Phenylobacterium deserti (DSM 103871, CCTCC AB 2016297, YIM 73061)

Name: Phenylobacterium deserti (DSM 103871, CCTCC AB 2016297, YIM 73061)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 158279

Type strain

Culture col. no. DSM 103871 CCTCC AB 2016297 YIM 73061 NCCP 697

NCBI tax ID(s) 1914756

Special Collections DSMZ Literature strains

Links

Phenylobacterium deserti DSM 103871 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from desert soil.

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

Name and taxonomic classification

SI-ID 401591

DSM 103871

@ref 20215

Last LPSN update 2025-12-16 10:07:59

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Caulobacterales

Family Caulobacteraceae

Genus Phenylobacterium

Species Phenylobacterium deserti

Full scientific name Phenylobacterium deserti Khan et al. 2017

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
65414	negative	1.4-2.9 µm	0.6-1.7 µm	rod-shaped
125438	negative				98.828
125439	negative				94.8

Pigmentation

@ref	Production	Name
65414		melanin pigment

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
64939	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
64939	positive	growth	37	mesophilic
65414	positive	growth	20-40
65414	positive	optimum	30-37	mesophilic

Culture pH

@ref	Ability	Type	PH
65414	positive	optimum	7.0
65414	positive	growth	5.0-8.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
65414	aerobe
125439	aerobe	97.1

Spore formation

@ref	Spore formation	Confidence
125438		92.826
125439		96.5

Observation

@ref	Observation
65414	predominant isoprenoid quinone is Q-10
65414	The polar lipid profile consists of phosphatidylglycerol and four unidentified glycolipids

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
65414	16004 ChEBI	(R)-lactate	-	carbon source
65414	16651 ChEBI	(S)-lactate	-	carbon source
65414	30916 ChEBI	2-oxoglutarate	-	carbon source
65414	73918 ChEBI	3-O-methyl-D-glucose	-	carbon source
65414	57606 ChEBI	5-oxoproline	-	carbon source
65414	13705 ChEBI	acetoacetate	+	carbon source
65414	17925 ChEBI	alpha-D-glucose	-	carbon source
65414	17057 ChEBI	cellobiose	-	carbon source
65414	18333 ChEBI	D-arabitol	-	carbon source
65414	29990 ChEBI	D-aspartate	+	carbon source
65414	78697 ChEBI	D-fructose 6-phosphate	+	carbon source
65414	28847 ChEBI	D-fucose	-	carbon source
65414	12936 ChEBI	D-galactose	-	carbon source
65414	8391 ChEBI	D-gluconate	+	carbon source
65414	15588 ChEBI	D-malate	+	carbon source
65414	16899 ChEBI	D-mannitol	-	carbon source
65414	17924 ChEBI	D-sorbitol	-	carbon source
65414	23652 ChEBI	dextrin	-	carbon source
65414	4853 ChEBI	esculin	+	hydrolysis
65414	15740 ChEBI	formate	-	carbon source
65414	71321 ChEBI	fusidate	+	carbon source
65414	5291 ChEBI	gelatin	-	carbon source
65414	5291 ChEBI	gelatin	+	hydrolysis
65414	15978 ChEBI	glycerol 3-phosphate	-	carbon source
65414	85249 ChEBI	hydroxyethylcellulose	-	assimilation
65414	17596 ChEBI	inosine	-	carbon source
65414	16467 ChEBI	L-arginine	+	carbon source
65414	29991 ChEBI	L-aspartate	+	carbon source
65414	18287 ChEBI	L-fucose	-	carbon source
65414	29985 ChEBI	L-glutamate	-	carbon source
65414	15971 ChEBI	L-histidine	+	carbon source
65414	15589 ChEBI	L-malate	+	carbon source
65414	17295 ChEBI	L-phenylalanine	+	carbon source
65414	62345 ChEBI	L-rhamnose	-	carbon source
65414	17306 ChEBI	maltose	-	carbon source
65414	320055 ChEBI	methyl beta-D-glucopyranoside	-	carbon source
65414		milk	+	assimilation
65414	17268 ChEBI	myo-inositol	+	carbon source
65414	63154 ChEBI	N-acetyl-beta-D-mannosamine	-	carbon source
65414	28037 ChEBI	N-acetylgalactosamine	-	carbon source
65414	506227 ChEBI	N-acetylglucosamine	-	carbon source
65414	35418 ChEBI	n-acetylneuraminate	+	carbon source
65414	17632 ChEBI	nitrate	+	reduction
65414	17309 ChEBI	pectin	-	carbon source
65414	17272 ChEBI	propionate	+	carbon source
65414	16634 ChEBI	raffinose	-	carbon source
65414	64103 ChEBI	sodium butyrate	-	carbon source
65414	75228 ChEBI	sodium lactate	-	carbon source
65414	28017 ChEBI	starch	-	assimilation
65414	17992 ChEBI	sucrose	-	carbon source
65414	27082 ChEBI	trehalose	-	carbon source
65414	32528 ChEBI	turanose	-	carbon source
65414	53424 ChEBI	tween 20	-	assimilation
65414	53423 ChEBI	tween 40	-	assimilation
65414	53425 ChEBI	tween 60	-	assimilation
65414	53426 ChEBI	tween 80	-	assimilation

