Allosphingosinicella indica (DSM 25434, CCM 7882, MTCC 10862)

Name: Allosphingosinicella indica (DSM 25434, CCM 7882, MTCC 10862)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14271

Type strain

Strain Designation Dd16

Culture col. no. DSM 25434 CCM 7882 MTCC 10862 Dd16

NCBI tax ID(s) 941907

Special Collections DSMZ Literature strains

History DSMZ <- R. Lal, Univ. Delhi, Dept. Zoology, India; Dd16

Allosphingosinicella indica Dd16 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from HCH-contaminated dump site.

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

Name and taxonomic classification

Culture Collection Numbers

DSM 25434 CCM 7882 MTCC 10862 Dd16

@ref 20215

Last LPSN update 2026-05-29 08:28:15

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Allosphingosinicella

Species Allosphingosinicella indica

Full scientific name Allosphingosinicella indica (Niharika et al. 2012) Hördt et al. 2020

Synonyms (1)

Sphingomonas indica

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
30344	negative	2.6 µm	0.9 µm	rod-shaped
125438	negative				96.328
125439	negative				93.854

Pigmentation

30344

Productionyes

Multimedia

@ref:	18036
multimedia content:	DSM_25434.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_25434.jpg
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
30344	positive	growth	04-28
30344	positive	optimum	28

Culture pH

@ref	Ability	Type	PH
30344	positive	optimum	7
30344	positive	growth	06-07

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30344	aerobe
125439	obligate aerobe	96.445

Spore formation

@ref	Spore formation	Confidence
30344
125439		97.793
125438		90.724

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30344	NaCl	positive	growth	0-2 %
30344	NaCl	positive	optimum	1 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30344	22599 ChEBI	arabinose	+	carbon source
30344	28757 ChEBI	fructose	+	carbon source
30344	28260 ChEBI	galactose	+	carbon source
30344	29864 ChEBI	mannitol	+	carbon source
30344	16634 ChEBI	raffinose	+	carbon source
30344	30911 ChEBI	sorbitol	+	carbon source
30344	17992 ChEBI	sucrose	+	carbon source
30344	27082 ChEBI	trehalose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
30344	catalase	+	1.11.1.6
30344	cytochrome oxidase	+	1.9.3.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	coenzyme A metabolism	100	4 of 4
66794	gluconeogenesis	100	8 of 8
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	methylglyoxal degradation	100	5 of 5
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	suberin monomers biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	ppGpp biosynthesis	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	palmitate biosynthesis	90.91	20 of 22
66794	chorismate metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	citric acid cycle	78.57	11 of 14
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	photosynthesis	78.57	11 of 14
66794	NAD metabolism	77.78	14 of 18
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	isoleucine metabolism	75	6 of 8
66794	butanoate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	glutamate and glutamine metabolism	75	21 of 28
66794	acetate fermentation	75	3 of 4
66794	peptidoglycan biosynthesis	73.33	11 of 15
66794	methionine metabolism	73.08	19 of 26
66794	histidine metabolism	72.41	21 of 29
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	propanol degradation	71.43	5 of 7
66794	tryptophan metabolism	71.05	27 of 38
66794	threonine metabolism	70	7 of 10
66794	propionate fermentation	70	7 of 10
66794	vitamin B1 metabolism	69.23	9 of 13
66794	phenylalanine metabolism	69.23	9 of 13
66794	alanine metabolism	68.97	20 of 29
66794	purine metabolism	67.02	63 of 94
66794	enterobactin biosynthesis	66.67	2 of 3
66794	flavin biosynthesis	66.67	10 of 15
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	arginine metabolism	66.67	16 of 24
66794	octane oxidation	66.67	2 of 3
66794	glycolysis	64.71	11 of 17
66794	lipid metabolism	64.52	20 of 31
66794	glutathione metabolism	64.29	9 of 14
66794	tyrosine metabolism	64.29	9 of 14
66794	vitamin B6 metabolism	63.64	7 of 11
66794	proline metabolism	63.64	7 of 11
66794	pentose phosphate pathway	63.64	7 of 11
66794	non-pathway related	63.16	24 of 38
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	lysine metabolism	59.52	25 of 42
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	leucine metabolism	53.85	7 of 13
66794	CMP-KDO biosynthesis	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	degradation of sugar alcohols	50	8 of 16
66794	Entner Doudoroff pathway	50	5 of 10
66794	catecholamine biosynthesis	50	2 of 4
66794	cysteine metabolism	50	9 of 18
66794	biotin biosynthesis	50	2 of 4
66794	sulfopterin metabolism	50	2 of 4
66794	ribulose monophosphate pathway	50	1 of 2
66794	starch degradation	50	5 of 10
66794	phenylmercury acetate degradation	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	quinate degradation	50	1 of 2
66794	ketogluconate metabolism	50	4 of 8
66794	toluene degradation	50	2 of 4
66794	pyrimidine metabolism	46.67	21 of 45
66794	urea cycle	46.15	6 of 13
66794	metabolism of disaccharids	45.45	5 of 11
66794	lipid A biosynthesis	44.44	4 of 9
66794	aspartate and asparagine metabolism	44.44	4 of 9
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	heme metabolism	42.86	6 of 14
66794	carotenoid biosynthesis	40.91	9 of 22
66794	glycine betaine biosynthesis	40	2 of 5
66794	D-cycloserine biosynthesis	40	2 of 5
66794	3-phenylpropionate degradation	40	6 of 15
66794	glycine metabolism	40	4 of 10
66794	gallate degradation	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	degradation of hexoses	38.89	7 of 18
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	polyamine pathway	34.78	8 of 23
66794	oxidative phosphorylation	34.07	31 of 91
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	ascorbate metabolism	31.82	7 of 22
66794	myo-inositol biosynthesis	30	3 of 10
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	cholesterol biosynthesis	27.27	3 of 11
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	degradation of pentoses	25	7 of 28
66794	dTDPLrhamnose biosynthesis	25	2 of 8
66794	phenol degradation	25	5 of 20
66794	alginate biosynthesis	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	degradation of sugar acids	24	6 of 25
66794	phenylpropanoid biosynthesis	23.08	3 of 13
66794	nitrate assimilation	22.22	2 of 9
66794	4-hydroxymandelate degradation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Engineered	#Built environment
#Engineered	#Contamination

