Department of Genetics and Genomic Sciences, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai. New York, NY, USA.
Department of Biological Sciences, CUNY Hunter College, New York, NY, USA.
Gut Microbes. 2022 Jan-Dec;14(1):2107866. doi: 10.1080/19490976.2022.2107866.
We present an overview of recent experimental and computational advances in technology used to characterize the microbiome, with a focus on how these developments improve our understanding of inflammatory bowel disease (IBD). Specifically, we present studies that make use of flow cytometry and metabolomics assays to provide a functional characterization of microbial communities. We also describe computational methods for strain-level resolution, temporal series, mycobiome and virome data, co-occurrence networks, and compositional data analysis. In addition, we review novel techniques to therapeutically manipulate the microbiome in IBD. We discuss the benefits and drawbacks of these technologies to increase awareness of specific biases, and to facilitate a more rigorous interpretation of results and their potential clinical application. Finally, we present future lines of research to better characterize the relation between microbial communities and IBD pathogenesis and progression.
我们介绍了用于描述微生物组的技术的最新实验和计算进展，重点介绍了这些进展如何增进我们对炎症性肠病 (IBD) 的理解。具体来说，我们介绍了利用流式细胞术和代谢组学分析来提供微生物群落功能特征的研究。我们还描述了用于菌株水平分辨率、时间序列、真菌组和病毒组数据、共生网络和组成数据分析的计算方法。此外，我们回顾了在 IBD 中治疗性操纵微生物组的新技术。我们讨论了这些技术的优缺点，以提高对特定偏差的认识，并促进对结果及其潜在临床应用的更严格解释。最后，我们提出了未来的研究方向，以更好地描述微生物群落与 IBD 发病机制和进展之间的关系。
