Herbaspirillum hiltneri (DSM 17495, CIP 109904, LMG 23131)

Name: Herbaspirillum hiltneri (DSM 17495, CIP 109904, LMG 23131)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11365

Type strain

Strain Designation N3

Culture col. no. DSM 17495 CIP 109904 LMG 23131 N3 UCCCB12

NCBI tax ID(s) 341045

Special Collections DSMZ CIP Literature strains UCCCB

History <- M. Rothballer, GSF - Dept. Rhizosphere Biol., Inst. Soil Ecol., Germany; N3 <- I. Klein M. Rothballer, GSF - Deptartment of Rhizosphere Biology, Inst. Soil Ecol., Germany; N3 < Klein, I. Department of Rhizosphere Biology, GSF - National Research Centre for Environment and Health CIP <- 2008, DSMZ <- M. Rothballer, GSF, Neuherberg, Germany: strain N3

Links

Herbaspirillum hiltneri N3 is an aerobe, Gram-negative, motile bacterium that was isolated from surface-sterilized wheat roots .

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

Name and taxonomic classification

SI-ID 297228

DSM 17495,LMG 23131,CCUG 54573,CIP 109904

@ref 20215

Last LPSN update 2026-02-09 11:20:32

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Oxalobacteraceae

Genus Herbaspirillum

Species Herbaspirillum hiltneri

Full scientific name Herbaspirillum hiltneri Rothballer et al. 2006

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31675	negative	1.6-2 µm	0.5-0.6 µm	rod-shaped
119899	negative			rod-shaped
125438	negative				97.5
125439	negative				98.4

Pigmentation

31675

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7022	NUTRIENT AGAR (DSMZ Medium 1)	Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
33337	MEDIUM 328- for nutrient agar		Distilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
119899	CIP Medium 328	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
7022	positive	growth	30
31675	positive	growth	26-34
31675	positive	optimum	26-34
33337	positive	growth	30
67772	positive	optimum	26-34

Culture pH

@ref	Ability	Type	PH
31675	positive	optimum	06-08
67772	positive	optimum	6.0-8.0
31675	positive	growth	06-08

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31675	aerobe
119899	obligate aerobe
125439	obligate aerobe	98.2

Spore formation

@ref	Spore formation	Confidence
31675
125439		97.7

Observation

31675

Observationaggregates in chains

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31675	22599 ChEBI	arabinose	+	carbon source
31675	33984 ChEBI	fucose	+	carbon source
31675	28260 ChEBI	galactose	+	carbon source
31675	17234 ChEBI	glucose	+	carbon source
31675	17754 ChEBI	glycerol	+	carbon source
31675	28087 ChEBI	glycogen	+	carbon source
31675	18403 ChEBI	L-arabitol	+	carbon source
31675	29864 ChEBI	mannitol	+	carbon source
31675	506227 ChEBI	N-acetylglucosamine	+	carbon source
119899	17632 ChEBI	nitrate	-	reduction
119899	16301 ChEBI	nitrite	-	reduction
31675	28044 ChEBI	phenylalanine	+	carbon source
31675	26986 ChEBI	threonine	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
119899	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
31675	catalase	+	1.11.1.6
119899	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
31675	cytochrome oxidase	+	1.9.3.1
68382	esterase (C 4)	-		from API zym
68382	esterase lipase (C 8)	-		from API zym
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	-		from API zym
119899	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
119899	urease	+	3.5.1.5
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
119899	-	+	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Host species
7022	surface-sterilized wheat roots (Triticum aestivum)		Oberpfalz, Neumarkt	Germany	DEU	Europe			Triticum aestivum
67772	Surface-sterilized wheat roots	2005	Baviera, Neumarkt in der Oberpfalz	Germany	DEU	Europe	49.2833	11.4667 49.2833/11.4667
119899	Environment, Soil, surface-sterilized wheat roots, Triticum aestivum		Oberpfalz	Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence DQ150563 (>99% sequence identity) for Herbaspirillum from Microbeatlas

Aquatic Samples	4
Soil Samples	3
Animal Samples	11
Plant Samples	3
Total Samples	21

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7022	1	Risk group (German classification) According to TRBA 466
67772	1
119899	1	Risk group (French 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	ASM126792v1 assembly for Herbaspirillum hiltneri N3	complete	GCA_001267925	1262470.4	2645728026	1262470	95.44

