Pedobacter quisquiliarum (CGMCC 1.15343, NBRC 111767, C62-2)

Name: Pedobacter quisquiliarum (CGMCC 1.15343, NBRC 111767, C62-2)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 158603

Type strain

Strain Designation C62-2

Culture col. no. CGMCC 1.15343 NBRC 111767 C62-2

NCBI tax ID(s) 1834438

Special Collections Literature strains

Links

Pedobacter quisquiliarum C62-2 is an aerobe, Gram-negative, rod-shaped prokaryote that forms circular colonies and was isolated from activated sludge.

Gram-negative rod-shaped colony-forming aerobe genome sequence 16S sequence

Name and taxonomic classification

SI-ID 272939

LMG 31388,NBRC 111767

@ref 20215

Last LPSN update 2025-12-16 10:08:04

Domain Pseudomonadati

Phylum Bacteroidota

Class Sphingobacteriia

Order Sphingobacteriales

Family Sphingobacteriaceae

Genus Pedobacter

Species Pedobacter quisquiliarum

Full scientific name Pedobacter quisquiliarum Zhang et al. 2018

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
65319	negative	0.7-1.8 µm	0.45-0.68 µm	rod-shaped
125439	negative				99.4
125438	negative				96.886

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
65319	1 mm	light-yellow	circular	3 days	R2A

Pigmentation

@ref	Production	Name
65319		flexirubin type pigments

Culture and growth conditions

Culture medium

@ref	Name	Growth
65319	Reasoner's 2A agar (R2A)

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
65319	positive	growth	20-37
65319	positive	optimum	30	mesophilic

Culture pH

@ref	Ability	Type	PH
65319	positive	optimum	7
65319	positive	growth	5-8

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
65319	aerobe
125439	obligate aerobe	95.2

Spore formation

@ref	Spore formation	Confidence
65319
125439		99.2

Halophily

@ref	Salt	Growth	Tested relation	Concentration
65319	NaCl	positive	growth	0-3 %(w/v)
65319	NaCl	positive	optimum	0 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
65319	16808 ChEBI	2-dehydro-D-gluconate	+	builds acid from
65319	58143 ChEBI	5-dehydro-D-gluconate	-	builds acid from
65319	27613 ChEBI	amygdalin	+	builds acid from
65319	18305 ChEBI	arbutin	+	builds acid from
65319	17057 ChEBI	cellobiose	+	builds acid from
65319	17108 ChEBI	D-arabinose	-	builds acid from
65319	18333 ChEBI	D-arabitol	-	builds acid from
65319	15824 ChEBI	D-fructose	+	builds acid from
65319	28847 ChEBI	D-fucose	-	builds acid from
65319	12936 ChEBI	D-galactose	+	builds acid from
65319	17634 ChEBI	D-glucose	+	builds acid from
65319	62318 ChEBI	D-lyxose	+	builds acid from
65319	16024 ChEBI	D-mannose	+	builds acid from
65319	16988 ChEBI	D-ribose	-	builds acid from
65319	16443 ChEBI	D-tagatose	-	builds acid from
65319	65327 ChEBI	D-xylose	+	builds acid from
65319	17113 ChEBI	erythritol	-	builds acid from
65319	4853 ChEBI	esculin	+	builds acid from
65319	4853 ChEBI	esculin	+	hydrolysis
65319	16813 ChEBI	galactitol	-	builds acid from
65319	28066 ChEBI	gentiobiose	+	builds acid from
65319	24265 ChEBI	gluconate	+	builds acid from
65319	17234 ChEBI	glucose	-	fermentation
65319	17754 ChEBI	glycerol	-	builds acid from
65319	28087 ChEBI	glycogen	-	builds acid from
65319	15443 ChEBI	inulin	+	builds acid from
65319	30849 ChEBI	L-arabinose	+	builds acid from
65319	18403 ChEBI	L-arabitol	-	builds acid from
65319	17266 ChEBI	L-sorbose	-	builds acid from
65319	65328 ChEBI	L-xylose	-	builds acid from
65319	17716 ChEBI	lactose	+	builds acid from
65319	17306 ChEBI	maltose	+	builds acid from
65319	29864 ChEBI	mannitol	-	builds acid from
65319	6731 ChEBI	melezitose	+	builds acid from
65319	28053 ChEBI	melibiose	+	builds acid from
65319	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from
65319	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from
65319	37657 ChEBI	methyl D-glucoside	+	builds acid from
65319	17268 ChEBI	myo-inositol	-	builds acid from
65319	506227 ChEBI	N-acetylglucosamine	+	builds acid from
65319	17632 ChEBI	nitrate	-	reduction
65319	16634 ChEBI	raffinose	+	builds acid from
65319	15963 ChEBI	ribitol	-	builds acid from
65319	17814 ChEBI	salicin	+	builds acid from
65319	30911 ChEBI	sorbitol	-	builds acid from
65319	28017 ChEBI	starch	+	builds acid from
65319	17992 ChEBI	sucrose	+	builds acid from
65319	27082 ChEBI	trehalose	+	builds acid from
65319	32528 ChEBI	turanose	+	builds acid from
65319	53426 ChEBI	tween 80	-	assimilation

