Noviherbaspirillum massiliense (DSM 25712, CSUR P159, JC206)

Name: Noviherbaspirillum massiliense (DSM 25712, CSUR P159, JC206)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24269

Type strain

Strain Designation JC206

Culture col. no. DSM 25712 CSUR P159 JC206

NCBI tax ID(s) 1465823

Special Collections DSMZ Literature strains Cadoret human gut

Links

Noviherbaspirillum massiliense JC206 is an aerobe, mesophilic, motile prokaryote that was isolated from human faeces of a healthy patient.

motile rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 402288

DSM 25712

@ref 20215

Last LPSN update 2025-12-16 09:52:49

Domain Pseudomonadati

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Oxalobacteraceae

Genus Noviherbaspirillum

Species Noviherbaspirillum massiliense

Full scientific name Noviherbaspirillum massiliense (Lagier et al. 2014) Chaudhary and Kim 2017

Synonyms (2)

Herbaspirillum massiliense
Noviherbaspirillum massiliense

Morphology

Cell morphology

@ref	Cell shape	Flagellum arrangement	Gram stain	Confidence
43245	rod-shaped	polar
125438			negative	96.994
125439			negative	95

Multimedia

@ref:	20983
multimedia content:	DSM_25712.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_25712.jpg
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
43245	Reasoner's 2A agar (R2A)
43245	nutritient agar (NA)
20983	COLUMBIA BLOOD AGAR (DSMZ Medium 429)	Medium recipe at MediaDive	Name: COLUMBIA BLOOD AGAR (DSMZ Medium 429) Composition: Horse blood 40.0 g/l Columbia agar base
43245	trypticase soy agar (TSA)

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
20983	positive	growth	37	mesophilic
43245	positive	optimum	37	mesophilic
43245	positive	growth	30-37	mesophilic

Physiology and metabolism

Oxygen tolerance

43245

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
125439		97.1

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43245	30089 ChEBI	acetate	+	carbon source
43245	28885 ChEBI	butanol	-	growth
43245	17968 ChEBI	butyrate	+	carbon source
43245	4853 ChEBI	esculin	+	hydrolysis
43245	16236 ChEBI	ethanol	-	growth
43245	28757 ChEBI	fructose	-	growth
43245	28260 ChEBI	galactose	-	growth
43245	24265 ChEBI	gluconate	-	growth
43245	17234 ChEBI	glucose	-	growth
43245	17754 ChEBI	glycerol	-	growth
43245	17716 ChEBI	lactose	-	growth
43245	17306 ChEBI	maltose	-	growth
43245	37684 ChEBI	mannose	-	growth
43245	17632 ChEBI	nitrate	-	reduction
43245	15361 ChEBI	pyruvate	-	carbon source
43245	26546 ChEBI	rhamnose	-	growth
43245	30911 ChEBI	sorbitol	-	growth
43245	30031 ChEBI	succinate	+	carbon source
43245	18222 ChEBI	xylose	-	growth

Metabolite production

@ref	Chebi-ID	Metabolite	Production
43245	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
43245	arginine dihydrolase	+	3.5.3.6
43245	catalase	+	1.11.1.6
43245	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Infection	#Patient	-
#Host	#Human	-
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
20983	human faeces of a healthy patient	Senegal	SEN	Africa
43245	faecal flora of a healthy patient	Senegal	SEN	Africa

Taxonmaps

69479

Global distribution of 16S sequence JN657219 (>99% sequence identity) for Noviherbaspirillum massiliense subclade from Microbeatlas

Aquatic Samples	140
Soil Samples	253
Animal Samples	716
Plant Samples	44
Total Samples	1153

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
20983	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	ASM31204v1 assembly for Noviherbaspirillum massiliense JC206	scaffold	GCA_000312045	1095769.4	2547132156	1095769	71.52

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20983	Herbaspirillum massiliense JC206 16S ribosomal RNA gene, partial sequence	JN657219	1489		1095769

GC content

@ref	GC-content (mol%)	Method
20983	59.73	sequence analysis
43245	59.73	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Noviherbaspirillum massiliense JC206
NCBI: GCA_000312045

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.10	no
125439	motility	BacteriaNetⓘ	yes	64.10	no
125439	gram_stain	BacteriaNetⓘ	negative	95.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	71.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Noviherbaspirillum massiliense JC206 JC206
NCBI: GCA_000312045.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.99	no
125438	anaerobic	anaerobicⓘ	no	95.65	yes
125438	aerobic	aerobicⓘ	yes	87.88	yes
125438	spore-forming	spore-formingⓘ	no	88.86	no
125438	thermophilic	thermophileⓘ	no	94.62	yes
125438	flagellated	motile2+ⓘ	yes	88.84	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Noviherbaspirillum aerium sp. nov., isolated from air.	Xue H, Piao CG, Lin YH, Bian DR, Li Y	Int J Syst Evol Microbiol	10.1099/ijsem.0.004537	2020
Phylogeny	Noviherbaspirillum denitrificans sp. nov., a denitrifying bacterium isolated from rice paddy soil and Noviherbaspirillum autotrophicum sp. nov., a denitrifying, facultatively autotrophic bacterium isolated from rice paddy soil and proposal to reclassify Herbaspirillum massiliense as Noviherbaspirillum massiliense comb. nov.	Ishii S, Ashida N, Ohno H, Segawa T, Yabe S, Otsuka S, Yokota A, Senoo K	Int J Syst Evol Microbiol	10.1099/ijsem.0.001875	2017
Phylogeny	Noviherbaspirillum agri sp. nov., isolated from reclaimed grassland soil, and reclassification of Herbaspirillum massiliense (Lagier et al., 2014) as Noviherbaspirillum massiliense comb. nov.	Chaudhary DK, Kim J	Int J Syst Evol Microbiol	10.1099/ijsem.0.001747	2017
Phylogeny	Noviherbaspirillum pedocola sp. nov., isolated from oil-contaminated experimental soil.	Chaudhary DK, Dahal RH, Hong Y	Arch Microbiol	10.1007/s00203-021-02295-6	2021
Phylogeny	Noviherbaspirillum galbum sp. nov., a bacterium isolated from soil.	Park Y, Maeng S, Lee SE, Han JH, Lee YK, Oh J, Jigden B, Kang JH, Kim MK	Arch Microbiol	10.1007/s00203-020-02076-7	2020
Genetics	Non-contiguous finished genome sequence and description of Herbaspirillum massiliense sp. nov.	Lagier JC, Gimenez G, Robert C, Raoult D, Fournier PE	Stand Genomic Sci	10.4056/sigs.3086474	2012

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 )
#20983	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25712
#43245	Satoshi Ishii, Naoaki Ashida, Hiroki Ohno, Takahiro Segawa, Shuhei Yabe, Shigeto Otsuka, Akira Yokota, Keishi Senoo: Noviherbaspirillum denitrificans sp. nov., a denitrifying bacterium isolated from rice paddy soil and Noviherbaspirillum autotrophicum sp. nov., a denitrifying, facultatively autotrophic bacterium isolated from rice paddy soil and proposal to reclassify Herbaspirillum massiliense as Noviherbaspirillum massiliense comb. nov.. IJSEM 67: 1841 - 1848 2017 ( DOI 10.1099/ijsem.0.001875 , PubMed 28629495 )
#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) .
#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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Noviherbaspirillum massiliense (DSM 25712, CSUR P159, JC206)

Name and taxonomic classification

Morphology

Cell morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000312045

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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