CD Genomics Blog

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Organisms live in an ecological context, and pure cultures rarely exist in nature. Microbial communities comprising microecology are one example of systems that are far from being pure culture which makes them dynamic in playing roles in the ecosystem.  Despite their abundance and ubiquity, our understanding of microecology, their interactions, and functions lag our knowledge of pure cultures. 

In the environment, microecology maintains stability and participate in the biochemical circulation of macronutrients thereby alleviating environmental pollution. Agriculture benefits from it in ways such as the increase in crop yields, animal productivity and health improvement, and microbial amendments. In medicine, it elucidates pathogenic mechanism which facilitates vaccine and drug development for human diseases. The human has its own microecology which plays roles in processes such as immune response and disease progression. Interaction of this microecology also produces a plethora of outcomes that can either be beneficial or harmful to one another.

Traditional methods can still be used but oftentimes, they can be laborious and time-consuming. With the advent of cutting-edge molecular biology tools, types and frequency of microorganisms, as well as their quality and quantity in the samples, can be measured through next-generation sequencing, long-read sequencing, Ion PGM, Nanopore systems, clone library, real-time qPCR, PCR-denaturing gradient gel electrophoresis (DGGE), and anaerobic culture. In pharmaceuticals, third-generation sequencing, SNP genotyping, and gene chip analysis are also used for identification and characterization. For microbial identification, the 16S ribosomal RNA is used for bacteria while the 18S rRNA and ITS regions are ideal for fungi.  Detection of novel microorganisms is made possible through short-read and full-length 16S/18S/ITS amplicon sequencing. Sequencing data is then processed through bioinformatics platforms for alignment, trimming, diversity analysis, correlation analysis, and taxonomic assignment. The only challenge here is the variety of source and collection methods where this microecology will come from. Afterward, the process is deviates depending on the desired outputs.

Through metagenomics, extremophiles found in volcanoes, deep seas, and radioactive regions can be explored. This unique microecology presents novel enzymes and biochemical pathways waiting to be discovered. Enzymes collected from them could be used for various industrial applications. The air has also its own share of microbial diversity which affects air quality and causes human diseases such as allergies and infections. Studying aerial microecology gives insights into its functions, structures, and relationships. Microecology in bodies of water including sewage controls water quality and biogeochemical processes. Studying its diversity allows us to create solutions for sewage treatment and water pollution. On the other hand, the soil microbiome is involved in toxin removal, decomposition, plant growth, and protection against pathogens.

Looking at the bigger picture, microecology research through sequencing helps us produce innovative desirable solutions such as microbial fertilizers, microbial fuel cells, healthy animals, potent probiotics, crop yield increase, and proper protocols for waste management. This can be utilized also in personalized medicine where alterations in humans and surrounding interacting microecology could be used as biomarkers for potential disease diagnosis and treatment. Rapid automated tests are also emerging which can be used in the food, cosmetics, and pharmaceutical industry.

References

  1. Shi HL, Lan YH, Hu ZC, et al. Microecology research: a new target for the prevention of asthma. Chinese Medical Journal. 2020, 133(22).
  2. Yan J, Wu X, Chen J, et al. Harnessing the strategy of metagenomics for exploring the intestinal microecology of sable (Martes zibellina), the national first-level protected animal. AMB Express. 2020, 10(1).

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