Name: Pelagirhabdus alkalitolerans S5
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 158524

Type strain:

Species: Pelagirhabdus alkalitolerans

Strain Designation: S5

Culture col. no.: KCTC 33632, CGMCC 1.15177

NCBI tax ID(s): 1612202 (species)

Special Collections

Section

When using BacDive for research please cite our paper

Pelagirhabdus alkalitolerans S5 is a facultative anaerobe, mesophilic, Gram-positive bacterium that forms circular colonies and was isolated from beach sediment sample.

colony-forming
Gram-positive
rod-shaped
facultative anaerobe
mesophilic
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	*Bacillota*
	Class	*Bacilli*
	Order	*Caryophanales*
	Family	*Bacillaceae*
	Genus	*Pelagirhabdus*
	Species	**Pelagirhabdus alkalitolerans**
	Full Scientific Name (LPSN)	Pelagirhabdus alkalitolerans Sultanpuram et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #23028]	Gram stain	positive

[Ref.: #23028]	Cell length	1.0-1.2 µm

[Ref.: #23028]	Cell width	0.3-0.4 µm

[Ref.: #23028]	Cell shape	rod-shaped

[Ref.: #23028]	Motility	no

[Ref.: #23028]	Colony size	0.8-1.0 mm
[Ref.: #23028]	Colony color	cream-coloured
[Ref.: #23028]	Colony shape	circular
[Ref.: #23028]	Cultivation medium used	alkaline medium

Information on culture and growth conditions Culture and growth conditions

[Ref.: #23028]

Culture medium

alkaline medium

[Ref.: #23028]

Culture medium growth

	Temperatures	Kind of temperature		Temperature
[Ref.: #23028]			optimum	37 °C
[Ref.: #23028]			growth	20-55 °C

	pH	Kind of pH		pH
[Ref.: #23028]			optimum	8.5-9.0
[Ref.: #23028]			growth	6.5-11.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #23028]	Oxygen tolerance	facultative anaerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %97.1

[Ref.: #23028]	Type of spore	endospore
[Ref.: #23028]	Ability of spore formation	no

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #23028]		NaCl		optimum	10	%(w/v)
[Ref.: #23028]		NaCl		growth	0-16	%(w/v)

[Ref.: #23028]

Observation

Neither gas nor acid are produced under aerobic or anaerobic conditions

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #23028]	ammonium chloride ChEBI	-	nitrogen source
[Ref.: #23028]	aspartate ChEBI	-	nitrogen source
[Ref.: #23028]	casein	-	hydrolysis
[Ref.: #23028]	cellobiose ChEBI	+	assimilation
[Ref.: #23028]	cellulose ChEBI	-	hydrolysis
[Ref.: #23028]	citrate ChEBI	-	assimilation
[Ref.: #23028]	D-arabinose ChEBI	+	assimilation
[Ref.: #23028]	D-galactose ChEBI	+	assimilation
[Ref.: #23028]	D-glucose ChEBI	+	assimilation
[Ref.: #23028]	D-mannitol ChEBI	+	assimilation
[Ref.: #23028]	D-ribose ChEBI	-	assimilation
[Ref.: #23028]	D-sorbitol ChEBI	-	carbon source
[Ref.: #23028]	D-xylose ChEBI	+	assimilation
[Ref.: #23028]	dna ChEBI	-	hydrolysis
[Ref.: #23028]	esculin ChEBI	-	hydrolysis
[Ref.: #23028]	ethanol ChEBI	-	assimilation
[Ref.: #23028]	fructose ChEBI	+	assimilation
[Ref.: #23028]	gelatin ChEBI	+	hydrolysis
[Ref.: #23028]	glucose ChEBI	-	fermentation
[Ref.: #23028]	glucose ChEBI	+	carbon source
[Ref.: #23028]	hippurate ChEBI	-	hydrolysis
[Ref.: #23028]	hypoxanthine ChEBI	-	hydrolysis
[Ref.: #23028]	inulin ChEBI	-	carbon source
[Ref.: #23028]	L-glutamate ChEBI	-	nitrogen source
[Ref.: #23028]	L-sorbose ChEBI	-	assimilation
[Ref.: #23028]	lactate ChEBI	-	assimilation
[Ref.: #23028]	lactose ChEBI	+	assimilation
[Ref.: #23028]	maltose ChEBI	+	assimilation
[Ref.: #23028]	mannose ChEBI	+	assimilation
[Ref.: #23028]	melibiose ChEBI	+	assimilation
[Ref.: #23028]	myo-inositol ChEBI	-	carbon source
[Ref.: #23028]	nitrate ChEBI	-	nitrogen source
[Ref.: #23028]	nitrate ChEBI	-	reduction
[Ref.: #23028]	nitrite ChEBI	+	nitrogen source
[Ref.: #23028]	raffinose ChEBI	+	assimilation
[Ref.: #23028]	rhamnose ChEBI	-	carbon source
[Ref.: #23028]	salicin ChEBI	-	carbon source
[Ref.: #23028]	starch ChEBI	-	assimilation
[Ref.: #23028]	starch ChEBI	-	hydrolysis
[Ref.: #23028]	sucrose ChEBI	+/-	assimilation
[Ref.: #23028]	trehalose ChEBI	-	carbon source
[Ref.: #23028]	tryptophan ChEBI	-	energy source
[Ref.: #23028]	tween 20 ChEBI	-	hydrolysis
[Ref.: #23028]	tween 40 ChEBI	-	hydrolysis
[Ref.: #23028]	tween 80 ChEBI	-	hydrolysis
[Ref.: #23028]	tyrosine ChEBI	-	hydrolysis
[Ref.: #23028]	urea ChEBI	+	hydrolysis
[Ref.: #23028]	urea ChEBI	+	nitrogen source
[Ref.: #23028]	xanthine ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #23028]	acetoin ChEBI	no
[Ref.: #23028]	hydrogen sulfide ChEBI	no
[Ref.: #23028]	indole ChEBI	no

