Herbaspirillum huttiense subsp. putei (DSM 21883, ATCC BAA-806, CCUG 49453)

Name: Herbaspirillum huttiense subsp. putei (DSM 21883, ATCC BAA-806, CCUG 49453)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11368

Type strain

Strain Designation 7-2

Culture col. no. DSM 21883 ATCC BAA-806 CCUG 49453 IAM 15032 JCM 21495 3 more

NCBI tax ID(s) 1235558 230311

Special Collections DSMZ CCUG JCM CIP

History <- CCUG <- A. Yokota, IAM; strain 7-2 IAM 15032 <-- A. Yokota 7-2.

Links

Herbaspirillum huttiense subsp. putei 7-2 is an aerobe bacterium that was isolated from well water.

aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 134429

ATCC BAA-806,IAM 15032,CCUG 49453,NBRC 102406,CIP 108607,JCM 21495,DSM 21883

@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 huttiense subsp. putei

Full scientific name Herbaspirillum huttiense subsp. putei (Ding and Yokota 2004) Dobritsa et al. 2010

Synonyms (1)

Herbaspirillum putei

BacDive ID	Other strains from **Herbaspirillum huttiense subsp. putei** (1)	Type strain
11358	H. huttiense subsp. putei 266, DSM 10281, ATCC 14670, JCM 21423, CCUG ... (type strain)

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	98
125439	negative	99.1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
16017	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

Culture temp

@ref	Growth	Type	Temperature (°C)
16017	positive	growth	22-37
58564	positive	growth	22-37
67770	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
58564	aerobe
125439	aerobe	90.3

Spore formation

@ref	Spore formation	Confidence
125439		99.2

Observation

67770

Observationquinones: Q-8

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	-
#Engineered	#Built environment	#Water reservoir (Aquarium/pool)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
16017	well water	Osaka	Japan	JPN	Asia
67770	Well water	Osaka	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB681762 (>99% sequence identity) for Herbaspirillum from Microbeatlas

Aquatic Samples	342
Soil Samples	197
Animal Samples	743
Plant Samples	411
Total Samples	1693

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16017	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
67770	Hputei1.0 assembly for Herbaspirillum huttiense subsp. putei IAM 15032	contig	GCA_000478365	1235558.4	2551306420	1235558	67.35

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Herbaspirillum huttiense subsp. putei gene for 16S rRNA, partial sequence, strain: NBRC 102406	AB681762	1458	1235558
16017	Herbaspirillum putei gene for 16S rRNA, partial sequence	AB109890	1496	1235558
16017	Herbaspirillum huttiense subsp. putei strain ATCC BAA-806 16S ribosomal RNA gene, partial sequence	EU046556	1455	1235558

GC content

@ref	GC-content (mol%)	Method
16017	66.2	high performance liquid chromatography (HPLC)
67770	62.1	high performance liquid chromatography (HPLC)
67770	62.9	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: Herbaspirillum huttiense subsp. putei IAM 15032
NCBI: GCA_000478365

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.20	no
125439	motility	BacteriaNetⓘ	yes	85.20	no
125439	gram_stain	BacteriaNetⓘ	negative	99.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	90.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Herbaspirillum huttiense subsp. putei IAM 15032
PATRIC: 1235558.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.00	no
125438	anaerobic	anaerobicⓘ	no	97.81	yes
125438	spore-forming	spore-formingⓘ	no	88.38	no
125438	aerobic	aerobicⓘ	yes	86.84	yes
125438	thermophilic	thermophileⓘ	no	98.99	yes
125438	flagellated	motile2+ⓘ	yes	80.79	no

