Name: Xylanibacter rarus 109
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 158435

Type strain:

Species: Xylanibacter rarus

Strain Designation: 109

Culture col. no.: DSM 105141, VKM B-2992

Strain history: <- V. Shcherbakova, Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Science, Pushchino, Russia; 109

NCBI tax ID(s): 1676614 (species)

SI-ID 402586

DSM 105141

Section

Xylanibacter rarus 109 is an obligate anaerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from feces adult human female, 43 years old.

colony-forming
Gram-negative
rod-shaped
mesophilic
obligate anaerobe
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	*Bacteroidota*
	Class	*Bacteroidia*
	Order	*Bacteroidales*
	Family	*Prevotellaceae*
	Genus	*Xylanibacter*
	Species	**Xylanibacter rarus**
	Full Scientific Name (LPSN)	Xylanibacter rarus corrig. (Efimov et al. 2018) Hitch et al. 2023

	Synonym	Prevotella rara
	Synonym	Xylanibacter rara

Information on morphological and physiological properties Morphology

[Ref.: #66770]	Gram stain	negative

[Ref.: #66770]	Cell shape	rod-shaped
[Ref.: #66770]	Cell shape	other

[Ref.: #66770]	Motility	no

[Ref.: #66770]	Type of hemolysis	beta
[Ref.: #66770]	Hemolysis ability	1
[Ref.: #66770]	Colony size	0.5 mm
[Ref.: #66770]	Colony color	colorless but after one week of incubation colonies develop light brown pigmentation.
[Ref.: #66770]	Colony shape	circular
[Ref.: #66770]	Incubation period	2 days
[Ref.: #66770]	Cultivation medium used	rich media

Information on culture and growth conditions Culture and growth conditions

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Culture medium

CHOPPED MEAT MEDIUM (DSMZ Medium 78)

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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

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Culture medium

rich media

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Culture medium growth

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Culture medium composition

expand / minimize

	Kind of temperature		Temperature
[Ref.: #65111]		growth	37 °C
[Ref.: #66770]	no	growth	30 °C
[Ref.: #66770]		optimum	37 °C
[Ref.: #66770]	no	growth	45 °C
[Ref.: #66770]		growth	32-42 °C

[Ref.: #65111]	Temperature range	mesophilic
[Ref.: #66770]	Temperature range	mesophilic
[Ref.: #66770]	Temperature range	thermophilic

	pH	Kind of pH		pH
[Ref.: #66770]			optimum	7-8
[Ref.: #66770]			growth	6-8

Information on physiology and metabolism Physiology and metabolism

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Oxygen tolerance

obligate anaerobe

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Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #66770]		NaCl	no	growth	>1	%(w/v)

