Pontibacter mucosus (DSM 100162, KCTC 42942, PB3)

Name: Pontibacter mucosus (DSM 100162, KCTC 42942, PB3)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132973

Type strain

Strain Designation PB3

Culture col. no. DSM 100162 KCTC 42942 PB3

NCBI tax ID(s) 1649266

Special Collections DSMZ KCTC Literature strains

Links

Pontibacter mucosus PB3 is an aerobe, Gram-negative, motile prokaryote that was isolated from hexachlorocyclohexane-contaminated pond sediment.

Gram-negative motile rod-shaped aerobe genome sequence 16S sequence

Name and taxonomic classification

SI-ID 24452

KCTC 42942

@ref 20215

Last LPSN update 2025-12-16 10:01:39

Domain Pseudomonadati

Phylum Bacteroidota

Class Cytophagia

Order Cytophagales

Family Hymenobacteraceae

Genus Pontibacter

Species Pontibacter mucosus

Full scientific name Pontibacter mucosus Nayyar et al. 2016

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Flagellum arrangement	Confidence
43975	negative	1.0-1.4 µm	0.3-0.7 µm	rod-shaped	gliding
67771				rod-shaped	gliding
67771	negative
125438	negative					97.5
125439	negative					98.9

Colony morphology

@ref	Colony color	Incubation period	Medium used
43975	pink	1 day	Luria-Bertani agar

Pigmentation

@ref	Production	Name
43975		Flexirubin-type pigments

Culture and growth conditions

Culture medium

@ref	Name	Growth
43975	Brain heart infusion agar
43975	LB (Luria-Bertani) MEDIUM
43975	Marine agar (MA)
43975	Nutrient agar (NA)
43975	Reasoner's 2A agar (R2A)
43975	Tryptic soya yeast agar

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
43975	positive	growth	5-45
43975	positive	optimum	28	mesophilic
67771	positive	growth	28	mesophilic

Culture pH

@ref	Ability	Type	PH
43975	positive	optimum	7.0-8.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
43975	aerobe
67771	aerobe

Spore formation

@ref	Spore formation	Confidence
125439		98.7

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43975	NaCl	positive	growth	0-10 %(w/v)
43975	NaCl	positive	optimum	1-2 %(w/v)

Observation

67771

Observationquinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43975		casein	+	carbon source
43975	16947 ChEBI	citrate	-	hydrolysis
43975	17108 ChEBI	D-arabinose	+	assimilation
43975	18333 ChEBI	D-arabitol	-	assimilation
43975	15824 ChEBI	D-fructose	+	assimilation
43975	12936 ChEBI	D-galactose	+	assimilation
43975	17634 ChEBI	D-glucose	+	assimilation
43975	16899 ChEBI	D-mannitol	+	assimilation
43975	16024 ChEBI	D-mannose	+	assimilation
43975	17924 ChEBI	D-sorbitol	-	assimilation
43975	17113 ChEBI	erythritol	-	assimilation
43975	4853 ChEBI	esculin	+	hydrolysis
43975	16813 ChEBI	galactitol	-	assimilation
43975	5291 ChEBI	gelatin	+	hydrolysis
43975	17368 ChEBI	hypoxanthine	+	carbon source
43975	15443 ChEBI	inulin	-	assimilation
43975	18287 ChEBI	L-fucose	+	assimilation
43975	62345 ChEBI	L-rhamnose	+	assimilation
43975	17266 ChEBI	L-sorbose	+	assimilation
43975	65328 ChEBI	L-xylose	-	assimilation
43975	17716 ChEBI	lactose	+	assimilation
43975	17306 ChEBI	maltose	+	assimilation
43975	28053 ChEBI	melibiose	+	assimilation
43975	17268 ChEBI	myo-inositol	-	assimilation
43975	17632 ChEBI	nitrate	-	reduction
43975	32032 ChEBI	potassium gluconate	-	assimilation
43975	16634 ChEBI	raffinose	+	assimilation
43975	28017 ChEBI	starch	+	hydrolysis
43975	17992 ChEBI	sucrose	+	assimilation
43975	53424 ChEBI	tween 20	+	hydrolysis
43975	53426 ChEBI	tween 80	+	hydrolysis
43975	16199 ChEBI	urea	+	hydrolysis
43975	15318 ChEBI	xanthine	+	carbon source
43975	17151 ChEBI	xylitol	-	assimilation
43975	18222 ChEBI	xylose	-	assimilation

