The arsenal of genes that microbes express reflect the way in which they sense their environment. We have previously reported that the rumen microbiome composition and its coding capacity are different in animals having distinct feed efficiency states, even when fed an identical diet. Here, we reveal that many microbial populations belonging to the bacteria and archaea domains show divergent proteome production in function of the feed efficiency state. Thus, proteomic data serve as a strong indicator of host feed efficiency state phenotype, overpowering predictions based on genomic and taxonomic information. We highlight protein production of specific phylogenies associated with each of the feed efficiency states. We also find remarkable plasticity of the proteome both in the individual population and at the community level, driven by niche partitioning and competition. These mechanisms result in protein production patterns that exhibit functional redundancy and checkerboard distribution that are tightly linked to the host feed efficiency phenotype. By linking microbial protein production and the ecological mechanisms that act within the microbiome feed efficiency states, our present work reveals a layer of complexity that bears immense importance to the current global challenges of food security and sustainability.

微生物表达的基因库反映了它们感知环境的方式。我们之前曾报道过，即使饲喂相同的饮食，具有不同饲料效率状态的动物的瘤胃微生物组组成及其编码能力也不同。在这里，我们揭示了许多属于细菌和古生菌领域的微生物种群在饲料效率状态的作用下表现出不同的蛋白质组生产。因此，蛋白质组数据作为宿主饲料效率状态表型的强有力指标，压倒了基于基因组和分类信息的预测。我们强调与每种饲料效率状态相关的特定系统发育的蛋白质生产。我们还发现蛋白质组在个体人群和社区水平上都具有显着的可塑性，由细分市场和竞争驱动。这些机制导致蛋白质生产模式表现出与宿主饲料效率表型密切相关的功能冗余和棋盘分布。通过将微生物蛋白质生产和在微生物组饲料效率状态中起作用的生态机制联系起来，我们目前的工作揭示了一层复杂性，这对当前全球粮食安全和可持续性挑战具有极其重要的意义。