Flavilitoribacter nigricans (DSM 23189, ATCC 23147, NBRC 102662)

Name: Flavilitoribacter nigricans (DSM 23189, ATCC 23147, NBRC 102662)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14047

Type strain

Strain Designation SS-2

Culture col. no. DSM 23189 ATCC 23147 NBRC 102662 NCIMB 1420 SS-2

NCBI tax ID(s) 70997

Special Collections DSMZ

Links

Flavilitoribacter nigricans SS-2 is a mesophilic prokaryote that was isolated from brown beach sand.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 45697

ATCC 23147,ATCC 19592,NCIMB 1420,NBRC 102662,DSM 23189

@ref 20215

Last LPSN update 2025-12-16 09:50:15

Domain Pseudomonadati

Phylum Bacteroidota

Class Saprospiria

Order Saprospirales

Family Lewinellaceae

Genus Flavilitoribacter

Species Flavilitoribacter nigricans

Full scientific name Flavilitoribacter nigricans (Lewin 1970) García-López et al. 2020

Synonyms (2)

Herpetosiphon nigricans
Lewinella nigricans

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	95.8
125438	negative	93.241

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
16743	REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c)		Medium recipe at MediaDive	Name: REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c) Composition: NaCl 19.45 g/l Agar 18.0 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l Na2CO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
16743	positive	growth	28	mesophilic

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		93.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	quinate degradation	100	2 of 2
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	gallate degradation	100	5 of 5
66794	glycogen metabolism	100	5 of 5
66794	kanosamine biosynthesis II	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	adipate degradation	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	octane oxidation	100	3 of 3
66794	vitamin E metabolism	100	4 of 4
66794	acetoin degradation	100	3 of 3
66794	palmitate biosynthesis	100	22 of 22
66794	biotin biosynthesis	100	4 of 4
66794	starch degradation	100	10 of 10
66794	ppGpp biosynthesis	100	4 of 4
66794	valine metabolism	100	9 of 9
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	denitrification	100	2 of 2
66794	suberin monomers biosynthesis	100	2 of 2
66794	ceramide biosynthesis	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	sulfopterin metabolism	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	cellulose degradation	100	5 of 5
66794	gluconeogenesis	100	8 of 8
66794	NAD metabolism	94.44	17 of 18
66794	phenylalanine metabolism	92.31	12 of 13
66794	Entner Doudoroff pathway	90	9 of 10
66794	threonine metabolism	90	9 of 10
66794	serine metabolism	88.89	8 of 9
66794	pyrimidine metabolism	88.89	40 of 45
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	4-hydroxymandelate degradation	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	ketogluconate metabolism	87.5	7 of 8
66794	flavin biosynthesis	86.67	13 of 15
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	photosynthesis	85.71	12 of 14
66794	heme metabolism	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	leucine metabolism	84.62	11 of 13
66794	degradation of sugar acids	84	21 of 25
66794	1,4-dihydroxy-6-naphthoate biosynthesis	83.33	5 of 6
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	purine metabolism	82.98	78 of 94
66794	alanine metabolism	82.76	24 of 29
66794	glycolysis	82.35	14 of 17
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	pentose phosphate pathway	81.82	9 of 11
66794	proline metabolism	81.82	9 of 11
66794	lysine metabolism	80.95	34 of 42
66794	glycine betaine biosynthesis	80	4 of 5
66794	3-chlorocatechol degradation	80	4 of 5
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	arginine metabolism	79.17	19 of 24
66794	tryptophan metabolism	78.95	30 of 38
66794	tyrosine metabolism	78.57	11 of 14
66794	glutathione metabolism	78.57	11 of 14
66794	degradation of hexoses	77.78	14 of 18
66794	methionine metabolism	76.92	20 of 26
66794	isoleucine metabolism	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	degradation of pentoses	75	21 of 28
66794	acetate fermentation	75	3 of 4
66794	lipid metabolism	74.19	23 of 31
66794	histidine metabolism	72.41	21 of 29
66794	cysteine metabolism	72.22	13 of 18
66794	propanol degradation	71.43	5 of 7
66794	citric acid cycle	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	non-pathway related	71.05	27 of 38
66794	phenol degradation	70	14 of 20
66794	urea cycle	69.23	9 of 13
66794	formaldehyde oxidation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	cyanate degradation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	nitrate assimilation	66.67	6 of 9
66794	d-xylose degradation	63.64	7 of 11
66794	ascorbate metabolism	63.64	14 of 22
66794	metabolism of disaccharids	63.64	7 of 11
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	degradation of sugar alcohols	62.5	10 of 16
66794	polyamine pathway	60.87	14 of 23
66794	myo-inositol biosynthesis	60	6 of 10
66794	4-hydroxyphenylacetate degradation	60	6 of 10
66794	propionate fermentation	60	6 of 10
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	isoprenoid biosynthesis	53.85	14 of 26
66794	phosphatidylethanolamine bioynthesis	53.85	7 of 13
66794	oxidative phosphorylation	50.55	46 of 91
66794	butanoate fermentation	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	grixazone biosynthesis	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	lactate fermentation	50	2 of 4
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	androgen and estrogen metabolism	50	8 of 16
66794	sphingosine metabolism	50	3 of 6
66794	cyclohexanol degradation	50	2 of 4
66794	toluene degradation	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	ethanol fermentation	50	1 of 2
66794	sulfate reduction	46.15	6 of 13
66794	vitamin B6 metabolism	45.45	5 of 11
66794	arachidonic acid metabolism	44.44	8 of 18
66794	allantoin degradation	44.44	4 of 9
66794	mevalonate metabolism	42.86	3 of 7
66794	factor 420 biosynthesis	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	3-phenylpropionate degradation	40	6 of 15
66794	coenzyme M biosynthesis	40	4 of 10
66794	lipoate biosynthesis	40	2 of 5
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	carnitine metabolism	37.5	3 of 8
66794	IAA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	carotenoid biosynthesis	31.82	7 of 22
66794	vitamin B1 metabolism	30.77	4 of 13
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	cholesterol biosynthesis	27.27	3 of 11
66794	catecholamine biosynthesis	25	1 of 4
66794	methanogenesis from CO2	25	3 of 12
66794	vitamin B12 metabolism	20.59	7 of 34

