McDonald Julie A K
Centre for Digestive and Gut Health, Imperial College London, London W2 1NY, U.K.
Emerg Top Life Sci. 2017 Nov 30;1(4):373-384. doi: 10.1042/ETLS20170045.
Gut microbiome studies have been gaining popularity over the years, especially with the development of new technologies (e.g. metataxonomics, metagenomics, metatranscriptomics, and metabonomics) that makes it easier for researchers to characterize the composition and functionality of these complex microbial communities. The goal of these studies is to identify a microorganism, group of microbes, or microbial metabolite which correlates with a disease state (e.g. inflammatory bowel disease, colorectal cancer, and obesity). Many of these are cross-sectional studies, where fecal samples from a group of diseased individuals are compared with those from a group of healthy individuals at a single time point. However, there are a wide range of variables that can affect the gut microbiota of humans which make mechanistic studies challenging. Longitudinal studies are required for research to more reliably correlate interventions or disease status to microbiota composition and functionality. However, longitudinal studies in humans and animals are difficult, expensive, and time-consuming. This review will discuss in vitro gut fermentation models and how they can be used to perform longitudinal studies that complement in vivo microbiome studies. Gut fermentation models support the growth of stable, reproducible, and diverse microbial communities in a tightly controlled environment set to mimic the conditions microbes encounter in the gastrointestinal tract. Gut fermentation models will make it easier for researchers to perform mechanistic studies and aid in the development of novel treatments that are both targeted and maintained over time.
近年来，肠道微生物组研究越来越受欢迎，尤其是随着新技术（如宏分类学、宏基因组学、宏转录组学和代谢组学）的发展，这些技术使研究人员更容易描述这些复杂微生物群落的组成和功能。这些研究的目标是确定与疾病状态（如炎症性肠病、结直肠癌和肥胖症）相关的一种微生物、一组微生物或微生物代谢物。其中许多是横断面研究，在单个时间点将一组患病个体的粪便样本与一组健康个体的粪便样本进行比较。然而，有多种变量会影响人类的肠道微生物群，这使得进行机制研究具有挑战性。为了更可靠地将干预措施或疾病状态与微生物群组成和功能联系起来，研究需要进行纵向研究。然而，在人类和动物中进行纵向研究既困难、昂贵又耗时。本综述将讨论体外肠道发酵模型以及如何利用它们进行纵向研究，以补充体内微生物组研究。肠道发酵模型支持在严格控制的环境中生长稳定、可重复且多样的微生物群落，该环境旨在模拟微生物在胃肠道中遇到的条件。肠道发酵模型将使研究人员更容易进行机制研究，并有助于开发随着时间推移既具有针对性又能持续有效的新型治疗方法。