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7022	Herbaspirillum hiltneri strain N3 16S ribosomal RNA gene, partial sequence	DQ150563	1478		1262470

GC content

@ref	GC-content (mol%)
7022	60.9
31675	60.9-61.5

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Herbaspirillum hiltneri N3
PATRIC: 1262470.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.20	no
125439	gram_stain	BacteriaNetⓘ	negative	98.40	no
125439	motility	BacteriaNetⓘ	yes	83.90	no
125439	spore_formation	BacteriaNetⓘ	no	97.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Herbaspirillum hiltneri N3 N3
NCBI: GCA_001267925.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.50	no
125438	anaerobic	anaerobicⓘ	no	97.83	yes
125438	aerobic	aerobicⓘ	yes	87.95	yes
125438	spore-forming	spore-formingⓘ	no	89.30	yes
125438	thermophilic	thermophileⓘ	no	96.99	no
125438	flagellated	motile2+ⓘ	yes	79.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Decrease in beneficial bacteria and increase in harmful bacteria in Gastrodia seedlings and their surrounding soil are mainly responsible for degradation of Gastrodia asexual propagation.	Wang X, Gao Y, Zang P, Zhang G, Yang X, Liu Q.	Front Plant Sci	10.3389/fpls.2024.1334958	2024
	Engineering Saccharomyces cerevisiae for growth on xylose using an oxidative pathway.	Tanaka K, Yukawa T, Bamba T, Wakiya M, Kumokita R, Jin YS, Kondo A, Hasunuma T.	Appl Microbiol Biotechnol	10.1007/s00253-025-13417-1	2025
	Isolation, identification and characterization of nitrogen fixing endophytic bacteria and their effects on cassava production.	Zhang X, Tong J, Dong M, Akhtar K, He B.	PeerJ	10.7717/peerj.12677	2022
Genetics	Genome comparison between clinical and environmental strains of Herbaspirillum seropedicae reveals a potential new emerging bacterium adapted to human hosts.	Faoro H, Oliveira WK, Weiss VA, Tadra-Sfeir MZ, Cardoso RL, Balsanelli E, Brusamarello-Santos LCC, Camilios-Neto D, Cruz LM, Raittz RT, Marques ACQ, LiPuma J, Fadel-Picheth CMT, Souza EM, Pedrosa FO.	BMC Genomics	10.1186/s12864-019-5982-9	2019
Enzymology	Recovery of Herbaspirillum species from persons with cystic fibrosis.	Spilker T, Uluer AZ, Marty FM, Yeh WW, Levison JH, Vandamme P, Lipuma JJ.	J Clin Microbiol	10.1128/jcm.00460-08	2008
Enzymology	Screening and characterization of endophytic Bacillus and Paenibacillus strains from medicinal plant Lonicera japonica for use as potential plant growth promoters.	Zhao L, Xu Y, Lai XH, Shan C, Deng Z, Ji Y.	Braz J Microbiol	10.1590/s1517-838246420140024	2015
Genetics	Complete Genome Sequence of Herbaspirillum hiltneri N3 (DSM 17495), Isolated from Surface-Sterilized Wheat Roots.	Guizelini D, Saizaki PM, Coimbra NA, Weiss VA, Faoro H, Sfeir MZ, Baura VA, Monteiro RA, Chubatsu LS, Souza EM, Cruz LM, Pedrosa FO, Raittz RT, Marchaukoski JN, Steffens MB	Genome Announc	10.1128/genomeA.01288-15	2015
Phylogeny	Herbaspirillum hiltneri sp. nov., isolated from surface-sterilized wheat roots.	Rothballer M, Schmid M, Klein I, Gattinger A, Grundmann S, Hartmann A	Int J Syst Evol Microbiol	10.1099/ijs.0.64031-0	2006

References

#7022	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17495
#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 )
#27953	IJSEM 1341 2006 ( DOI 10.1099/ijs.0.64031-0 , PubMed 16738112 )
#31675	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 #27953
#33337	; Curators of the CIP;
#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) .
#67772	The University of Coimbra Bacteria Culture Collection (UCCCB) ; Curators of the UCCCB;
#68382	Automatically annotated from API zym .
#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 .
#119899	Collection of Institut Pasteur ; Curators of the CIP; CIP 109904
#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 )

Rate our new design

Content

About us

Herbaspirillum hiltneri (DSM 17495, CIP 109904, LMG 23131)

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

Metabolite production

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001267925

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media