Currently described members of Elusimicrobia, a relatively recently defined phylum, are animal-associated and rely on fermentation. However, free-living Elusimicrobia have been detected in sediments, soils and groundwater, raising questions regarding their metabolic capacities and evolutionary relationship to animal-associated species. Here, we analyzed 94 draft-quality, non-redundant genomes, including 30 newly reconstructed genomes, from diverse animal-associated and natural environments. Genomes group into 12 clades, 10 of which previously lacked reference genomes. Groundwater-associated Elusimicrobia are predicted to be capable of heterotrophic or autotrophic lifestyles, reliant on oxygen or nitrate/nitrite-dependent respiration, or a variety of organic compounds and Rhodobacter nitrogen fixation (Rnf) complex-dependent acetogenesis with hydrogen and carbon dioxide as the substrates. Genomes from two clades of groundwater-associated Elusimicrobia often encode a new group of nitrogenase paralogs that co-occur with an extensive suite of radical S-Adenosylmethionine (SAM) proteins. We identified similar genomic loci in genomes of bacteria from the Gracilibacteria phylum and the Myxococcales order and predict that the gene clusters reduce a tetrapyrrole, possibly to form a novel cofactor. The animal-associated Elusimicrobia clades nest phylogenetically within two free-living-associated clades. Thus, we propose an evolutionary trajectory in which some Elusimicrobia adapted to animal-associated lifestyles from free-living species via genome reduction.

目前描述的Elusimicrobia成员是一个相对较新定义的门，与动物相关并且依赖于发酵。然而，在沉积物、土壤和地下水中发现了自由生活的Elusimicrobia，这引发了关于它们的代谢能力和与动物相关物种的进化关系的问题。在这里，我们分析了来自不同动物相关环境和自然环境的 94 个草稿质量的非冗余基因组，包括 30 个新重建的基因组。基因组分为 12 个进化枝，其中 10 个以前缺乏参考基因组。地下水相关的Elusimicrobia预计能够进行异养或自养生活方式，依赖氧气或硝酸盐/亚硝酸盐依赖性呼吸，或以氢气和二氧化碳为底物的多种有机化合物和红杆菌固氮（Rnf）复合物依赖性乙酸生成。来自两个与地下水相关的Elusimicrobia进化枝的基因组通常编码一组新的固氮酶旁系同源物，它们与大量自由基 S-腺苷甲硫氨酸 (SAM) 蛋白共存。我们在来自 Gracilibacteria phylum 和Myxococcales目的细菌基因组中鉴定了相似的基因组位点，并预测基因簇减少了四吡咯，可能形成一种新的辅助因子。动物相关的Elusimicrobia进化枝在系统发育上嵌套在两个自由生活相关的进化枝中。因此，我们提出了一个进化轨迹，其中一些Elusimicrobia通过基因组减少适应了来自自由生活物种的动物相关生活方式。