Antibiotic resistance

@ref	ChEBI	Metabolite	Sensitivity conc.	Resistance conc.
65414	2637	amikacin	30 µg (disc)
65414	3517	cefuroxime sodium		30 µg (disc)
65414	17698	chloramphenicol	30 µg (disc)
65414	100241	ciprofloxacin		30 µg (disc)
65414	48923	erythromycin		15 µg (disc)
65414	17833	gentamicin	10 µg (disc)
65414	100246	norfloxacin		10 µg (disc)
65414	28368	novobiocin		30 µg (disc)
65414	7809	oxacillin		30 µg (disc)
65414	18208	penicillin g		10 µg (disc)
65414	8232	piperacillin		30 µg (disc)
65414	8309	polymyxin b		30 µg (disc)
65414	9332	sulfamethoxazole		30 µg (disc)
65414	27902	tetracycline	30 µg (disc)
65414	28001	vancomycin	30 µg (disc)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
65414	15138 ChEBI	sulfide

Enzymes

@ref	Value	Activity	Ec
65414	acid phosphatase	+	3.1.3.2
65414	alkaline phosphatase	+	3.1.3.1
65414	alpha-glucosidase	+	3.2.1.20
65414	beta-glucuronidase	+	3.2.1.31
65414	catalase	+	1.11.1.6
65414	cystine arylamidase	+	3.4.11.3
65414	cytochrome oxidase	+	1.9.3.1
65414	esterase (C 4)	+
65414	esterase Lipase (C 8)	+
65414	leucine arylamidase	+	3.4.11.1
65414	valine arylamidase	+

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	biotin biosynthesis	100	4 of 4
66794	kanosamine biosynthesis II	100	2 of 2
66794	Entner Doudoroff pathway	100	10 of 10
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	octane oxidation	100	3 of 3
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	butanoate fermentation	100	4 of 4
66794	valine metabolism	100	9 of 9
66794	quinate degradation	100	2 of 2
66794	ethanol fermentation	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	taurine degradation	100	1 of 1
66794	ceramide biosynthesis	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	phenylalanine metabolism	92.31	12 of 13
66794	threonine metabolism	90	9 of 10
66794	serine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	gluconeogenesis	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	propanol degradation	85.71	6 of 7
66794	leucine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	alanine metabolism	82.76	24 of 29
66794	proline metabolism	81.82	9 of 11
66794	flavin biosynthesis	80	12 of 15
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	starch degradation	80	8 of 10
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	propionate fermentation	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	citric acid cycle	78.57	11 of 14
66794	d-mannose degradation	77.78	7 of 9
66794	isoleucine metabolism	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	glutamate and glutamine metabolism	75	21 of 28
66794	ketogluconate metabolism	75	6 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	methionine metabolism	73.08	19 of 26
66794	vitamin B6 metabolism	72.73	8 of 11
66794	pentose phosphate pathway	72.73	8 of 11
66794	d-xylose degradation	72.73	8 of 11
66794	cysteine metabolism	72.22	13 of 18
66794	tyrosine metabolism	71.43	10 of 14
66794	heme metabolism	71.43	10 of 14
66794	lysine metabolism	71.43	30 of 42
66794	glycolysis	70.59	12 of 17
66794	myo-inositol biosynthesis	70	7 of 10
66794	vitamin B1 metabolism	69.23	9 of 13
66794	purine metabolism	69.15	65 of 94
66794	degradation of sugar alcohols	68.75	11 of 16
66794	acetoin degradation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	lipid metabolism	64.52	20 of 31
66794	pyrimidine metabolism	64.44	29 of 45
66794	glutathione metabolism	64.29	9 of 14
66794	metabolism of disaccharids	63.64	7 of 11
66794	non-pathway related	63.16	24 of 38
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	gallate degradation	60	3 of 5
66794	degradation of sugar acids	60	15 of 25
66794	lipoate biosynthesis	60	3 of 5
66794	histidine metabolism	58.62	17 of 29
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	degradation of hexoses	55.56	10 of 18
66794	tryptophan metabolism	55.26	21 of 38
66794	arginine metabolism	54.17	13 of 24
66794	urea cycle	53.85	7 of 13
66794	degradation of pentoses	53.57	15 of 28
66794	3-phenylpropionate degradation	53.33	8 of 15
66794	ascorbate metabolism	50	11 of 22
66794	ribulose monophosphate pathway	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	pantothenate biosynthesis	50	3 of 6
66794	cyclohexanol degradation	50	2 of 4
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	4-hydroxymandelate degradation	44.44	4 of 9
66794	nitrate assimilation	44.44	4 of 9
66794	cardiolipin biosynthesis	42.86	3 of 7
66794	oxidative phosphorylation	42.86	39 of 91
66794	arachidonate biosynthesis	40	2 of 5
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	glycine betaine biosynthesis	40	2 of 5
66794	elloramycin biosynthesis	40	2 of 5
66794	sulfate reduction	38.46	5 of 13
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	carotenoid biosynthesis	36.36	8 of 22
66794	phenol degradation	35	7 of 20
66794	arachidonic acid metabolism	33.33	6 of 18
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	polyamine pathway	30.43	7 of 23
66794	coenzyme M biosynthesis	30	3 of 10
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	cholesterol biosynthesis	27.27	3 of 11
66794	lactate fermentation	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	chlorophyll metabolism	22.22	4 of 18

