哥伦比亚大学医学中心Harris H. Wang小组经过不懈努力对肠道微生物生物地理学进行了空间宏基因组表征。 相关论文于2019年8月发表在《自然—生物技术》上。

该研究组通过测序（MaPS-seq）进行宏基因组图采样，MaPS-seq是一种独立于培养的方法，用于以微米级分辨率表征微生物组的空间组织。完整的微生物样品被固定在凝胶基质中，冷冻破碎成颗粒。邻近的微生物类群的粒子通过基于液滴的封装、条形码16S rRNA扩增和深度测序。对小鼠肠道三个区域的分析揭示了不同种类的微生物分布，在特定分类群之间有正相关和负相关。研究团队鉴定了所有肠室中类杆菌分类群之间的强相关性，并表明细菌的系统发育聚集局部区域与饮食扰动有关。空间宏基因组学可用于研究复杂生境中的微生物生物地理学。

据了解，空间结构对自然生态系统的维护很重要。包括肠道微生物的许多微生物群落,都具有复杂的空间组构。绘制细菌的生物地理学图可以揭示群落功能背后的相互作用,但是现有的方法不足以描述数百种自然界中已发现的微生物。

附：英文原文

Title: Spatial metagenomic characterization of microbial biogeography in the gut

Author: Ravi U. Sheth, Mingqiang Li, Weiqian Jiang, Peter A. Sims, Kam W. Leong, Harris H. Wang

Issue&Volume: Volume 37 Issue 8

Abstract: Spatial structuring is important for the maintenance of natural ecological systems. Many microbial communities, including the gut microbiome, display intricate spatial organization. Mapping the biogeography of bacteria can shed light on interactions that underlie community functions, but existing methods cannot accommodate the hundreds of species that are found in natural microbiomes. Here we describe metagenomic plot sampling by sequencing (MaPS-seq), a culture-independent method to characterize the spatial organization of a microbiome at micrometer-scale resolution. Intact microbiome samples are immobilized in a gel matrix and cryofractured into particles. Neighboring microbial taxa in the particles are then identified by droplet-based encapsulation, barcoded 16S rRNA amplification and deep sequencing. Analysis of three regions of the mouse intestine revealed heterogeneous microbial distributions with positive and negative co-associations between specific taxa. We identified robust associations between Bacteroidales taxa in all gut compartments and showed that phylogenetically clustered local regions of bacteria were associated with a dietary perturbation. Spatial metagenomics could be used to study microbial biogeography in complex habitats.

DOI: 10.1038/s41587-019-0183-2

Source: https://www.nature.com/articles/s41587-019-0183-2