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Identification of Rare Bacterial Pathogens by 16S rRNA Gene Sequencing and MALDI-TOF MS
Published on: July 11, 2016
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Sphingobacterium humi sp. nov., isolated from soil
Yunhee Lee1, Hyun Mi Jin2, Hye Su Jung1
1Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea.
International Journal of Systematic and Evolutionary Microbiology
|September 26, 2017
Summary
A novel bacterium, Sphingobacterium humi sp. nov. strain D1T, was discovered in South Korean soil. This facultatively aerobic, Gram-negative bacterium exhibits unique fatty acid profiles and represents a new species within the Sphingobacterium genus.
Area of Science:
- Microbiology
- Bacteriology
- Genomics
Background:
- The genus Sphingobacterium comprises Gram-negative, rod-shaped bacteria known for their characteristic sphingolipids.
- Understanding bacterial diversity in soil ecosystems is crucial for ecological and biotechnological applications.
Purpose of the Study:
- To isolate and characterize a novel bacterial strain from soil in South Korea.
- To determine the taxonomic position of the novel isolate using polyphasic characterization, including chemotaxonomic and phylogenetic analyses.
Main Methods:
- Isolation and cultivation of bacteria from soil samples.
- Gram staining, motility tests, and assessment of oxidase and catalase activities.
- Determination of growth conditions (temperature, pH, salinity).
- Chemotaxonomic analyses: respiratory quinone, major fatty acids, and polar lipid profiling.
- Genomic DNA extraction and G+C content determination.
- 16S rRNA gene sequencing for phylogenetic analysis.
- DNA-DNA hybridization for relatedness studies.
Main Results:
- Strain D1T is a Gram-negative, facultatively aerobic, non-motile rod.
- Optimal growth occurs at 30-37°C, pH 7.0-8.0, and 0.0-1.0% NaCl.
- Menaquinone 7 (MK-7) was the sole respiratory quinone; major fatty acids included iso-C15:0, iso-C17:0 3-OH, and summed feature 3.
- Sphingolipids were detected, consistent with the genus Sphingobacterium.
- The G+C content of the genomic DNA was 43.6 mol%.
- Phylogenetic analysis placed strain D1T within the genus Sphingobacterium, closely related to Sphingobacterium hotanense XH4T (98.1% 16S rRNA similarity).
- DNA-DNA relatedness between strain D1T and Sphingobacterium cellulitidis R-53603T was 43.1±0.7%.
Conclusions:
- Strain D1T represents a novel species of the genus Sphingobacterium based on distinct phenotypic, chemotaxonomic, and molecular characteristics.
- The proposed name for this new species is Sphingobacterium humi sp. nov.
- The type strain is D1T (=KACC 18595T=JCM 31225T).
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