Fatty acid profile

Metadata FA analysis

@ref

65414

Fatty acid	Percentage
C18:1ω7c and/or C 18:1ω6c	46.4
C16:0	27.9
C19:0cycloω8c	5.3
C16:1ω6c and/or C16:1ω7c	4.6
C12:0	4.5
C12:1 3OH	3.2
C16:1ω11c	2.1
C14:0	1.6
C17:1ω8c	0.7
C12:0 3OH	0.6
C18:0	0.5
C15:0 3OH	0.5

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Desert
#Environmental	#Terrestrial	#Soil
#Condition	#Xerophilic	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
64939	desert soil	Punjab, Cholistan Desert, (42° 27' N 60° 57' E)	Pakistan	PAK	Asia	42.45	60.95 42.45/60.95
65414	the Cholistan desert	Punjab	Pakistan	PAK	Asia

Taxonmaps

69479

Global distribution of 16S sequence LC193944 (>99% sequence identity) for Phenylobacterium deserti subclade from Microbeatlas

Aquatic Samples	389
Soil Samples	1687
Animal Samples	313
Plant Samples	59
Total Samples	2448

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
64939	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM325470v1 assembly for Phenylobacterium deserti YIM 73061	contig	GCA_003254705	1914756.3	2840414474	1914756	76.69

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
64939	Phenylobacterium sp. YIM 73061 gene for 16S ribosomal RNA, partial sequence	LC193944	1469		1914756

GC content

@ref	GC-content (mol%)	Method
64939	66.8	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Phenylobacterium deserti YIM 73061
NCBI: GCA_003254705

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.50	no
125439	motility	BacteriaNetⓘ	yes	64.40	no
125439	gram_stain	BacteriaNetⓘ	negative	94.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	97.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Phenylobacterium deserti strain YIM 73061
PATRIC: 1914756.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.83	yes
125438	anaerobic	anaerobicⓘ	no	96.76	no
125438	spore-forming	spore-formingⓘ	no	92.83	no
125438	aerobic	aerobicⓘ	yes	86.69	yes
125438	thermophilic	thermophileⓘ	no	96.78	no
125438	flagellated	motile2+ⓘ	yes	72.54	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Phenylobacterium deserti sp. nov., isolated from desert soil.	Khan IU, Hussain F, Habib N, Wadaan MAM, Ahmed I, Im WT, Hozzein WN, Zhi XY, Li WJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.002366	2017
Phylogeny	Phenylobacterium soli sp. nov., isolated from arsenic and cadmium contaminated farmland soil.	Li X, Yu Y, Choi L, Song Y, Wu M, Wang G, Li M	Int J Syst Evol Microbiol	10.1099/ijsem.0.003325	2019

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 )
#64939	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 103871
#65414	Inam Ullah Khan, Firasat Hussain, Neeli Habib, Mohammed A. M. Wadaan, Iftikhar Ahmed, Wan-Taek Im, Wael N. Hozzein, Xiao-Yang Zhi, Wen-Jun Li: Phenylobacterium deserti sp. nov., isolated from desert soil. IJSEM 67: 4722 - 4727 2017 ( DOI 10.1099/ijsem.0.002366 , PubMed 28984224 )
#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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Phenylobacterium deserti (DSM 103871, CCTCC AB 2016297, YIM 73061)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Enzymes

Pathway annotation

Fatty acid profile?

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003254705

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

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Fatty acid profile