Name: Tessaracoccus flavus RP1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 132480

Type strain:

Species: Tessaracoccus flavus

Strain Designation: RP1

Culture col. no.: DSM 100159, KCTC 39686, MCC 2769

Strain history: <- R. Lal, Univ. Delhi, Dept. Zoology, India; RP1 <- R. Kumari

NCBI tax ID(s): 1610493 (species)

Section

Tessaracoccus flavus RP1 is a facultative anaerobe, Gram-positive, coccus-shaped bacterium that forms circular colonies and was isolated from drainage system of a lindane-producing unit.

coccus-shaped
colony-forming
Gram-positive
facultative anaerobe
16S sequence
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	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Propionibacteriales*
	Family	*Propionibacteriaceae*
	Genus	*Tessaracoccus*
	Species	**Tessaracoccus flavus**
	Full Scientific Name (LPSN)	Tessaracoccus flavus Kumari et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #43695]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #43695]	Cell length	0.4-1 µm

[Ref.: #43695]	Cell shape	coccus-shaped

[Ref.: #43695]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %91.54

[Ref.: #43695]	Colony color	Yellow
[Ref.: #43695]	Colony shape	circular
[Ref.: #43695]	Incubation period	2 days
[Ref.: #43695]	Cultivation medium used	Luria Bertani agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43695]

Culture medium

LB (Luria-Bertani) MEDIUM

[Ref.: #43695]

Culture medium growth

	Temperatures	Kind of temperature		Temperature
[Ref.: #43695]			growth	15-45 °C
[Ref.: #43695]			optimum	28 °C

[Ref.: #43695]

Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #43695]			optimum	8
[Ref.: #43695]			growth	7-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43695]

Oxygen tolerance

facultative anaerobe

[Ref.: #43695]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %92
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.994

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43695]		NaCl		growth	0-7	%(w/v)
[Ref.: #43695]		NaCl		optimum	5	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43695]	casein	-	hydrolysis
[Ref.: #43695]	D-arabinose ChEBI	+	assimilation
[Ref.: #43695]	D-arabinose ChEBI	+	builds acid from
[Ref.: #43695]	D-fructose ChEBI	+	assimilation
[Ref.: #43695]	D-fructose ChEBI	+	builds acid from
[Ref.: #43695]	D-galactose ChEBI	+	assimilation
[Ref.: #43695]	D-galactose ChEBI	+	builds acid from
[Ref.: #43695]	D-glucose ChEBI	+	assimilation
[Ref.: #43695]	D-glucose ChEBI	+	builds acid from
[Ref.: #43695]	D-mannitol ChEBI	+	assimilation
[Ref.: #43695]	D-mannitol ChEBI	+	builds acid from
[Ref.: #43695]	D-mannose ChEBI	+	assimilation
[Ref.: #43695]	D-mannose ChEBI	+	builds acid from
[Ref.: #43695]	D-sorbitol ChEBI	+	assimilation
[Ref.: #43695]	D-sorbitol ChEBI	+	builds acid from
[Ref.: #43695]	D-sorbose ChEBI	-	assimilation
[Ref.: #43695]	erythritol ChEBI	+	assimilation
[Ref.: #43695]	erythritol ChEBI	+	builds acid from
[Ref.: #43695]	esculin ChEBI	+	hydrolysis
[Ref.: #43695]	galactitol ChEBI	-	assimilation
[Ref.: #43695]	gelatin ChEBI	-	hydrolysis
[Ref.: #43695]	hypoxanthine ChEBI	-	hydrolysis
[Ref.: #43695]	L-arabinose ChEBI	+	assimilation
[Ref.: #43695]	L-arabinose ChEBI	+	builds acid from
[Ref.: #43695]	maltose ChEBI	+	assimilation
[Ref.: #43695]	maltose ChEBI	+	builds acid from
[Ref.: #43695]	nitrate ChEBI	+	reduction
[Ref.: #43695]	raffinose ChEBI	-	assimilation
[Ref.: #43695]	starch ChEBI	-	hydrolysis
[Ref.: #43695]	sucrose ChEBI	+	assimilation
[Ref.: #43695]	sucrose ChEBI	+	builds acid from
[Ref.: #43695]	trehalose ChEBI	+	assimilation
[Ref.: #43695]	trehalose ChEBI	+	builds acid from
[Ref.: #43695]	tween 20 ChEBI	-	hydrolysis
[Ref.: #43695]	tween 80 ChEBI	-	hydrolysis
[Ref.: #43695]	urea ChEBI	-	hydrolysis
[Ref.: #43695]	xanthine ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #43695]	amikacin ChEBI				yes	30	µg (disc)
[Ref.: #43695]	ampicillin ChEBI				yes	10	µg (disc)
[Ref.: #43695]	chloramphenicol ChEBI	yes	30	µg (disc)
[Ref.: #43695]	ciprofloxacin ChEBI				yes	5	µg (disc)
[Ref.: #43695]	gentamicin ChEBI	yes	10	µg (disc)
[Ref.: #43695]	kanamycin ChEBI	yes	30	µg (disc)
[Ref.: #43695]	nalidixic acid ChEBI				yes	30	µg (disc)
[Ref.: #43695]	oxytetracycline ChEBI				yes	30	µg (disc)
[Ref.: #43695]	penicillin g ChEBI				yes	10	µg (disc)
[Ref.: #43695]	polymyxin b ChEBI	yes	300	µg (disc)
[Ref.: #43695]	rifampicin ChEBI	yes	5	µg (disc)
[Ref.: #43695]	tetracycline ChEBI				yes	30	µg (disc)
[Ref.: #43695]	vancomycin ChEBI	yes	30	µg (disc)
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #43695]		hydrogen sulfide ChEBI	no
[Ref.: #43695]		indole ChEBI	no