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Observation

The 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 activity	Kind of utilization tested
[Ref.: #66770]	cellobiose ChEBI	+	fermentation
[Ref.: #66770]	D-glucose ChEBI	+	fermentation
[Ref.: #66770]	D-mannitol ChEBI	-	fermentation
[Ref.: #66770]	D-mannose ChEBI	-	fermentation
[Ref.: #66770]	D-sorbitol ChEBI	-	fermentation
[Ref.: #66770]	D-xylose ChEBI	+	fermentation
[Ref.: #66770]	esculin ChEBI	+	hydrolysis
[Ref.: #66770]	gelatin ChEBI	+	hydrolysis
[Ref.: #66770]	glycerol ChEBI	-	fermentation
[Ref.: #66770]	L-arabinose ChEBI	+	fermentation
[Ref.: #66770]	L-rhamnose ChEBI	+	fermentation
[Ref.: #66770]	lactose ChEBI	-	fermentation
[Ref.: #66770]	maltose ChEBI	+	fermentation
[Ref.: #66770]	melezitose ChEBI	-	fermentation
[Ref.: #66770]	raffinose ChEBI	+	fermentation
[Ref.: #66770]	salicin ChEBI	-	fermentation
[Ref.: #66770]	sucrose ChEBI	+	fermentation
[Ref.: #66770]	trehalose ChEBI	-	fermentation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #66770]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #66770]	6-phospho-beta-galactosidase	-	3.2.1.85
[Ref.: #66770]	alanine arylamidase	+	3.4.11.2
[Ref.: #66770]	alkaline phosphatase	+	3.1.3.1
[Ref.: #66770]	alpha-arabinosidase	+	3.2.1.55
[Ref.: #66770]	alpha-fucosidase	-	3.2.1.51
[Ref.: #66770]	alpha-galactosidase	+	3.2.1.22
[Ref.: #66770]	alpha-glucosidase	+	3.2.1.20
[Ref.: #66770]	arginine arylamidase	-
[Ref.: #66770]	arginine dihydrolase	-	3.5.3.6
[Ref.: #66770]	beta-galactosidase	-	3.2.1.23
[Ref.: #66770]	beta-glucosidase	+	3.2.1.21
[Ref.: #66770]	beta-glucuronidase	-	3.2.1.31
[Ref.: #66770]	catalase	-	1.11.1.6
[Ref.: #66770]	glutamate decarboxylase	-	4.1.1.15
[Ref.: #66770]	glutamyl-glutamate arylamidase	+
[Ref.: #66770]	glycin arylamidase	-
[Ref.: #66770]	histidine arylamidase	-
[Ref.: #66770]	leucine arylamidase	-	3.4.11.1
[Ref.: #66770]	leucyl glycin arylamidase	+	3.4.11.1
[Ref.: #66770]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #66770]	nitrate reductase	-	1.7.99.4
[Ref.: #66770]	phenylalanine arylamidase	-
[Ref.: #66770]	proline-arylamidase	-	3.4.11.5
[Ref.: #66770]	pyroglutamic acid arylamidase	-
[Ref.: #66770]	serine arylamidase	-
[Ref.: #66770]	tyrosine arylamidase	-
[Ref.: #66770]	urease	-	3.5.1.5
	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.: #65111]	Sample type/isolated from	feces adult human female, 43 years old
[Ref.: #65111]	Geographic location (country and/or sea, region)	Moscow
[Ref.: #65111]	Country	Russia
[Ref.: #65111]	Country ISO 3 Code	RUS
[Ref.: #65111]	Continent	Europe

[Ref.: #66770]	Sample type/isolated from	stool sample from a 43-year-old healthy Russian female
[Ref.: #66770]	Sampling date	2013-03-21
[Ref.: #66770]	Geographic location (country and/or sea, region)	Moscow
[Ref.: #66770]	Country	Russia
[Ref.: #66770]	Country ISO 3 Code	RUS
[Ref.: #66770]	Continent	Europe
[Ref.: #66770]	Enrichment culture	EG agar
[Ref.: #66770]	Enrichment culture composition	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.
[Ref.: #66770]	Enrichment culture duration	3 days
[Ref.: #66770]	Enrichment culture temperature	37 ̊C
[Ref.: #66770]	Isolation/enrichment procedure	Plates were incubated in an atmosphere of 85 % N2 +10 % H2 +5 % CO2 at 37°C for 72 h in anaerobic jars.
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

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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

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.: #66770]	Prevotella rara strain 109 16S ribosomal RNA gene, partial sequence	KX198132	1535	ENA	1676614 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Prevotella rara 109	GCA_001275135	contig	GenBank	1676614 tax ID	*
[Ref.: #66792]	Prevotella rara 109	2639762917	draft	JGI IMG/M	1676614 tax ID	*

[Ref.: #65111]	GC-content	45.7 mol%
[Ref.: #66770]	GC-content	45.7 mol%	genome sequence analysis

Availability in culture collections External links

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Culture collection no.

DSM 105141, VKM B-2992

[Ref.: #111236]

SI-ID 402586

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 .

#111236

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-ID402586.1 )

* These data were automatically processed and therefore are not curated

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