Comparison of Different Approaches for Microbial Community Investigation of Arctic Ocean Samples

• Main Author: GAMBARDELLA, NICOLA
• Other Authors: VEZZI, ALESSANDRO
• Language: unknown
• Published: 2023
• Subjects: Metagenomics; Arctic; Comparison; Bioinformatics; Ocean; Arctic Ocean; Pacific
• Online Access: https://hdl.handle.net/20.500.12608/61232

none Modern microbial ecology offers a plethora of approaches for investigating microbial populations. The Arctic Ocean is an example of an environment that is difficult to research without the use of such tools, and the benefits and drawbacks of each are still unclear. A computational comparison of primary methodologies was undertaken in this study with the intention of increasing clarity and assisting future investigations. ASV were estimated using full-16S gene sequencing on the Pacific Bioscience platform, whereas metagenome-assembled-genomes (MAGs) were obtained using shotgun sequencing on the Illumina NovaSeq platform. Furthermore, the entire 16S gene sequence was divided into its well-known hypervariable regions in order to compare how those regions affect the results. The evaluation of the influence of such strategies in the community description revealed a complex picture, which is discussed in this paper. Modern microbial ecology offers a plethora of approaches for investigating microbial populations. The Arctic Ocean is an example of an environment that is difficult to research without the use of such tools, and the benefits and drawbacks of each are still unclear. A computational comparison of primary methodologies was undertaken in this study with the intention of increasing clarity and assisting future investigations. ASV were estimated using full-16S gene sequencing on the Pacific Bioscience platform, whereas metagenome-assembled-genomes (MAGs) were obtained using shotgun sequencing on the Illumina NovaSeq platform. Furthermore, the entire 16S gene sequence was divided into its well-known hypervariable regions in order to compare how those regions affect the results. The evaluation of the influence of such strategies in the community description revealed a complex picture, which is discussed in this paper.