Strain identifier
BacDive ID: 162645
Type strain: 
Species: Noviherbaspirillum humi
Strain history: S.-S. Lee U15.
NCBI tax ID(s): 1688639 (species)
version 9.3 (current version)
General
@ref: 67770
BacDive-ID: 162645
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Noviherbaspirillum humi JCM 19873 is a mesophilic, Gram-negative bacterium that was isolated from Soil of Sadky region.
NCBI tax id
- NCBI tax id: 1688639
- Matching level: species
strain history
- @ref: 67770
- history: S.-S. Lee U15.
doi: 10.13145/bacdive162645.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Oxalobacteraceae
- genus: Noviherbaspirillum
- species: Noviherbaspirillum humi
- full scientific name: Noviherbaspirillum humi Sundararaman et al. 2017
@ref: 67770
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Oxalobacteraceae
genus: Noviherbaspirillum
species: Noviherbaspirillum humi
full scientific name: Noviherbaspirillum humi Sundararaman et al. 2017
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 125438 | negative | 97.994 |
| 125439 | negative | 98.7 |
Culture and growth conditions
culture temp
- @ref: 67770
- growth: positive
- type: growth
- temperature: 30
Physiology and metabolism
oxygen tolerance
- @ref: 125439
- oxygen tolerance: aerobe
- confidence: 93.5
spore formation
- @ref: 125439
- spore formation: no
- confidence: 97.1
Isolation, sampling and environmental information
isolation
- @ref: 67770
- sample type: Soil of Sadky region
- country: Ukraine
- origin.country: UKR
- continent: Europe
taxonmaps
- @ref: 69479
- File name: preview.99_27399.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_3405;97_16521;98_20502;99_27399&stattab=map
- Last taxonomy: Noviherbaspirillum humi subclade
- 16S sequence: KP763493
- Sequence Identity:
- Total samples: 603
- soil counts: 327
- aquatic counts: 66
- animal counts: 97
- plant counts: 113
Sequence information
16S sequences
- @ref: 67770
- description: Noviherbaspirillum humi strain U15 16S ribosomal RNA gene, partial sequence
- accession: KP763493
- length: 1442
- database: nuccore
- NCBI tax ID: 1688639
Genome sequences
- @ref: 67770
- description: Noviherbaspirillum humi U15
- accession: GCA_900188095
- assembly level: scaffold
- database: ncbi
- NCBI tax ID: 1688639
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 97.994 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 97.581 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 89.251 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 85.31 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 95.335 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 82.004 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 97.1 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 73.9 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 98.7 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | aerobe | 93.5 |
External links
@ref: 67770
culture collection no.: JCM 19873, KEMB 7305-102
literature
- topic: Phylogeny
- Pubmed-ID: 26940744
- title: Noviherbaspirillum humi sp. nov., isolated from soil.
- authors: Sundararaman A, Srinivasan S, Lee SS
- journal: Antonie Van Leeuwenhoek
- DOI: 10.1007/s10482-016-0670-0
- year: 2016
- mesh: Bacterial Typing Techniques, DNA, Bacterial/genetics, Oxalobacteraceae/*classification/genetics/*isolation & purification, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Soil Microbiology, Ukraine
- topic2: Phenotype
Reference
| @id | authors | title | doi/url |
|---|---|---|---|
| 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 | 10.1099/ijsem.0.004332 |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |
| 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 | https://microbeatlas.org/ |
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | 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 | https://github.com/GenomeNet/deepG |