	Metabolite	Voges-Proskauer-test	Methylred-test	Indole test
[Ref.: #23028]	acetoin ChEBI	-
[Ref.: #23028]	glucose ChEBI		-
[Ref.: #23028]	indole ChEBI			-

	Enzyme	Enzyme activity	EC number
[Ref.: #23028]	catalase	+	1.11.1.6
[Ref.: #23028]	cytochrome oxidase	-	1.9.3.1
[Ref.: #23028]	lipase	-
[Ref.: #23028]	tryptophan deaminase	-	4.1.99.1
[Ref.: #23028]	urease	+	3.5.1.5

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #23028]

Fatty acid	Percentage
C15:0 anteiso	27.9
C16:0	21.5
C15:0 iso	13.1
C14:0	9.6
C13:0 iso	4.9
C13:0 anteiso	4.8

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	chorismate metabolism	100	9 of 9
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	aerobactin biosynthesis	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	purine metabolism	67.02	63 of 94
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	pyrimidine metabolism	64.44	29 of 45
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	non-pathway related	63.16	24 of 38
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	oxidative phosphorylation	59.34	54 of 91
[Ref.: #66794]	methionine metabolism	57.69	15 of 26
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	CO2 fixation in Crenarchaeota	55.56	5 of 9
[Ref.: #66794]	tryptophan metabolism	55.26	21 of 38
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	cholesterol biosynthesis	54.55	6 of 11
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	degradation of pentoses	53.57	15 of 28
[Ref.: #66794]	alanine metabolism	51.72	15 of 29
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	isoprenoid biosynthesis	46.15	12 of 26
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	lipid metabolism	45.16	14 of 31
[Ref.: #66794]	degradation of hexoses	44.44	8 of 18
[Ref.: #66794]	degradation of sugar acids	44	11 of 25
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	glutathione metabolism	42.86	6 of 14
[Ref.: #66794]	propionate fermentation	40	4 of 10
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	lysine metabolism	38.1	16 of 42
[Ref.: #66794]	degradation of sugar alcohols	37.5	6 of 16
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	reductive acetyl coenzyme A pathway	28.57	2 of 7
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	phenol degradation	25	5 of 20
[Ref.: #66794]	biotin biosynthesis	25	1 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	25	2 of 8
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	sulfate reduction	23.08	3 of 13
[Ref.: #66794]	carotenoid biosynthesis	22.73	5 of 22
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
		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.: #23028]	Sample type/isolated from	beach sediment sample
[Ref.: #23028]	Geographic location (country and/or sea, region)	Pingaleshwar beach
[Ref.: #23028]	Country	India
[Ref.: #23028]	Country ISO 3 Code	IND
[Ref.: #23028]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Coast
#Environmental	#Terrestrial	#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.: #23028]	Pelagirhabdus alkalitolerans partial 16S rRNA gene, type strain S5T	LN812018		GenBank ENA

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pelagirhabdus alkalitolerans S5	GCA_900096905	scaffold	GenBank ENA	1612202 tax ID	*
[Ref.: #66792]	Pelagirhabdus alkalitolerans S5	2671180221	draft	JGI IMG/M	1612202 tax ID	*

[Ref.: #23028]

GC-content

40.8 mol%

high performance liquid chromatography (HPLC)

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: Pelagirhabdus alkalitolerans S5 NCBI: GCA_900096905.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	85.181	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	82.25	no
[Ref.: #125438]	aerobic	aerobicⓘ	no	85.742	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	yes	55.177	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	93.701	no
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	82.776	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pelagirhabdus alkalitolerans S5 NCBI: GCA_900096905
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	yes	85.7
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	79.5
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	variable	76.5
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	97.1

Availability in culture collections External links

[Ref.: #23028]

Culture collection no.

KCTC 33632, CGMCC 1.15177

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pelagirhabdus alkalitolerans gen. nov., sp. nov., an alkali-tolerant and thermotolerant bacterium isolated from beach sediment, and reclassification of Amphibacillus fermentum as Pelagirhabdus fermentum comb. nov.	Sultanpuram VR, Mothe T, Chintalapati S, Chintalapati VR	Int J Syst Evol Microbiol	10.1099/ijsem.0.000678	2015	*

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 )

#23028

Vishnuvardhan Reddy Sultanpuram,Thirumala Mothe,Sasikala Chintalapati,Venkata Ramana Chintalapati: Pelagirhabdus alkalitolerans gen. nov., sp. nov., an alkali-tolerant and thermotolerant bacterium isolated from beach sediment, and reclassification of Amphibacillus fermentum as Pelagirhabdus fermentum comb. nov.. IJSEM 66: 84 - 90 2016 ( DOI 10.1099/ijsem.0.000678 , PubMed 26475440 )

#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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#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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