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Coast
#Environmental	#Terrestrial	#Sandy

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
16743	brown beach sand	near Lagos	Nigeria	NGA	Africa

Taxonmaps

69479

Global distribution of 16S sequence AM295255 (>99% sequence identity) for Flavilitoribacter nigricans subclade from Microbeatlas

Aquatic Samples	2249
Soil Samples	223
Animal Samples	129
Plant Samples	49
Total Samples	2650

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16743	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM264659v1 assembly for Flavilitoribacter nigricans DSM 23189 = NBRC 102662	contig	GCA_002646595	1122177.3	2881388915	1122177	48.26

Genome browser: GCA_002646595

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Lewinella nigricans 16S ribosomal RNA gene, partial sequence	AF039294	1445	70997
20218	Lewinella nigricans partial 16S rRNA gene, type strain ATCC 23147T	AM295255	1414	70997
16743	Lewinella nigricans gene for 16S ribosomal RNA, partial sequence	AB301615	1449	1122177

GC content

@ref	GC-content (mol%)
16743	53.1
16743	53.0

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Flavilitoribacter nigricans DSM 23189 = NBRC 102662
NCBI: GCA_002646595

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	93.10	no
125439	motility	BacteriaNetⓘ	no	68.50	no
125439	gram_stain	BacteriaNetⓘ	negative	95.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	77.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Lewinella nigricans DSM 23189 = NBRC 102662
PATRIC: 1122177.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	93.24	no
125438	anaerobic	anaerobicⓘ	no	93.58	no
125438	spore-forming	spore-formingⓘ	no	84.72	no
125438	aerobic	aerobicⓘ	yes	79.23	no
125438	thermophilic	thermophileⓘ	no	95.96	yes
125438	flagellated	motile2+ⓘ	no	81.25	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes.	Garcia-Lopez M, Meier-Kolthoff JP, Tindall BJ, Gronow S, Woyke T, Kyrpides NC, Hahnke RL, Goker M.	Front Microbiol	10.3389/fmicb.2019.02083	2019
Phylogeny	Lewinella agarilytica sp. nov., a novel marine bacterium of the phylum Bacteroidetes, isolated from beach sediment.	Lee SD	Int J Syst Evol Microbiol	10.1099/ijs.0.65254-0	2007

References

#16743	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23189
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#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 .
#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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Flavilitoribacter nigricans (DSM 23189, ATCC 23147, NBRC 102662)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002646595

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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