Discovering a New Bacteria in Sweet Potato Soil

Jim Crocker
10th April, 2024

Discovering a New Bacteria in Sweet Potato Soil

Image Source: Natural Science News, 2024

Key Findings

  • Scientists discovered a new bacteria, Saccharopolyspora ipomoeae, in a Thai sweet potato field
  • This new strain could be a source of compounds for developing new antibiotics
  • The strain's genetic identity confirms it's a unique species within the Saccharopolyspora genus
In the quest to discover new antibiotics and other therapeutic agents, scientists have turned to the soil beneath our feet—quite literally. A team from Rajamangala University of Technology Suvarnabhumi has isolated a previously unknown species of bacteria from a sweet potato field, which could potentially be a new source of medically useful compounds[1]. This discovery adds a new member to the genus Saccharopolyspora, a group already known for producing natural products with significant pharmacological potential[2]. The genus Saccharopolyspora is part of a larger family of bacteria called actinomycetes, which are renowned for their ability to produce secondary metabolites—chemicals that can have various biological activities, including antibacterial properties[2]. These organisms are found in diverse environments, from terrestrial to marine, and they have been a goldmine for drug discovery. The new strain, named Saccharopolyspora ipomoeae, was identified through a meticulous process that is part of what scientists call a "polyphasic taxonomic approach." To determine if this strain was indeed something new, researchers compared its genetic material to that of other known species. They focused on the 16S rRNA gene, a part of the genome commonly used to identify and classify bacteria. The analysis showed that while related to other Saccharopolyspora species, strain TS4A08T had less than the threshold similarity in its genetic codes that scientists use to delineate one species from another. Further confirmation came from advanced genomic analyses. Using tools like CheckM, researchers can assess the quality of a genome, ensuring that the data they are looking at is complete and not contaminated by other genetic material[3]. This is crucial when claiming the discovery of a new species. Additionally, QUAST, another tool, helps scientists compare genome assemblies to check for errors and verify the accuracy of the genetic sequencing[4]. The new strain's genome was sequenced, and its size and G + C content, which refers to the proportion of the genome made up by guanine (G) and cytosine (C) bases, were determined to be characteristic of its genus. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values, which are measures of genetic similarity, were below the accepted thresholds for defining a new species, further supporting the claim. The researchers also looked at the physical and chemical characteristics of the strain. They found that it grew well in a range of temperatures and pH levels and could tolerate varying concentrations of salt. Its cell wall contained specific amino acids, and the fatty acid profile matched what is typically seen in Saccharopolyspora species. Moreover, the presence of certain sugars and the predominant isoprenologue, a type of molecule associated with the cell's membrane, were consistent with the genus's known properties. The discovery of Saccharopolyspora ipomoeae is more than just an addition to a list of bacterial species. It is a potential treasure trove for new drugs. Previous studies have shown that actinomycetes, and Saccharopolyspora in particular, are sources of chemical diversity and novel natural products with interesting pharmacological effects[2]. With the growing problem of antibiotic resistance, finding new compounds that can be developed into drugs is of paramount importance. This research not only expands our knowledge of the biodiversity of actinomycetes but also provides a foundation for further studies that could lead to the development of new therapeutic agents. The work done by the team at Rajamangala University of Technology Suvarnabhumi exemplifies the intricate process of discovering and characterizing new species with the potential to benefit human health. As such, strain TS4A08T, now known as Saccharopolyspora ipomoeae, stands as a promising candidate for future bioprospecting efforts aimed at combating diseases and improving medical treatments.

AgriculturePlant Science

References

Main Study

1) Saccharopolyspora ipomoeae sp. nov., an Actinomycete Isolated from Sweet Potato Field Soils.

Published 8th April, 2024

https://doi.org/10.1007/s00284-024-03661-5

Related Studies

2) Saccharopolyspora: an underexplored source for bioactive natural products.

https://doi.org/10.1111/jam.14360

3) CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.

https://doi.org/10.1101/gr.186072.114

4) QUAST: quality assessment tool for genome assemblies.

https://doi.org/10.1093/bioinformatics/btt086


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