BACKGROUND The assembly of animal microbiomes is influenced by multiple environmental factors and host genetics, although the relative importance of these factors remains unclear. Bifidobacteria (genus Bifidobacterium, phylum Actinobacteria) are common first colonizers of gut microbiomes in humans and inhabit other mammals, social insects, food, and sewages. In humans, the presence of bifidobacteria in the gut has been correlated with health-promoting benefits. Here, we compared the genome sequences of a subset of the over 400 Bifidobacterium strains publicly available to investigate the adaptation of bifidobacteria diversity. We tested 1) whether bifidobacteria show a phylogenetic signal with their isolation sources (hosts and environments) and 2) whether key traits encoded by the bifidobacteria genomes depend on the host or environment from which they were isolated. We analyzed Bifidobacterium genomes available in the PATRIC and NCBI repositories and identified the hosts and/or environment from which they were isolated. A multilocus phylogenetic analysis was conducted to compare the genetic relatedness the strains harbored by different hosts and environments. Furthermore, we examined differences in genomic traits and genes related to amino acid biosynthesis and degradation of carbohydrates. RESULTS We found that bifidobacteria diversity appears to have evolved with their hosts as strains isolated from the same host were non-randomly associated with their phylogenetic relatedness. Moreover, bifidobacteria isolated from different sources displayed differences in genomic traits such as genome size and accessory gene composition and on particular traits related to amino acid production and degradation of carbohydrates. In contrast, when analyzing diversity within human-derived bifidobacteria, we observed no phylogenetic signal or differences on specific traits (amino acid biosynthesis genes and CAZymes). CONCLUSIONS Overall, our study shows that bifidobacteria diversity is strongly adapted to specific hosts and environments and that several genomic traits were associated with their isolation sources. However, this signal is not observed in human-derived strains alone. Looking into the genomic signatures of bifidobacteria strains in different environments can give insights into how this bacterial group adapts to their environment and what types of traits are important for these adaptations.

中文翻译：

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双歧杆菌与其宿主和环境之间的进化关系。


背景动物微生物组的组装受到多种环境因素和宿主遗传学的影响，尽管这些因素的相对重要性仍不清楚。双歧杆菌（双歧杆菌属，放线菌门）是人类肠道微生物群中常见的第一定殖者，栖息在其他哺乳动物、社会性昆虫、食物和污水中。在人类中，肠道中双歧杆菌的存在与促进健康的益处相关。在这里，我们比较了公开的 400 多种双歧杆菌菌株中一部分的基因组序列，以研究双歧杆菌多样性的适应情况。我们测试了 1) 双歧杆菌是否显示出与其分离来源（宿主和环境）相关的系统发育信号，以及 2) 双歧杆菌基因组编码的关键性状是否取决于其分离的宿主或环境。我们分析了 PATRIC 和 NCBI 存储库中提供的双歧杆菌基因组，并确定了它们分离的宿主和/或环境。进行多位点系统发育分析，以比较不同宿主和环境所携带的菌株的遗传相关性。此外，我们检查了与氨基酸生物合成和碳水化合物降解相关的基因组特征和基因的差异。结果我们发现，双歧杆菌多样性似乎随宿主一起进化，因为从同一宿主分离的菌株与其系统发育相关性非随机相关。此外，从不同来源分离的双歧杆菌在基因组特征（例如基因组大小和辅助基因组成）以及与氨基酸产生和碳水化合物降解相关的特定特征上表现出差异。 相反，在分析人源双歧杆菌的多样性时，我们没有观察到系统发育信号或特定性状（氨基酸生物合成基因和 CAZymes）的差异。结论总的来说，我们的研究表明双歧杆菌多样性强烈适应特定的宿主和环境，并且一些基因组特征与其分离来源相关。然而，仅在人类来源的菌株中并未观察到该信号。研究不同环境中双歧杆菌菌株的基因组特征可以深入了解该细菌群如何适应其环境以及哪些类型的性状对于这些适应很重要。