Name: Pontibacter mucosus PB3
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 132973

Type strain:

Species: Pontibacter mucosus

Strain Designation: PB3

Culture col. no.: DSM 100162, KCTC 42942

Strain history: <- Rup Lal, Univ. of Delhi, India

NCBI tax ID(s): 1649266 (species)

Special Collections

Section

When using BacDive for research please cite our paper

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Bacteroidota*
	Class	*Cytophagia*
	Order	*Cytophagales*
	Family	*Hymenobacteraceae*
	Genus	*Pontibacter*
	Species	**Pontibacter mucosus**
	Full Scientific Name (LPSN)	Pontibacter mucosus Nayyar et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #43975]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #125438]	Gram stain	negative Confidence in %97.5
[Ref.: #125439]	Gram stain	negative Confidence in %98.9

[Ref.: #43975]	Cell length	1.0-1.4 µm

[Ref.: #43975]	Cell width	0.3-0.7 µm

[Ref.: #43975]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #43975]	Motility	yes
[Ref.: #67771]	Motility	yes

[Ref.: #43975]	Flagellum arrangement	gliding
[Ref.: #67771]	Flagellum arrangement	gliding

[Ref.: #43975]	Colony color	pink
[Ref.: #43975]	Incubation period	1 day
[Ref.: #43975]	Cultivation medium used	Luria-Bertani agar

[Ref.: #43975]	Pigment production	no
[Ref.: #43975]	Pigment name	Flexirubin-type pigments

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43975]

Culture medium

Brain heart infusion agar

[Ref.: #43975]

Culture medium growth

[Ref.: #43975]

Culture medium

LB (Luria-Bertani) MEDIUM

[Ref.: #43975]

Culture medium growth

[Ref.: #43975]

Culture medium

Marine agar (MA)

[Ref.: #43975]

Culture medium growth

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Culture medium

Nutrient agar (NA)

[Ref.: #43975]

Culture medium growth

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Culture medium

Reasoner's 2A agar (R2A)

[Ref.: #43975]

Culture medium growth

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Culture medium

Tryptic soya yeast agar

[Ref.: #43975]

Culture medium growth

		Temperature
[Ref.: #43975]	growth	5-45 °C
[Ref.: #43975]	optimum	28 °C
[Ref.: #67771]	growth	28 °C

	pH	Kind of pH		pH
[Ref.: #43975]			optimum	7.0-8.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43975]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #125439]

Ability of spore formation

no Confidence in %98.7

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43975]		NaCl		growth	0-10	%(w/v)
[Ref.: #43975]		NaCl		optimum	1-2	%(w/v)

[Ref.: #67771]

Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43975]	casein	+	carbon source
[Ref.: #43975]	citrate ChEBI	-	hydrolysis
[Ref.: #43975]	D-arabinose ChEBI	+	assimilation
[Ref.: #43975]	D-arabitol ChEBI	-	assimilation
[Ref.: #43975]	D-fructose ChEBI	+	assimilation
[Ref.: #43975]	D-galactose ChEBI	+	assimilation
[Ref.: #43975]	D-glucose ChEBI	+	assimilation
[Ref.: #43975]	D-mannitol ChEBI	+	assimilation
[Ref.: #43975]	D-mannose ChEBI	+	assimilation
[Ref.: #43975]	D-sorbitol ChEBI	-	assimilation
[Ref.: #43975]	erythritol ChEBI	-	assimilation
[Ref.: #43975]	esculin ChEBI	+	hydrolysis
[Ref.: #43975]	galactitol ChEBI	-	assimilation
[Ref.: #43975]	gelatin ChEBI	+	hydrolysis
[Ref.: #43975]	hypoxanthine ChEBI	+	carbon source
[Ref.: #43975]	inulin ChEBI	-	assimilation
[Ref.: #43975]	L-fucose ChEBI	+	assimilation
[Ref.: #43975]	L-rhamnose ChEBI	+	assimilation
[Ref.: #43975]	L-sorbose ChEBI	+	assimilation
[Ref.: #43975]	L-xylose ChEBI	-	assimilation
[Ref.: #43975]	lactose ChEBI	+	assimilation
[Ref.: #43975]	maltose ChEBI	+	assimilation
[Ref.: #43975]	melibiose ChEBI	+	assimilation
[Ref.: #43975]	myo-inositol ChEBI	-	assimilation
[Ref.: #43975]	nitrate ChEBI	-	reduction
[Ref.: #43975]	potassium gluconate ChEBI	-	assimilation
[Ref.: #43975]	raffinose ChEBI	+	assimilation
[Ref.: #43975]	starch ChEBI	+	hydrolysis
[Ref.: #43975]	sucrose ChEBI	+	assimilation
[Ref.: #43975]	tween 20 ChEBI	+	hydrolysis
[Ref.: #43975]	tween 80 ChEBI	+	hydrolysis
[Ref.: #43975]	urea ChEBI	+	hydrolysis
[Ref.: #43975]	xanthine ChEBI	+	carbon source
[Ref.: #43975]	xylitol ChEBI	-	assimilation
[Ref.: #43975]	xylose ChEBI	-	assimilation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #43975]	gentamicin ChEBI				yes	10	µg (disc)
[Ref.: #43975]	kanamycin ChEBI				yes	30	µg (disc)
[Ref.: #43975]	penicillin ChEBI	yes	10	µg (disc)
[Ref.: #43975]	polymyxin b ChEBI	yes	300	µg (disc)
[Ref.: #43975]	tetracycline ChEBI	yes	30	µg (disc)

