Herbiconiux flava (DSM 26474, NBRC 16403, VKM Ac-2058)

Name: Herbiconiux flava (DSM 26474, NBRC 16403, VKM Ac-2058)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7512

Type strain

Culture col. no. DSM 26474 NBRC 16403 VKM Ac-2058

NCBI tax ID(s) 881268

Special Collections DSMZ Literature strains

Links

Herbiconiux flava DSM 26474 is an aerobe, mesophilic, Gram-positive prokaryote that was isolated from Phyllosphere Carex sp..

Gram-positive rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 49556

LMG 22541,DSM 14595,IFO 16235,VKM Ac-2058,IFO 16403,VKM Ac-2085,KCTC 13907,JCM 11431,NBRC 16235,ATCC BAA-401,CIP 107131,NCIMB 13882,IAM 15144,NBRC 16403,DSM 26474

@ref 20215

Last LPSN update 2025-12-16 09:48:36

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Microbacteriaceae

Genus Herbiconiux

Species Herbiconiux flava

Full scientific name Herbiconiux flava Hamada et al. 2012

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
30227	positive	01-02 µm	0.5-0.7 µm	rod-shaped
125439	positive					98.5

Pigmentation

30227

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
18237	PP-MEDIUM (DSMZ Medium 513)		Medium recipe at MediaDive	Name: PP-MEDIUM (DSMZ Medium 513) Composition: Agar 15.0 g/l Polypeptone 10.0 g/l Yeast extract 2.0 g/l MgSO4 x 7 H2O 1.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
18237	positive	growth	28	mesophilic
30227	positive	growth	05-37
30227	positive	optimum	28	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
30227	positive	optimum	7
30227	positive	growth	05-09	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30227	aerobe
125438	aerobe	90.214
125439	obligate aerobe	98.9

Spore formation

30227

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30227	NaCl	positive	growth	0-3 %

Murein

@ref	Murein short key	Type
18237	B07	B2gamma {Gly} [L-Dab] D-Glu-D-Dab

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30227	17057 ChEBI	cellobiose	+	carbon source
30227	4853 ChEBI	esculin	+	hydrolysis
30227	28757 ChEBI	fructose	+	carbon source
30227	28260 ChEBI	galactose	+	carbon source
30227	17234 ChEBI	glucose	+	carbon source
30227	17754 ChEBI	glycerol	+	carbon source
30227	17306 ChEBI	maltose	+	carbon source
30227	29864 ChEBI	mannitol	+	carbon source
30227	37684 ChEBI	mannose	+	carbon source
30227	17814 ChEBI	salicin	+	carbon source
30227	17992 ChEBI	sucrose	+	carbon source
30227	18222 ChEBI	xylose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
30227	catalase	+	1.11.1.6

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
18237	Phyllosphere Carex sp.	Carex	Belgorod region	Russia	RUS	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
18237	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	ASM1340986v1 assembly for Herbiconiux flava DSM 26474	contig	GCA_013409865	881268.3	2844852863	881268	76.72
124043	ASM2792202v1 assembly for Herbiconiux flava VKM Ac-2058	scaffold	GCA_027922025	881268.6	8118457815	881268	76.67

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Curtobacterium sp. VKM Ac-2058 gene for 16S ribosomal RNA, partial sequence	AB042093	1510		123319
18237	Herbiconiux flava gene for 16S rRNA, partial sequence	AB583921	1480		881268

GC content

@ref	GC-content (mol%)
18237	71.0
30227	71

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Herbiconiux flava DSM 26474
NCBI: GCA_013409865

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	69.20	no
125439	motility	BacteriaNetⓘ	no	65.00	no
125439	gram_stain	BacteriaNetⓘ	positive	98.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Herbiconiux flava strain DSM 26474
PATRIC: 881268.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	89.77	no
125438	anaerobic	anaerobicⓘ	no	98.40	no
125438	aerobic	aerobicⓘ	yes	90.21	yes
125438	spore-forming	spore-formingⓘ	no	79.10	no
125438	thermophilic	thermophileⓘ	no	97.00	yes
125438	flagellated	motile2+ⓘ	no	89.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Pangenome analysis of the genus Herbiconiux and proposal of four new species associated with Chinese medicinal plants.	Deng Y, Jiang ZM, Han XF, Su J, Yu LY, Liu WH, Zhang YQ.	Front Microbiol	10.3389/fmicb.2023.1119226	2023
Phylogeny	Description of Herbiconiux flava sp. nov. and emended description of the genus Herbiconiux.	Hamada M, Komukai C, Tamura T, Evtushenko LI, Vinokurova NG, Suzuki KI	Int J Syst Evol Microbiol	10.1099/ijs.0.031260-0	2011

References

#18237	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26474
#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 )
#30227	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 #26570 (see below)
#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) .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Herbiconiux flava (DSM 26474, NBRC 16403, VKM Ac-2058)

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

Halophily

Murein

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_013409865

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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