Literature

Topic	Title	Authors	Journal	DOI	Year
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
Phylogeny	Genomic insights into two new subspecies of Herbaspirillum huttiense strains isolated from diseased foliage in Florida.	Poudel M, Sharma A, Minsavage GV, Fullem K, Huguet-Tapia J, Norman DJ, Goss EM, Harmon CL, Jones JB.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006597	2024
	The role and significance of the oncobiota in selected cancers: a review.	Walczak LJ, Kosikowska U, Herbet M.	Clin Exp Med	10.1007/s10238-025-01598-y	2025
	Isolation of cadmium-resistance and siderophore-producing endophytic bacteria and their potential use for soil cadmium remediation.	Li Y, Wei S, Chen X, Dong Y, Zeng M, Yan C, Hou L, Jiao R.	Heliyon	10.1016/j.heliyon.2023.e17661	2023
Metabolism	Discovery of novel pathways for carbohydrate metabolism.	Stack TMM, Gerlt JA.	Curr Opin Chem Biol	10.1016/j.cbpa.2020.09.005	2021
	The Liver Microbiome Is Implicated in Cancer Prognosis and Modulated by Alcohol and Hepatitis B.	Chakladar J, Wong LM, Kuo SZ, Li WT, Yu MA, Chang EY, Wang XQ, Ongkeko WM.	Cancers (Basel)	10.3390/cancers12061642	2020
	Biochemical characteristics, adhesion, and cytotoxicity of environmental and clinical isolates of Herbaspirillum spp.	Marques AC, Paludo KS, Dallagassa CB, Surek M, Pedrosa FO, Souza EM, Cruz LM, LiPuma JJ, Zanata SM, Rego FG, Fadel-Picheth CM.	J Clin Microbiol	10.1128/jcm.02192-14	2015
	The genome of the endophytic bacterium H. frisingense GSF30(T) identifies diverse strategies in the Herbaspirillum genus to interact with plants.	Straub D, Rothballer M, Hartmann A, Ludewig U.	Front Microbiol	10.3389/fmicb.2013.00168	2013
Metabolism	Bacterial Small RNAs in the Genus Herbaspirillum spp.	Carvalho Garcia A, Dos Santos VLP, Santos Cavalcanti TC, Collaco LM, Graf H.	Int J Mol Sci	10.3390/ijms20010046	2018
Enzymology	Structure and function of aldopentose catabolism enzymes involved in oxidative non-phosphorylative pathways.	Ren Y, Eronen V, Blomster Andberg M, Koivula A, Hakulinen N.	Biotechnol Biofuels Bioprod	10.1186/s13068-022-02252-5	2022
	Herbaspirillum Infection in Humans: A Case Report and Review of Literature.	Dhital R, Paudel A, Bohra N, Shin AK.	Case Rep Infect Dis	10.1155/2020/9545243	2020
Enzymology	Crystal structure of L-2-keto-3-deoxyfuconate 4-dehydrogenase reveals a unique binding mode as a alpha-furanosyl hemiketal of substrates.	Akagashi M, Watanabe S, Kwiatkowski S, Drozak J, Terawaki SI, Watanabe Y.	Sci Rep	10.1038/s41598-024-65627-8	2024
Genetics	Draft Genome Sequence of Herbaspirillum huttiense subsp. putei IAM 15032, a Strain Isolated from Well Water.	de Souza V, Piro VC, Faoro H, Tadra-Sfeir MZ, Chicora VK, Guizelini D, Weiss V, Vialle RA, Monteiro RA, Steffens MB, Marchaukoski JN, Pedrosa FO, Cruz LM, Chubatsu LS, Raittz RT	Genome Announc	10.1128/genomeA.00252-12	2013
Metabolism	Substrate and metabolic promiscuities of d-altronate dehydratase family proteins involved in non-phosphorylative d-arabinose, sugar acid, l-galactose and l-fucose pathways from bacteria.	Watanabe S, Fukumori F, Watanabe Y	Mol Microbiol	10.1111/mmi.14259	2019
Metabolism	Novel non-phosphorylative pathway of pentose metabolism from bacteria.	Watanabe S, Fukumori F, Nishiwaki H, Sakurai Y, Tajima K, Watanabe Y	Sci Rep	10.1038/s41598-018-36774-6	2019
Phylogeny	Reclassification of Herbaspirillum putei as a later heterotypic synonym of Herbaspirillum huttiense, with the description of H. huttiense subsp. huttiense subsp. nov. and H. huttiense subsp. putei subsp. nov., comb. nov., and description of Herbaspirillum aquaticum sp. nov.	Dobritsa AP, Reddy MCS, Samadpour M	Int J Syst Evol Microbiol	10.1099/ijs.0.009381-0	2009
Phylogeny	Proposals of Curvibacter gracilis gen. nov., sp. nov. and Herbaspirillum putei sp. nov. for bacterial strains isolated from well water and reclassification of [Pseudomonas] huttiensis, [Pseudomonas] lanceolata, [Aquaspirillum] delicatum and [Aquaspirillum] autotrophicum as Herbaspirillum huttiense comb. nov., Curvibacter lanceolatus comb. nov., Curvibacter delicatus comb. nov. and Herbaspirillum autotrophicum comb. nov.	Ding L, Yokota A	Int J Syst Evol Microbiol	10.1099/ijs.0.02975-0	2004

References

#16017	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21883
#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 )
#58564	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 49453
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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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Herbaspirillum huttiense subsp. putei (DSM 21883, ATCC BAA-806, CCUG 49453)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000478365

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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