Standard microbial evolutionary ontology is organized according to a nested hierarchy of entities at various levels of biological organization. It typically detects and defines these entities in relation to the most stable aspects of evolutionary processes, by identifying lineages evolving by a process of vertical inheritance from an ancestral entity. However, recent advances in microbiology indicate that such an ontology has important limitations. The various dynamics detected within microbiological systems reveal that a focus on the most stable entities (or features of entities) over time inevitably underestimates the extent and nature of microbial diversity. These dynamics are not the outcome of the process of vertical descent alone. Other processes, often involving causal interactions between entities from distinct levels of biological organisation, or operating at different time scales, are responsible not only for the destabilisation of pre-existing entities, but also for the emergence and stabilisation of novel entities in the microbial world. In this article we consider microbial entities as more or less stabilised functional wholes, and sketch a network-based ontology that can represent a diverse set of processes including, for example, as well as phylogenetic relations, interactions that stabilise or destabilise the interacting entities, spatial relations, ecological connections, and genetic exchanges. We use this pluralistic framework for evaluating (i) the existing ontological assumptions in evolution (e.g. whether currently recognized entities are adequate for understanding the causes of change and stabilisation in the microbial world), and (ii) for identifying hidden ontological kinds, essentially invisible from within a more limited perspective. We propose to recognize additional classes of entities that provide new insights into the structure of the microbial world, namely “processually equivalent” entities, “processually versatile” entities, and “stabilized” entities.

中文翻译：

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迈向过程微生物本体

标准的微生物进化本体是根据生物组织不同层次的实体嵌套层次结构组织的。它通常通过识别通过祖先实体的垂直继承过程进化的谱系，来检测和定义与进化过程最稳定方面相关的这些实体。然而，微生物学的最新进展表明，这种本体具有重要的局限性。在微生物系统中检测到的各种动态表明，随着时间的推移，关注最稳定的实体（或实体的特征）不可避免地低估了微生物多样性的范围和性质。这些动态不仅仅是垂直下降过程的结果。其他流程，通常涉及来自不同生物组织层次的实体之间的因果相互作用，或在不同的时间尺度上运行，不仅导致预先存在的实体不稳定，而且还导致微生物世界中新实体的出现和稳定。在本文中，我们将微生物实体视为或多或少稳定的功能整体，并勾勒出一个基于网络的本体，该本体可以表示一系列不同的过程，包括例如系统发育关系、稳定或破坏相互作用实体的相互作用、空间关系、生态联系和遗传交换。我们使用这个多元框架来评估（i）进化中现有的本体论假设（例如 当前公认的实体是否足以理解微生物世界中变化和稳定的原因），以及（ii）识别隐藏的本体类型，从更有限的角度来看基本上是不可见的。我们建议识别其他类别的实体，它们为微生物世界的结构提供了新的见解，即“过程等效”实体、“过程通用”实体和“稳定”实体。