Segmented filamentous bacteria (SFB) are unique immune modulatory bacteria colonizing the small intestine of a variety of animals in a host-specific manner. SFB exhibit filamentous growth and attach to the host’s intestinal epithelium, offering a physical route of interaction. SFB affect functions of the host immune system, among them IgA production and T-cell maturation. Until now, no human-specific SFB genome has been reported. Here, we report the metagenomic reconstruction of an SFB genome from a human ileostomy sample. Phylogenomic analysis clusters the genome with SFB genomes from mouse, rat and turkey, but the genome is genetically distinct, displaying 65–71% average amino acid identity to the others. By screening human faecal metagenomic datasets, we identified individuals carrying sequences identical to the new SFB genome. We thus conclude that a unique SFB variant exists in humans and foresee a renewed interest in the elucidation of SFB functionality in this environment.

节段丝状细菌 (SFB) 是独特的免疫调节细菌，以宿主特异性方式定植于各种动物的小肠。SFB 表现出丝状生长并附着在宿主的肠上皮上，提供了一种物理相互作用途径。SFB 影响宿主免疫系统的功能，其中包括 IgA 产生和 T 细胞成熟。到目前为止，还没有人类特异性 SFB 基因组的报道。在这里，我们报告了来自人类回肠造口术样本的 SFB 基因组的宏基因组重建。系统基因组分析将基因组与来自小鼠、大鼠和火鸡的 SFB 基因组聚类，但基因组在遗传上是不同的，与其他基因组显示 65-71% 的平均氨基酸同一性。通过筛选人类粪便宏基因组数据集，我们确定了携带与新 SFB 基因组相同的序列的个体。