402586

VKM B-2992,DSM 105141

@ref 20215

Last LPSN update 2026-05-29 08:43:58

Domain Bacteria

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Prevotellaceae

Genus Prevotella

Species Prevotella rara

Full scientific name Prevotella rara Efimov et al. 2018

Synonyms (2)

Xylanibacter rarus
Xylanibacter rara

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
66770	negative	rod-shaped
66770		other
125439	negative		98.515

Colony morphology

@ref	Type of hemolysis	Hemolysis ability	Colony size	Colony color	Colony shape	Incubation period	Medium used
66770	beta	1	0.5 mm	colorless but after one week of incubation colonies develop light brown pigmentation.	circular	2 days	rich media

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
65111	CHOPPED MEAT MEDIUM (DSMZ Medium 78)		Medium recipe at MediaDive	Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water
66770	rich media			with defibrinated sheep blood

Culture temp

@ref	Growth	Type	Temperature (°C)
65111	positive	growth	37
66770	negative	growth	30
66770	positive	optimum	37
66770	negative	growth	45
66770	positive	growth	32-42

Culture pH

@ref	Ability	Type	PH
66770	positive	optimum	7-8
66770	positive	growth	6-8

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
66770	obligate anaerobe
125439	obligate anaerobe	99.85

Spore formation

@ref	Spore formation	Confidence
66770
125439		99.981

Halophily

@ref	Salt	Growth	Tested relation	Concentration
66770	NaCl		growth	>1 %(w/v)

Observation

66770

ObservationThe morphology of the cells greatly depended on the culture medium in which the strain was incubated. Most cells grown in Anaerobe Basal Broth (Oxoid) after 72 h of incubation were short rods (0.3-0.4 x 0.9-1.4 µm), while cells grown on Anaerobe Basal Agar (Oxoid) in Petri dishes without blood, were longer (0.50-0.55 x 1.0-8.0 µm). On SchaedlerAnaerobe Broth (Oxoid) the length of the cells varied from short rods (0.3-0.4 x 1.2-2.3 µm) to long filamentous forms reaching 20 µm, with some filamento

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
66770	17057 ChEBI	cellobiose	+	fermentation
66770	17634 ChEBI	D-glucose	+	fermentation
66770	16899 ChEBI	D-mannitol	-	fermentation
66770	16024 ChEBI	D-mannose	-	fermentation
66770	17924 ChEBI	D-sorbitol	-	fermentation
66770	65327 ChEBI	D-xylose	+	fermentation
66770	4853 ChEBI	esculin	+	hydrolysis
66770	5291 ChEBI	gelatin	+	hydrolysis
66770	17754 ChEBI	glycerol	-	fermentation
66770	30849 ChEBI	L-arabinose	+	fermentation
66770	62345 ChEBI	L-rhamnose	+	fermentation
66770	17716 ChEBI	lactose	-	fermentation
66770	17306 ChEBI	maltose	+	fermentation
66770	6731 ChEBI	melezitose	-	fermentation
66770	16634 ChEBI	raffinose	+	fermentation
66770	17814 ChEBI	salicin	-	fermentation
66770	17992 ChEBI	sucrose	+	fermentation
66770	27082 ChEBI	trehalose	-	fermentation

Metabolite production

@ref	Chebi-ID	Metabolite	Production
66770	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
66770	6-phospho-beta-galactosidase	-	3.2.1.85
66770	alanine arylamidase	+	3.4.11.2
66770	alkaline phosphatase	+	3.1.3.1
66770	alpha-arabinosidase	+	3.2.1.55
66770	alpha-fucosidase	-	3.2.1.51
66770	alpha-galactosidase	+	3.2.1.22
66770	alpha-glucosidase	+	3.2.1.20
66770	arginine arylamidase	-
66770	arginine dihydrolase	-	3.5.3.6
66770	beta-galactosidase	-	3.2.1.23
66770	beta-glucosidase	+	3.2.1.21
66770	beta-glucuronidase	-	3.2.1.31
66770	catalase	-	1.11.1.6
66770	glutamate decarboxylase	-	4.1.1.15
66770	glutamyl-glutamate arylamidase	+
66770	glycin arylamidase	-
66770	histidine arylamidase	-
66770	leucine arylamidase	-	3.4.11.1
66770	leucyl glycin arylamidase	+	3.4.11.1
66770	N-acetyl-beta-glucosaminidase	-	3.2.1.52
66770	nitrate reductase	-	1.7.99.4
66770	phenylalanine arylamidase	-
66770	proline-arylamidase	-	3.4.11.5
66770	pyroglutamic acid arylamidase	-
66770	serine arylamidase	-
66770	tyrosine arylamidase	-
66770	urease	-	3.5.1.5

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)
#Host	#Human	#Female

Isolation

@ref	Sample type	Host species	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Enrichment culture	Enrichment culture composition	Enrichment culture duration	Enrichment culture temperature	Isolation procedure
65111	feces adult human female, 43 years old	Homo sapiens		Moscow	Russia	RUS	Europe
66770	stool sample from a 43-year-old healthy Russian female	Homo sapiens	2013-03-21	Moscow	Russia	RUS	Europe	EG agar	supplemented with 5 % (v/v) defibrinated sheep blood. EG medium base consisted of (per 100 ml): 0.24 g Lab-Lemco powder (Oxoid), 1.0 g Proteose peptone No. 3 (BD-Difco), 0.5 g yeast extract, 0.4 g Na2HPO4, 0.15 g glucose, 0.05 g soluble starch, 0.02 g L-cystine, 1.5 g agar and 0.05 g L-cysteine. HCl. H2O.	3 days	37	Plates were incubated in an atmosphere of 85 % N2 +10 % H2 +5 % CO2 at 37°C for 72 h in anaerobic jars.

Taxonmaps

69479

Global distribution of 16S sequence KX198132 (>99% sequence identity) for Prevotella rara from Microbeatlas

Aquatic Samples	448
Soil Samples	143
Animal Samples	9336
Plant Samples	33
Total Samples	9960

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	IMG accession	NCBI tax ID	Score
66792	ASM127513v1 assembly for Xylanibacter rarus 109	contig	GCA_001275135	2639762917	1676614	60.66

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
66770	Xylanibacter rarus strain 109 16S ribosomal RNA gene, partial sequence	KX198132	1535		1676614

GC content

@ref	GC-content (mol%)	Method
65111	45.7
66770	45.7	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM127513v1 assembly for Xylanibacter rarus 109
NCBI: GCA_001275135

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	99.85	no
125439	motility	BacteriaNetⓘ	no	84.59	no
125439	gram_stain	BacteriaNetⓘ	negative	98.52	no
125439	spore_formation	BacteriaNetⓘ	no	99.98	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Prevotella rara sp. nov., isolated from human faeces.	Efimov BA, Chaplin AV, Shcherbakova VA, Suzina NE, Podoprigora IV, Shkoporov AN	Int J Syst Evol Microbiol	10.1099/ijsem.0.003066	2018

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 )
#65111	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 105141
#66770	Boris A. Efimov, Andrei V. Chaplin, Victoria A. Shcherbakova, Natalia E. Suzina, Irina V. Podoprigora, Andrei N. Shkoporov: Prevotella rara sp. nov., isolated from human faeces. IJSEM 68: 3818 - 3825 2018 ( DOI 10.1099/ijsem.0.003066 , PubMed 30339117 )
#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) .
#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 .
#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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Prevotella rara (DSM 105141, VKM B-2992, 109)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_001275135

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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