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #43695]		catalase	+	1.11.1.6
[Ref.: #43695]		cytochrome oxidase	-	1.9.3.1

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #43695]

Fatty acid	Percentage
C18:1ω7c / C18:1ω6c	73
11-methyl C18:1ω7c	13.2
C16:0	7.7
C18:0	3.1
C16:1ω7c / C16:1ω6c	1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	degradation of sugar alcohols	81.25	13 of 16
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	pyrimidine metabolism	75.56	34 of 45
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	biotin biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	lactate fermentation	75	3 of 4
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	purine metabolism	71.28	67 of 94
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	alanine metabolism	68.97	20 of 29
[Ref.: #66794]	glutamate and glutamine metabolism	67.86	19 of 28
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	nitrate assimilation	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	non-pathway related	65.79	25 of 38
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	degradation of pentoses	64.29	18 of 28
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	carnitine metabolism	62.5	5 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	histidine metabolism	58.62	17 of 29
[Ref.: #66794]	oxidative phosphorylation	58.24	53 of 91
[Ref.: #66794]	lipid metabolism	58.06	18 of 31
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	metabolism of disaccharids	54.55	6 of 11
[Ref.: #66794]	methionine metabolism	53.85	14 of 26
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	tryptophan metabolism	52.63	20 of 38
[Ref.: #66794]	lysine metabolism	52.38	22 of 42
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	coenzyme A metabolism	50	2 of 4
[Ref.: #66794]	degradation of hexoses	50	9 of 18
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	ascorbate metabolism	45.45	10 of 22
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	arginine metabolism	41.67	10 of 24
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	phenylacetate degradation (aerobic)	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	carotenoid biosynthesis	36.36	8 of 22
[Ref.: #66794]	degradation of sugar acids	36	9 of 25
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	35.29	6 of 17
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	flavin biosynthesis	33.33	5 of 15
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	vitamin B12 metabolism	23.53	8 of 34
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
[Ref.: #66794]	polyamine pathway	21.74	5 of 23
		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.: #24269]	Sample type/isolated from	drainage system of a lindane-producing unit
[Ref.: #24269]	Geographic location (country and/or sea, region)	Uttar Pradesh, Lucknow, Chinhat (26° 54' N 81° 09' E)
[Ref.: #24269]	Country	India
[Ref.: #24269]	Country ISO 3 Code	IND
[Ref.: #24269]	Continent	Asia
[Ref.: #24269]	Geographic location	26.9000°/81.1500°

[Ref.: #43695]	Sample type/isolated from	The drainage system of a lindane-producing unit
[Ref.: #43695]	Geographic location (country and/or sea, region)	India
[Ref.: #43695]	Country	India
[Ref.: #43695]	Country ISO 3 Code	IND
[Ref.: #43695]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Industrial	-
#Engineered	#Waste	#Industrial wastewater
#Engineered	#Industrial	#Plant (Factory)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KP265298 (>99% sequence identity) for Tessaracoccus flavus subclade from Microbeatlas

Aquatic Samples	165
Soil Samples	110
Animal Samples	456
Plant Samples	13
Total Samples	744

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.: #24269]	Tessaracoccus flavus strain RP1 16S ribosomal RNA gene, partial sequence	KP265298	1396	ENA	1610493 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Tessaracoccus flavus RP1	GCA_900107385	contig	GenBank	1610493 tax ID	*
[Ref.: #66792]	Tessaracoccus flavus RP1	GCA_001997295	complete	GenBank	1610493 tax ID	*
[Ref.: #66792]	Tessaracoccus flavus strain RP1T	1610493.4	complete	PATRIC	1610493 tax ID	*

[Ref.: #43695]	GC-content	66.7 mol%	Thermal denaturation, fluorometry
[Ref.: #24269]	GC-content	66.7 mol%	fluorimetric

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: Tessaracoccus flavus RP1 NCBI: GCA_001997295.1
[Ref.: #69481]	spore-forming	no	92	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Tessaracoccus flavus RP1 NCBI: GCA_001997295.1
[Ref.: #69480]	flagellated	no	98.056	yes
[Ref.: #69480]	gram-positive	yes	90.23	no
[Ref.: #69480]	anaerobic	no	97.914	yes
[Ref.: #69480]	aerobic	yes	79.51	no
[Ref.: #69480]	halophile	no	93.25	no
[Ref.: #69480]	spore-forming	no	94.81	yes
[Ref.: #69480]	glucose-util	yes	88.793	yes
[Ref.: #69480]	thermophile	no	96.887	yes
[Ref.: #69480]	glucose-ferment	no	63.062	no
[Ref.: #69480]	motile	no	94.297	no

Availability in culture collections External links

[Ref.: #24269]

Culture collection no.

DSM 100159, KCTC 39686, MCC 2769

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Tessaracoccus flavus sp. nov., isolated from the drainage system of a lindane-producing factory.	Kumari R, Singh P, Schumann P, Lal R	Int J Syst Evol Microbiol	10.1099/ijsem.0.000958	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 )

#24269

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100159

#43695

Rashmi Kumari, Priya Singh, Peter Schumann, Rup Lal: Tessaracoccus flavus sp. nov., isolated from the drainage system of a lindane-producing factory. IJSEM 66: 1862 - 1868 2016 ( DOI 10.1099/ijsem.0.000958 , PubMed 26869509 )

#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 )

#69479

João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .

#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

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