	Metabolite production	Metabolite	Production
[Ref.: #43975]		hydrogen sulfide ChEBI	no
[Ref.: #43975]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #43975]	beta-galactosidase	+	3.2.1.23
[Ref.: #43975]	catalase	+	1.11.1.6
[Ref.: #43975]	cytochrome oxidase	+	1.9.3.1
[Ref.: #43975]	DNase	+

Fatty acid profile

Metadata FA analysis

Reference

[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

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

[Ref.: #24761]	Sample type/isolated from	hexachlorocyclohexane-contaminated pond sediment
[Ref.: #24761]	Geographic location (country and/or sea, region)	Uttar Pradesh, Lucknow, Chinhat (26° 53' 8.903'' N; 81° 20' 22.495'' E)
[Ref.: #24761]	Country	India
[Ref.: #24761]	Country ISO 3 Code	IND
[Ref.: #24761]	Continent	Asia
[Ref.: #24761]	Geographic location	26.8858°/81.3396°

[Ref.: #43975]	Sample type/isolated from	pond sediment near a hexachlorocyclohexane-producing factory, located at Chinhat, Lucknow, India
[Ref.: #43975]	Geographic location (country and/or sea, region)	Chinhat, Lucknow
[Ref.: #43975]	Country	India
[Ref.: #43975]	Country ISO 3 Code	IND
[Ref.: #43975]	Continent	Asia
[Ref.: #43975]	Geographic location	26.8858°/81.3396°
[Ref.: #43975]	Enrichment culture	Luria-Bertani agar
[Ref.: #43975]	Enrichment culture duration	1-2 days
[Ref.: #43975]	Enrichment culture temperature	28 ̊C

[Ref.: #67771]	Sample type/isolated from	From pond sediment containing discarded waste of hexachlorocyclohexane isomers near the India Pesticide Limited factory
[Ref.: #67771]	Geographic location (country and/or sea, region)	Uttar Pradesh, Lucknow, Chinhat, Lucknow
[Ref.: #67771]	Country	India
[Ref.: #67771]	Country ISO 3 Code	IND
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Contamination	-
#Environmental	#Aquatic	#Pond (small)
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

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.: #24761]	Pontibacter mucosus strain PB3 16S ribosomal RNA gene, partial sequence	KP861851	1432	GenBank ENA	1649266 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pontibacter mucosus DSM 100162	GCA_003054055	contig	GenBank ENA	1649266 tax ID	*
[Ref.: #66792]	Pontibacter mucosus strain DSM 100162	1649266.3	wgs	PATRIC	1649266 tax ID	*
[Ref.: #66792]	Pontibacter mucosus DSM 100162	2734482255	draft	JGI IMG/M	1649266 tax ID	*

[Ref.: #43975]	GC-content	53.5 mol%	real time PCR (RTD-PCR)
[Ref.: #24761]	GC-content	53.5 mol%	fluorimetric
[Ref.: #67771]	GC-content	53.5 mol%

Data predicted using genome information as a basis Genome-based predictions

	Model	Trait	Prediction	Confidence in %	In training data
	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.: #125438]	gram-positive	gram-positiveⓘ	no	97.5	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	97.018	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	84	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	85.224	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	96.961	no
[Ref.: #125438]	motile2+	flagellatedⓘ	no	85.5	yes

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pontibacter mucosus DSM 100162 NCBI: GCA_003054055
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	98.7
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	59.8
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	98.9
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate anaerobe	67.7

Availability in culture collections External links

[Ref.: #24761]

Culture collection no.

DSM 100162, KCTC 42942

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 .

* These data were automatically processed and therefore are not curated

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Pontibacter mucosus strain DSM 100162

Pontibacter mucosus DSM 100162

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