Navgire Gauri S, Goel Neha, Sawhney Gifty, Sharma Mohit, Kaushik Prashant, Mohanta Yugal Kishore, Mohanta Tapan Kumar, Al-Harrasi Ahmed
Department of Microbiology, Savitribai Phule Pune University, Pune, Maharastra, 411007, India.
Department of Genetics and Tree Improvement, Forest Research Institute, 248006, Dehradun, India.
Biol Proced Online. 2022 Nov 19;24(1):18. doi: 10.1186/s12575-022-00179-7.
Advances in next-generation sequencing technologies have accelerated the momentum of metagenomic studies, which is increasing yearly. The metagenomics field is one of the versatile applications in microbiology, where any interaction in the environment involving microorganisms can be the topic of study. Due to this versatility, the number of applications of this omics technology reached its horizons. Agriculture is a crucial sector involving crop plants and microorganisms interacting together. Hence, studying these interactions through the lenses of metagenomics would completely disclose a new meaning to crop health and development. The rhizosphere is an essential reservoir of the microbial community for agricultural soil. Hence, we focus on the R&D of metagenomic studies on the rhizosphere of crops such as rice, wheat, legumes, chickpea, and sorghum. These recent developments are impossible without the continuous advancement seen in the next-generation sequencing platforms; thus, a brief introduction and analysis of the available sequencing platforms are presented here to have a clear picture of the workflow. Concluding the topic is the discussion about different pipelines applied to analyze data produced by sequencing techniques and have a significant role in interpreting the outcome of a particular experiment. A plethora of different software and tools are incorporated in the automated pipelines or individually available to perform manual metagenomic analysis. Here we describe 8-10 advanced, efficient pipelines used for analysis that explain their respective workflows to simplify the whole analysis process.
新一代测序技术的进步加速了宏基因组学研究的发展势头，该研究每年都在增加。宏基因组学领域是微生物学中用途广泛的应用之一，环境中任何涉及微生物的相互作用都可以成为研究主题。由于其用途广泛，这种组学技术的应用数量已达到极限。农业是一个关键领域，涉及作物植物和微生物的相互作用。因此，通过宏基因组学的视角研究这些相互作用将为作物健康和发育完全揭示新的意义。根际是农业土壤微生物群落的重要储存库。因此，我们专注于对水稻、小麦、豆类、鹰嘴豆和高粱等作物根际的宏基因组学研究的研发。如果没有下一代测序平台的不断进步，这些最新进展是不可能实现的；因此，这里对可用的测序平台进行简要介绍和分析，以便清楚了解工作流程。最后讨论的是应用于分析测序技术产生的数据的不同流程，这些流程在解释特定实验的结果方面发挥着重要作用。大量不同的软件和工具被纳入自动化流程或单独提供以进行手动宏基因组分析。在这里，我们描述8 - 10种用于分析的先进、高效流程，并解释它们各自的工作流程，以简化整个分析过程。
