Kauter Anne, Epping Lennard, Semmler Torsten, Antao Esther-Maria, Kannapin Dania, Stoeckle Sabita D, Gehlen Heidrun, Lübke-Becker Antina, Günther Sebastian, Wieler Lothar H, Walther Birgit
Advanced Light and Electron Microscopy (ZBS-4), Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany.
Microbial Genomics (NG1), Robert Koch Institute, Berlin, Germany.
Anim Microbiome. 2019 Nov 13;1(1):14. doi: 10.1186/s42523-019-0013-3.
Understanding the complex interactions of microbial communities including bacteria, archaea, parasites, viruses and fungi of the gastrointestinal tract (GIT) associated with states of either health or disease is still an expanding research field in both, human and veterinary medicine. GIT disorders and their consequences are among the most important diseases of domesticated Equidae, but current gaps of knowledge hinder adequate progress with respect to disease prevention and microbiome-based interventions. Current literature on enteral microbiomes mirrors a vast data and knowledge imbalance, with only few studies tackling archaea, viruses and eukaryotes compared with those addressing the bacterial components.Until recently, culture-dependent methods were used for the identification and description of compositional changes of enteral microorganisms, limiting the outcome to cultivatable bacteria only. Today, next generation sequencing technologies provide access to the entirety of genes (microbiome) associated with the microorganisms of the equine GIT including the mass of uncultured microbiota, or "microbial dark matter".This review illustrates methods commonly used for enteral microbiome analysis in horses and summarizes key findings reached for bacteria, viruses and fungi so far. Moreover, reasonable possibilities to combine different explorative techniques are described. As a future perspective, knowledge expansion concerning beneficial compositions of microorganisms within the equine GIT creates novel possibilities for early disorder diagnostics as well as innovative therapeutic approaches. In addition, analysis of shotgun metagenomic data enables tracking of certain microorganisms beyond species barriers: transmission events of bacteria including pathogens and opportunists harboring antibiotic resistance factors between different horses but also between humans and horses will reach new levels of depth concerning strain-level distinctions.
了解胃肠道（GIT）中包括细菌、古菌、寄生虫、病毒和真菌在内的微生物群落与健康或疾病状态之间的复杂相互作用，在人类医学和兽医学领域仍是一个不断拓展的研究领域。胃肠道疾病及其后果是家养马科动物最重要的疾病之一，但目前的知识空白阻碍了在疾病预防和基于微生物组的干预方面取得足够进展。目前关于肠道微生物组的文献反映出巨大的数据和知识失衡，与针对细菌成分的研究相比，只有少数研究涉及古菌、病毒和真核生物。直到最近，依赖培养的方法仍被用于鉴定和描述肠道微生物的组成变化，其结果仅限于可培养的细菌。如今，新一代测序技术使人们能够获取与马胃肠道微生物相关的全部基因（微生物组），包括大量未培养的微生物群，即“微生物暗物质”。本综述阐述了马肠道微生物组分析常用的方法，并总结了目前在细菌、病毒和真菌方面取得的主要研究成果。此外，还描述了结合不同探索技术的合理可能性。从未来前景来看，关于马胃肠道内有益微生物组成的知识扩展为早期疾病诊断和创新治疗方法创造了新的可能性。此外，鸟枪法宏基因组数据分析能够追踪跨越物种屏障的某些微生物：包括携带抗生素抗性因子的病原体和机会致病菌在内的细菌在不同马匹之间以及人与马之间的传播事件，在菌株水平区分方面将达到新的深度。
