Phycicoccus sp. (DSM 102498, Root101)

Name: Phycicoccus sp. (DSM 102498, Root101)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132324

Type strain

Strain Designation Root101

Culture col. no. DSM 102498 Root101

NCBI tax ID(s) 1902410

Special Collections DSMZ Arabidopsis

History DSMZ <- P. Schulze-Lefert, Max Planck Institute for Plant Breeding Research, Cologne, Germany; Root101 <- Y. Bai

Links

Root101 is a bacterium that was isolated from roots of Arabidopsis thaliana ecotype Shakdara .

genome sequence Bacteria

Name and taxonomic classification

SI-ID 404049

DSM 102498

@ref 20215

Last LPSN update 2026-05-29 08:37:49

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Intrasporangiaceae

Genus Phycicoccus

Full scientific name Phycicoccus Lee 2006

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	positive	92.573
125439	positive	97.377

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
24113	TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)		Medium recipe at MediaDive	Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
24113	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)		Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
24113	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125438	aerobe	91.687
125439	obligate aerobe	94.161

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root (Rhizome)

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
24113	roots of Arabidopsis thaliana ecotype Shakdara (Sha)	Arabidopsis thaliana	Cologne (50.958N 6.856E)	Germany	DEU	Europe	50.958	6.856 50.958/6.856

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	Root101 assembly for Phycicoccus sp. Root101	contig	GCA_001426245	1736421.3	2643221624	1736421	75.3

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Root101 assembly for Phycicoccus sp. Root101
BV-BRC: 1736421.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	94.16	no
125439	motility	BacteriaNetⓘ	no	82.65	no
125439	gram_stain	BacteriaNetⓘ	positive	97.38	no
125439	spore_formation	BacteriaNetⓘ	no	77.79	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Phycicoccus sp. Root101
PATRIC: 1736421.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	92.57	no
125438	anaerobic	anaerobicⓘ	no	98.72	no
125438	spore-forming	spore-formingⓘ	no	60.19	no
125438	aerobic	aerobicⓘ	yes	91.69	no
125438	thermophilic	thermophileⓘ	no	95.00	no
125438	flagellated	motile2+ⓘ	no	76.50	no

Literature

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 )
#24113	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 102498
#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) .
#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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