Name: Bacteroides kribbi R2F3-3-3
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 158671

Type strain:

Species: Bacteroides kribbi

Strain Designation: R2F3-3-3

Culture col. no.: KCTC 15460, JCM 31391

NCBI tax ID(s): 1912894 (species)

Section

Bacteroides kribbi R2F3-3-3 is an anaerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from the faeces of a healthy adult.

colony-forming
Gram-negative
rod-shaped
anaerobe
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	*Bacteroidaceae*
	Genus	*Bacteroides*
	Species	**Bacteroides kribbi**
	Full Scientific Name (LPSN)	Bacteroides kribbi Shin et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #65401]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.999

[Ref.: #65401]	Cell length	0.4-0.7 µm

[Ref.: #65401]	Cell width	0.2-0.3 µm

[Ref.: #65401]	Cell shape	rod-shaped

[Ref.: #65401]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %90.095

[Ref.: #65401]	Colony size	1 mm
[Ref.: #65401]	Colony color	creamy
[Ref.: #65401]	Colony shape	circular
[Ref.: #65401]	Cultivation medium used	Reinforced Clostridial Medium

Information on culture and growth conditions Culture and growth conditions

	Temperatures	Kind of temperature		Temperature
[Ref.: #65401]			growth	15-40 °C
[Ref.: #65401]			optimum	37 °C

[Ref.: #65401]

Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #65401]			optimum	6.5
[Ref.: #65401]			growth	5.5-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #65401]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.379

[Ref.: #65401]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.995
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

[Ref.: #65401]	Observation	isolates grow in the presence of bile
[Ref.: #65401]	Observation	the sole quinone is MK-10, the major polar lipid is PE, and other minor lipids are PN, five PLs (PL1-PL5) and two unidenti-fied ALs (AL1-AL2)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #65401]	cellobiose ChEBI	+	assimilation
[Ref.: #65401]	esculin ChEBI	+	hydrolysis
[Ref.: #65401]	gelatin ChEBI	+	hydrolysis
[Ref.: #65401]	glucose ChEBI	+	assimilation
[Ref.: #65401]	glucose ChEBI	+	fermentation
[Ref.: #65401]	glycerol ChEBI	-	assimilation
[Ref.: #65401]	L-arabinose ChEBI	+	assimilation
[Ref.: #65401]	lactose ChEBI	+	assimilation
[Ref.: #65401]	maltose ChEBI	+	assimilation
[Ref.: #65401]	mannitol ChEBI	+	assimilation
[Ref.: #65401]	mannose ChEBI	+	assimilation
[Ref.: #65401]	melezitose ChEBI	+	assimilation
[Ref.: #65401]	nitrate ChEBI	-	reduction
[Ref.: #65401]	raffinose ChEBI	+	assimilation
[Ref.: #65401]	rhamnose ChEBI	+	assimilation
[Ref.: #65401]	salicin ChEBI	-	assimilation
[Ref.: #65401]	sorbitol ChEBI	+	assimilation
[Ref.: #65401]	sucrose ChEBI	+	assimilation
[Ref.: #65401]	trehalose ChEBI	+	assimilation
[Ref.: #65401]	urea ChEBI	-	assimilation
[Ref.: #65401]	xylose ChEBI	+	assimilation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #65401]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #65401]	6-phospho-beta-galactosidase	-	3.2.1.85
[Ref.: #65401]	alkaline phosphatase	-	3.1.3.1
[Ref.: #65401]	alpha-arabinosidase	-	3.2.1.55
[Ref.: #65401]	alpha-fucosidase	-	3.2.1.51
[Ref.: #65401]	alpha-galactosidase	+	3.2.1.22
[Ref.: #65401]	alpha-glucosidase	+	3.2.1.20
[Ref.: #65401]	arginine arylamidase	-
[Ref.: #65401]	arginine dihydrolase	-	3.5.3.6
[Ref.: #65401]	beta-galactosidase	+	3.2.1.23
[Ref.: #65401]	beta-glucuronidase	-	3.2.1.31
[Ref.: #65401]	catalase	-	1.11.1.6
[Ref.: #65401]	cytochrome oxidase	-	1.9.3.1
[Ref.: #65401]	glycin arylamidase	-
[Ref.: #65401]	histidine arylamidase	-
[Ref.: #65401]	leucine arylamidase	-	3.4.11.1
[Ref.: #65401]	leucyl glycin arylamidase	-	3.4.11.1
[Ref.: #65401]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #65401]	phenylalanine arylamidase	-
[Ref.: #65401]	proline-arylamidase	-	3.4.11.5
[Ref.: #65401]	pyroglutamic acid arylamidase	+
[Ref.: #65401]	pyroglutamic acid arylamidase	-
[Ref.: #65401]	serine arylamidase	-
[Ref.: #65401]	tyrosine arylamidase	-
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #65401]

Fatty acid	Percentage
C15:0 anteiso	39.3
C16:0 3OH	11.8
C15:0 iso	10.8
iso-C17:03-OH and/or C18:2 DMA	10
iso-C15:0 and/or unknown 13.570	5.5
C14:0	4.3
C16:0	4
C13:1 cis 12 and/or C 14:0	3.3
anteiso-C17:0 3-OH	2.7
C15:0	2.1
C18:1 cis9	2
anteiso-C15:0 DMA	1.1

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #65401]	Sample type/isolated from	the faeces of a healthy adult
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Bacteroides kribbi JCM 31391	GCA_007341395	contig	GenBank	1912894 tax ID	*
[Ref.: #66792]	Bacteroides kribbi strain JCM 31391	1912894.3	wgs	PATRIC	1912894 tax ID	*

[Ref.: #65401]

GC-content

42.4-42.6 mol%

high performance liquid chromatography (HPLC)

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: Bacteroides kribbi strain JCM 31391 PATRIC: 1912894.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Bacteroides kribbi strain JCM 31391 PATRIC: 1912894.3
[Ref.: #69480]	motile	no	92.217	yes
[Ref.: #69480]	gram-positive	no	97.446	yes
[Ref.: #69480]	anaerobic	yes	95.573	yes
[Ref.: #69480]	aerobic	no	96.372	no
[Ref.: #69480]	halophile	no	92.167	no
[Ref.: #69480]	spore-forming	no	94.362	yes
[Ref.: #69480]	glucose-util	yes	90.284	yes
[Ref.: #69480]	flagellated	no	97.31	no
[Ref.: #69480]	thermophile	no	99.611	yes
[Ref.: #69480]	glucose-ferment	yes	76.112	yes

Availability in culture collections External links

[Ref.: #65401]

Culture collection no.

KCTC 15460, JCM 31391

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Bacteroides koreensis sp. nov. and Bacteroides kribbi sp. nov., two new members of the genus Bacteroides.	Shin Y, Park SJ, Paek J, Kim JS, Rhee MS, Kim H, Kook JK, Chang YH	Int J Syst Evol Microbiol	10.1099/ijsem.0.002226	2017	*

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 )

#65401

Yeseul Shin, Soo-Je Park, Jayoung Paek, Joong-Su Kim, Moon-Soo Rhee, Hongik Kim, Joong-Ki Kook, Young-Hyo Chang: Bacteroides koreensis sp. nov. and Bacteroides kribbi sp. nov., two new members of the genus Bacteroides. IJSEM 67: 4352 - 4357 2017 ( DOI 10.1099/ijsem.0.002226 , PubMed 28945536 )

#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) .

#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 )

* 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 Bacteroides kribbi in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Bacteroides kribbi strain JCM 31391

Bacteroides kribbi strain JCM 31391

Change proposal

Change proposal