（1）The identification of processes activated by specific microbes during microbiota colonization of plant roots has been hampered by technical constraints in metatranscriptomics.在微生物组定殖植物根系的过程中，鉴定特定微生物所激活的生理过程一直受到宏转录组学技术限制的阻碍。

（2）These include lack of reference genomes, high representation of host or microbial rRNA sequences in datasets, or difficulty to experimentally validate gene functions.这些限制包括：缺乏参考基因组、数据集中宿主或微生物rRNA序列占比过高，以及难以通过实验验证基因功能。

Genome-resolved metatranscriptomics reveals conserved root colonization determinants in a synthetic microbiota

摘要

（1）The identification of processes activated by specific microbes during microbiota colonization of plant roots has been hampered by technical constraints in metatranscriptomics.在微生物组定殖植物根系的过程中，鉴定特定微生物所激活的生理过程一直受到宏转录组学技术限制的阻碍。

（2）These include lack of reference genomes, high representation of host or microbial rRNA sequences in datasets, or difficulty to experimentally validate gene functions.这些限制包括：缺乏参考基因组、数据集中宿主或微生物rRNA序列占比过高，以及难以通过实验验证基因功能。

（3）Here, we recolonized germ-free Arabidopsis thaliana with a synthetic, yet representative root microbiota comprising 106 genome-sequenced bacterial and fungal isolates.在此，我们使用一个包含106株已完成基因组测序的细菌和真菌分离株的合成型（但仍具代表性）根系微生物组，对无菌拟南芥进行了再定殖实验。

（4）We used multi-kingdom rRNA depletion, deep RNA-sequencing and read mapping against reference microbial genomes to analyse the in planta metatranscriptome of abundant colonizers.我们采用跨界的rRNA去除技术、深度RNA测序以及将序列比对到微生物参考基因组的方法，分析了高丰度定殖菌在植物体内的宏转录组。

（5）We identified over 3,000 microbial genes that were differentially regulated at the soil-root interface.我们鉴定出超过3000个在土壤-根系界面差异调控的微生物基因。

（6）Translation and energy production processes were consistently activated in planta, and their induction correlated with bacterial strains‘ abundance in roots.翻译和能量生产过程在植物体内被一致激活，并且这些过程的诱导与细菌菌株在根系中的丰度相关。

（7）Finally, we used targeted mutagenesis to show that several genes consistently induced by multiple bacteria are required for root colonization in one of the abundant bacterial strains (a genetically tractable Rhodanobacter).最后，我们通过靶向诱变证明，在一种丰度较高的细菌菌株（一株遗传上易操作的罗丹诺杆菌属细菌）中，多个被多种细菌一致诱导的基因是其根系定殖所必需的。

（8）Our results indicate that microbiota members activate strain-specific processes but also common gene sets to colonize plant roots.我们的研究结果表明，微生物组成员在定殖植物根系时，既会激活菌株特异性的生理过程，也会激活共有的基因集。

（9）Result

（10） High-resolution read mapping against host and SynCom reference genomes将RNA-seq测序得到的读段（reads）比对到拟南芥基因组和106株微生物的参考基因组上，以区分哪些RNA来自植物、哪些来自微生物

（11） RNA-Seq read mapping reveals SynCom structure at the root interface 通过比对结果，确定在根系界面（根表+根内）哪些微生物成功定殖、相对丰度如何

Figure 1a 展示的是84株细菌的全基因组系统发育树以及它们在基质和根系样本中的转录组检测概况。

（12） Extensive transcriptional reprogramming during root colonization at a strain-level resolution 在单个菌株的精度上，分析微生物在定殖根系时发生了哪些基因表达变化（与纯培养相比，哪些基因上调/下调）

（13） A core transcriptional response is activated by multiple strains in roots 发现不同菌株在定殖根系时，有一组共同的基因被激活（可能是定殖所需的核心功能，如营养代谢、胁迫响应等）

表1 | 根系 vs 基质中最显著上调的50个细菌基因

（14） Activation of multiple biological processes associate with bacterial abundance in roots 某些代谢通路（如能量生产、翻译等）的激活程度与细菌在根系的定殖丰度呈正相关——定殖越多的菌，这些通路越活跃

（15） Genes consistently induced by multiple bacteria in roots promote host colonization通过基因敲除实验证明，那些在多个菌株中都被诱导表达的基因，确实是细菌成功定殖根系所必需的

These include lack of reference genomes, high representation of host or microbial rRNA sequences in datasets, or difficulty to experimentally validate gene functions.这些限制包括：缺乏参考基因组、数据集中宿主或微生物rRNA序列占比过高，以及难以通过实验验证基因功能。