The human gastrointestinal tract, skin and mucosal surfaces are inhabited by a complex system of bacteria, viruses, fungi, archaea, protists, and eukaryotic parasites with predominance of bacteria and bacterial viruses (bacteriophages). Collectively these microbes form the microbiota of the microecosystem of humans. Recent advancement in technologies for nucleic acid isolation from various environmental samples, feces and body secretions and advancements in shotgun throughput massive parallel DNA and RNA sequencing along with 16S ribosomal gene sequencing have unraveled the identity of otherwise unknown microbial entities constituting the human microecosystem. The improved transcriptome analysis, technological developments in biochemical analytical methods and availability of complex bioinformatics tools have allowed us to begin to understand the metabolome of the microbiome and the biochemical pathways and potential signal transduction pathways in human cells in response to microbial infections and their products. Also, developments in human whole genome sequencing, targeted gene sequencing of histocompatibility genes and other immune response associated genes by Next Generation Sequencing (NGS) have allowed us to have a better conceptualization of immune responses, and alloimmune responses. These modern technologies have enabled us to dive into the intricate relationship between commensal symbiotic and pathogenic microbiome and immune system. For the most part, the commensal symbiotic microbiota helps to maintain normal immune homeostasis besides providing healthy nutrients, facilitating digestion, and protecting the skin, mucosal and intestinal barriers. However, changes in diets, administration of therapeutic agents like antibiotics, chemotherapeutic agents, immunosuppressants etc. along with certain host factors including human histocompatibility antigens may alter the microbial ecosystem balance by causing changes in microbial constituents, hierarchy of microbial species and even dysbiosis. Such alterations may cause immune dysregulation, breach of barrier protection and lead to immunopathogenesis rather than immune homeostasis. The effects of human microbiome on immunity, health and disease are currently under intense research with cutting edge technologies in molecular biology, biochemistry, and bioinformatics along with tremendous ability to characterize immune response at single cell level. This review will discuss the contemporary status on human microbiome immune system interactions and their potential effects on health, immune homeostasis and allograft transplantation.

人类胃肠道、皮肤和粘膜表面居住着一个由细菌、病毒、真菌、古细菌、原生生物和真核寄生虫组成的复杂系统，其中以细菌和细菌病毒（噬菌体）为主。这些微生物共同构成了人类微生态系统的微生物群。从各种环境样品、粪便和身体分泌物中分离核酸的技术的最新进展，以及鸟枪法大规模平行 DNA 和 RNA 测序以及 16S 核糖体基因测序的进步，揭示了构成人类微生态系统的其他未知微生物实体的身份。改进的转录组分析，生化分析方法的技术发展和复杂生物信息学工具的可用性使我们开始了解微生物组的代谢组以及人体细胞中响应微生物感染及其产物的生化途径和潜在的信号转导途径。此外，通过下一代测序 (NGS) 在人类全基因组测序、组织相容性基因和其他免疫反应相关基因的靶向基因测序方面的发展使我们能够更好地概念化免疫反应和同种免疫反应。这些现代技术使我们能够深入研究共生共生和致病微生物组与免疫系统之间的复杂关系。在大多数情况下，除了提供健康的营养、促进消化、保护皮肤、粘膜和肠道屏障外，共生共生微生物群还有助于维持正常的免疫稳态。然而，饮食的变化、抗生素、化学治疗剂、免疫抑制剂等治疗剂的使用以及某些宿主因素（包括人类组织相容性抗原）可能会通过引起微生物成分、微生物种类等级甚至生态失调的变化来改变微生物生态系统平衡。这种改变可能导致免疫失调，破坏屏障保护并导致免疫发病机制而不是免疫稳态。人类微生物组对免疫、健康和疾病的影响目前正在利用分子生物学、生物化学、和生物信息学以及在单细胞水平上表征免疫反应的巨大能力。本综述将讨论人类微生物组免疫系统相互作用的当代现状及其对健康、免疫稳态和同种异体移植的潜在影响。