Chapter 12: Human microbiome analysis.

Humans are essentially sterile during gestation, but during and after birth, every body surface, including the skin, mouth, and gut, becomes host to an enormous variety of microbes, bacterial, archaeal, fungal, and viral. Under normal circumstances, these microbes help us to digest our food and to maintain our immune systems, but dysfunction of the human microbiota has been linked to conditions ranging from inflammatory bowel disease to antibiotic-resistant infections. Modern high-throughput sequencing and bioinformatic tools provide a powerful means of understanding the contribution of the human microbiome to health and its potential as a target for therapeutic interventions. This chapter will first discuss the historical origins of microbiome studies and methods for determining the ecological diversity of a microbial community. Next, it will introduce shotgun sequencing technologies such as metagenomics and metatranscriptomics, the computational challenges and methods associated with these data, and how they enable microbiome analysis. Finally, it will conclude with examples of the functional genomics of the human microbiome and its influences upon health and disease.

在妊娠期，人类本质上是无菌的，但在出生期间和出生之后，包括皮肤、口腔和肠道在内的每个身体表面都会成为种类繁多的微生物（细菌、古菌、真菌和病毒）的宿主。在正常情况下，这些微生物帮助我们消化食物并维持免疫系统，但人类微生物群落的功能失调与从炎症性肠病到抗生素耐药性感染等多种疾病有关。现代高通量测序和生物信息学工具为理解人类微生物组对健康的贡献及其作为治疗干预靶点的潜力提供了有力手段。本章将首先讨论微生物组研究的历史起源以及确定微生物群落生态多样性的方法。接下来，将介绍鸟枪法测序技术，如宏基因组学和宏转录组学，与这些数据相关的计算挑战和方法，以及它们如何实现微生物组分析。最后，将以人类微生物组的功能基因组学及其对健康和疾病的影响的实例作为结尾。