Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
The Broad Institute, Cambridge, MA, USA.
Nat Microbiol. 2018 Mar;3(3):356-366. doi: 10.1038/s41564-017-0084-4. Epub 2018 Jan 15.
The gut microbiome is intimately related to human health, but it is not yet known which functional activities are driven by specific microorganisms' ecological configurations or transcription. We report a large-scale investigation of 372 human faecal metatranscriptomes and 929 metagenomes from a subset of 308 men in the Health Professionals Follow-Up Study. We identified a metatranscriptomic 'core' universally transcribed over time and across participants, often by different microorganisms. In contrast to the housekeeping functions enriched in this core, a 'variable' metatranscriptome included specialized pathways that were differentially expressed both across participants and among microorganisms. Finally, longitudinal metagenomic profiles allowed ecological interaction network reconstruction, which remained stable over the six-month timespan, as did strain tracking within and between participants. These results provide an initial characterization of human faecal microbial ecology into core, subject-specific, microorganism-specific and temporally variable transcription, and they differentiate metagenomically versus metatranscriptomically informative aspects of the human faecal microbiome.
肠道微生物组与人类健康密切相关，但目前尚不清楚哪些功能活动是由特定微生物的生态结构或转录驱动的。我们报告了对来自健康专业人员随访研究中 308 名男性的一部分的 372 个人类粪便宏转录组和 929 个宏基因组的大规模研究。我们鉴定了一个在时间和参与者之间普遍转录的宏转录组“核心”，通常由不同的微生物转录。与这个核心中富含的管家功能相反，一个“可变”的宏转录组包括专门的途径，这些途径在参与者之间和微生物之间都有差异表达。最后，纵向宏基因组谱允许重建生态相互作用网络，该网络在六个月的时间跨度内保持稳定，参与者内和参与者之间的菌株跟踪也是如此。这些结果初步描述了人类粪便微生物组的核心、个体特异性、微生物特异性和时间变化的转录，并区分了宏基因组学和宏转录组学对人类粪便微生物组的信息方面。
