Department of Molecular Virology and Microbiology, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA.
Anim Health Res Rev. 2012 Jun;13(1):40-53. doi: 10.1017/S1466252312000126.
Analysis of microbial communities using high throughput sequencing methods began in the mid 2000s permitting the production of 1000s to 10,000s of sequence reads per sample and megabases of data per sequence run. This then unprecedented depth of sequencing allowed, for the first time, the discovery of the 'rare biosphere' in environmental samples. The technology was quickly applied to studies in several human subjects. Perhaps these early studies served as a reminder that though the microbes that inhabit mammals are known to outnumber host cells by an order of magnitude or more, most of these are unknown members of our second genome, or microbiome (as coined by Joshua Lederberg), because of our inability to culture them. High throughput methods for microbial 16S ribosomal RNA gene and whole genome shotgun (WGS) sequencing have now begun to reveal the composition and identity of archaeal, bacterial and viral communities at many sites, in and on the human body. Surveys of the microbiota of food production animals have been published in the past few years and future studies should benefit from protocols and tools developed from large-scale human microbiome studies. Nevertheless, production animal-related resources, such as improved host genome assemblies and increased numbers and diversity of host-specific microbial reference genome sequences, will be needed to permit meaningful and robust analysis of 16S rDNA and WGS sequence data.
使用高通量测序方法分析微生物群落始于 21 世纪中期，每个样本可产生数千到数万条序列读取，每个序列运行可产生兆碱基的数据。这种前所未有的测序深度首次允许在环境样本中发现“稀有生物圈”。该技术很快被应用于多项人类研究中。也许这些早期的研究提醒我们，尽管栖息在哺乳动物体内的微生物数量是宿主细胞的数量级或更多，但由于我们无法培养它们，其中大多数都是我们第二基因组（或微生物组，由 Joshua Lederberg 创造）的未知成员。微生物 16S 核糖体 RNA 基因和全基因组鸟枪法（WGS）测序的高通量方法现在已经开始揭示人体内外许多部位的古细菌、细菌和病毒群落的组成和特征。在过去的几年中，已经发表了关于食品生产动物微生物群的调查，未来的研究应该受益于从大规模人类微生物组研究中开发的协议和工具。然而，为了允许对 16S rDNA 和 WGS 序列数据进行有意义和稳健的分析，还需要与生产动物相关的资源，例如改进的宿主基因组组装，以及更多和更多样化的宿主特异性微生物参考基因组序列。
