Microbiome Sequencing

Medicine  The relationship between composition and function of microflora and disease (such as diabetes, obesity, hypertensiony; microbiall medicine (intestinal tract, stomach, all cavities)

Agriculture  Different microflora structures will affect plant growth,plantpathogenic bacteria, microbial control (soill, root system, endomycorrhiza)

Animal Husbandry The difference in microorganism species and function (rumen,intestinal tract) under different nutrition condition or immunity levels

Environmental Treatment  Micro-ecological changes (waste water, sludge) during environmental treatment

lndustry  Microflora ad function changes(distillers' grains, yogurt, cultured microflora) during fermentation

Biollogical Energy  Microorganism composition and function (activated sludge, marine microorganism) in renewable biological resources

Targeted vs. Comprehensive Analysis: The 16S (for bacteria) and 18S (for eukaryotes) rRNA gene sequencing, along with ITS (Internal Transcribed Spacer) sequencing, are targeted approaches that focus on specific regions of the genome to identify and classify microorganisms. In contrast, Shotgun Metagenomics Sequencing provides a comprehensive analysis, sequencing all the DNA present in a sample, which allows for the identification of bacteria, viruses, fungi, and other microorganisms without prior knowledge of their presence.

Resolution and Diversity: 16S 18S ITS sequencing can accurately classify microorganisms at the genus or species level, depending on the microbial community’s complexity and the targeted region’s variability. Shotgun Metagenomics Sequencing, however, can potentially offer higher resolution down to the strain level and uncover a broader diversity of microorganisms, including those not detectable by targeted methods.

Functional Insights: While 16S, 18S, and ITS sequencing are excellent for identifying which microorganisms are present, Shotgun Metagenomics Sequencing goes a step further by providing insights into the functional potential of the microbial community. This means it can reveal what genes are present and infer the metabolic pathways and resistance genes, offering a deeper understanding of microbial functions and interactions.

Data Complexity and Analysis: Shotgun Sequencing Metagenomics generates a vast amount of data, covering the entire genomic content of a sample, which requires more substantial computational resources and more complex bioinformatics analyses compared to the targeted sequencing of 16S, 18S, and ITS. This means that while Shotgun Metagenomics offers a more detailed view, it also demands more in terms of data handling and interpretation.

Application-Specific Suitability: The choice between these methods depends on the study’s goals. For studies focused on microbial identification and diversity, 16S, 18S, and ITS sequencing might suffice. However, for comprehensive analysis that requires understanding the functional capabilities of a microbial community, Shotgun Sequencing Metagenomics is more appropriate.