Antibiotic resistance

@ref	ChEBI	Metabolite	Resistance conc.	Sensitivity conc.
43975	17833	gentamicin	10 µg (disc)
43975	6104	kanamycin	30 µg (disc)
43975	17334	penicillin		10 µg (disc)
43975	8309	polymyxin b		300 µg (disc)
43975	27902	tetracycline		30 µg (disc)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
43975	16136 ChEBI	hydrogen sulfide
43975	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
43975	beta-galactosidase	+	3.2.1.23
43975	catalase	+	1.11.1.6
43975	cytochrome oxidase	+	1.9.3.1
43975	DNase	+

Fatty acid profile

Metadata FA analysis

@ref

43975

Fatty acid	Percentage
C17:1 iso I /C17:1 anteiso B	27.4
C15:0 iso	20.38
C16:1ω5c	6.82
C15:0 iso 3OH	5.4
C17:0 iso 3OH	3.93
C20:0	3.69
C18:0	3.3
C16:1ω6c / C16:1ω7c	3.18
C17:1ω6c	2.47
C16:0	2.39
C18:1ω9c	1.55
C17:0	1.53
C16:0 2OH	1.05
iso-C15:1 H / C13:0 OH	0.85

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Contamination	-
#Environmental	#Aquatic	#Pond (small)
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture	Enrichment culture duration	Enrichment culture temperature
24761	hexachlorocyclohexane-contaminated pond sediment	Uttar Pradesh, Lucknow, Chinhat (26° 53' 8.903'' N; 81° 20' 22.495'' E)	India	IND	Asia	26.8858	81.3396 26.8858/81.3396
43975	pond sediment near a hexachlorocyclohexane-producing factory, located at Chinhat, Lucknow, India	Chinhat, Lucknow	India	IND	Asia	26.8858	81.3396 26.8858/81.3396	Luria-Bertani agar	1-2 days	28
67771	From pond sediment containing discarded waste of hexachlorocyclohexane isomers near the India Pesticide Limited factory	Uttar Pradesh, Lucknow, Chinhat, Lucknow	India	IND	Asia

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM305405v1 assembly for Pontibacter mucosus DSM 100162	contig	GCA_003054055	1649266.3	2734482255	1649266	69.22

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24761	Pontibacter mucosus strain PB3 16S ribosomal RNA gene, partial sequence	KP861851	1432		1649266

GC content

@ref	GC-content (mol%)	Method
43975	53.5	real time PCR (RTD-PCR)
24761	53.5	fluorimetric
67771	53.5

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pontibacter mucosus DSM 100162
NCBI: GCA_003054055

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.70	no
125439	motility	BacteriaNetⓘ	no	59.80	no
125439	gram_stain	BacteriaNetⓘ	negative	98.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	67.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pontibacter mucosus strain DSM 100162
PATRIC: 1649266.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.50	no
125438	anaerobic	anaerobicⓘ	no	97.02	yes
125438	spore-forming	spore-formingⓘ	no	84.00	no
125438	aerobic	aerobicⓘ	yes	85.22	yes
125438	thermophilic	thermophileⓘ	no	96.96	no
125438	flagellated	motile2+ⓘ	no	85.50	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pontibacter mangrovi sp. nov., isolated from mangrove sediment.	Mo KL, Wang L, Wu QJ, Ye L, Liu XD, Hu YH, Huang HQ	Int J Syst Evol Microbiol	10.1099/ijsem.0.004280	2020
Phylogeny	Pontibacter mucosus sp. nov., isolated from hexachlorocyclohexane-contaminated pond sediment.	Nayyar N, Kohli P, Mahato NK, Lal R	Int J Syst Evol Microbiol	10.1099/ijsem.0.001013	2016

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 )
#24761	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100162
#43975	Namita Nayyar, Puneet Kohli, Nitish Kumar Mahato, Rup Lal: Pontibacter mucosus sp. nov., isolated from hexachlorocyclohexane-contaminated pond sediment. IJSEM 66: 2234 - 2240 2016 ( DOI 10.1099/ijsem.0.001013 , PubMed 26961966 )
#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) .
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 )

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Pontibacter mucosus (DSM 100162, KCTC 42942, PB3)

Name and taxonomic classification