Horizontal gene transfer via plasmids plays a pivotal role in microbial evolution. The forces that shape plasmidomes functionality and distribution in natural environments are insufficiently understood. Here, we present a comparative study of plasmidomes across adjacent microbial environments present in different individual rumen microbiomes. Our findings show that the rumen plasmidome displays enormous unknown functional potential currently unannotated in available databases. Nevertheless, this unknown functionality is conserved and shared with published rat gut plasmidome data. Moreover, the rumen plasmidome is highly diverse compared with the microbiome that hosts these plasmids, across both similar and different rumen habitats. Our analysis demonstrates that its structure is shaped more by stochasticity than selection. Nevertheless, the plasmidome is an active partner in its intricate relationship with the host microbiome with both interacting with and responding to their environment.

中文翻译：

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揭示质粒组分布及其与宿主微生物组的相互作用。

通过质粒的水平基因转移在微生物进化中起关键作用。在自然环境中塑造质粒组功能和分布的力量尚不充分了解。在这里，我们提出了跨瘤胃微生物组中存在的相邻微生物环境中的质粒组的比较研究。我们的发现表明，瘤胃质粒组显示出目前尚未在可用数据库中注释的巨大未知功能潜力。然而，这种未知的功能得以保留并与已发表的大鼠肠道质粒组数据共享。而且，瘤胃质粒组与宿主这些质粒的微生物组相比，在相似和不同的瘤胃生境中都具有高度的多样性。我们的分析表明，它的结构更多地是由随机性决定，而不是选择。尽管如此，