Metabolite production

@ref	Chebi-ID	Metabolite
65319	15688 ChEBI	acetoin
65319	16136 ChEBI	hydrogen sulfide
65319	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
65319	15688 ChEBI	acetoin	-

Enzymes

@ref	Value	Activity	Ec
65319	acid phosphatase	+	3.1.3.2
65319	alkaline phosphatase	+	3.1.3.1
65319	alpha-chymotrypsin	-	3.4.21.1
65319	alpha-fucosidase	-	3.2.1.51
65319	alpha-galactosidase	-	3.2.1.22
65319	alpha-glucosidase	-	3.2.1.20
65319	alpha-mannosidase	-	3.2.1.24
65319	arginine dihydrolase	-	3.5.3.6
65319	beta-galactosidase	-	3.2.1.23
65319	beta-glucosidase	-	3.2.1.21
65319	beta-glucuronidase	-	3.2.1.31
65319	catalase	+	1.11.1.6
65319	cystine arylamidase	-	3.4.11.3
65319	cytochrome oxidase	+	1.9.3.1
65319	esterase (C 4)	+
65319	esterase Lipase (C 8)	+
65319	leucine arylamidase	+	3.4.11.1
65319	lipase (C 14)	-
65319	N-acetyl-beta-glucosaminidase	+	3.2.1.52
65319	naphthol-AS-BI-phosphohydrolase	+
65319	urease	-	3.5.1.5
65319	valine arylamidase	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Waste	#Activated sludge

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture	Enrichment culture temperature	Isolation procedure
65319	activated sludge	Shanghang county, Fujian Province	China	CHN	Asia	25.6286	116.82 25.6286/116.82	R2A	30	Activated sludge (1 g) was incubated at 30°C using R2A agar (Difco). After enriching three times, the enriched culture was serially diluted (10-fold) intubes containing 0.9 ml of R2A broth. Aliquots of 0.2 ml were spread on R2A agar plates to cultivate separated colonies.

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1464217v1 assembly for Pedobacter quisquiliarum CGMCC 1.15343	contig	GCA_014642175	1834438.3	2996083331	1834438	72.87

16S sequences

@ref	Description	Accession	Database
65319	Pedobacter quisquiliarum strain C62-2 16S ribosomal RNA gene, partial sequence	KU973598

GC content

@ref	GC-content (mol%)	Method
65319	43.2	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pedobacter quisquiliarum CGMCC 1.15343
NCBI: GCA_014642175

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.20	no
125439	motility	BacteriaNetⓘ	no	60.30	no
125439	gram_stain	BacteriaNetⓘ	negative	99.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	95.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pedobacter quisquiliarum strain CGMCC 1.15343
PATRIC: 1834438.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.89	yes
125438	anaerobic	anaerobicⓘ	no	96.87	yes
125438	spore-forming	spore-formingⓘ	no	88.32	no
125438	aerobic	aerobicⓘ	yes	86.87	yes
125438	thermophilic	thermophileⓘ	no	98.13	yes
125438	flagellated	motile2+ⓘ	no	86.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pedobacter quisquiliarum sp. nov., isolated from activated sludge.	Zhang B, Liu ZQ, Zheng YG	Int J Syst Evol Microbiol	10.1099/ijsem.0.002531	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 )
#65319	Bo Zhang, Zhi-Qiang Liu, Yu-Guo Zheng: Pedobacter quisquiliarum sp. nov., isolated from activated sludge. IJSEM 68: 438 - 442 2018 ( DOI 10.1099/ijsem.0.002531 , PubMed 29231155 )
#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) .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#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 )

Rate our new design

Content

About us

Pedobacter quisquiliarum (CGMCC 1.15343, NBRC 111767, C62-2)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_014642175

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media