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
18036	HCH-contaminated dump site	Uttar Pradesh, Lucknow, Ummari village (27° 00' N, 81° 09' E)	India	IND	Asia	27	81.15 27/81.15

Taxonmaps

69479

Global distribution of 16S sequence HQ449390 (>99% sequence identity) for Allosphingosinicella indica subclade from Microbeatlas

Aquatic Samples	10
Soil Samples	65
Animal Samples	7
Plant Samples	16
Total Samples	98

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
18036	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	IMG-taxon 2708742536 annotated assembly for Allosphingosinicella indica Dd16	chromosome	GCA_900177405	941907.3	2708742536	941907	88.63

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
18036	Sphingomonas indica strain Dd16 16S ribosomal RNA gene, partial sequence	HQ449390	1449		941907

GC content

@ref	GC-content (mol%)	Method
18036	65.8	fluorimetric
30344	65.8

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: IMG-taxon 2708742536 annotated assembly for Allosphingosinicella indica Dd16
NCBI: GCA_900177405

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	96.45	no
125439	gram_stain	BacteriaNetⓘ	negative	93.85	no
125439	motility	BacteriaNetⓘ	yes	45.43	no
125439	spore_formation	BacteriaNetⓘ	no	97.79	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Allosphingosinicella indica Dd16
NCBI: GCA_900177405.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.33	yes
125438	anaerobic	anaerobicⓘ	no	95.88	yes
125438	aerobic	aerobicⓘ	yes	82.72	yes
125438	spore-forming	spore-formingⓘ	no	90.72	no
125438	thermophilic	thermophileⓘ	no	91.27	no
125438	flagellated	motile2+ⓘ	yes	50.24	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.	Hordt A, Lopez MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Goker M.	Front Microbiol	10.3389/fmicb.2020.00468	2020

References

#18036	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25434
#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 )
#26685	IJSEM 2997 2012 ( DOI 10.1099/ijs.0.033845-0 , PubMed 22307515 )
#30344	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26685
#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 .

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Allosphingosinicella indica (DSM 25434, CCM 7882, MTCC 10862)

Name and taxonomic classification

Culture Collection Numbers

Morphology

Cell morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900177405

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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