Comprehensive analysis of 84 Faecalibacterium prausnitzii strains uncovers their genetic diversity, functional characteristics, and potential risks.
Comprehensive analysis of 84 Faecalibacterium prausnitzii strains uncovers their genetic diversity, functional characteristics, and potential risks.
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DOI：
10.3389/fcimb.2022.919701
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发表时间：
2022
影响因子：
5.7
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中科院分区：
文献类型：
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prausnitzii粪杆菌是一种有益的人体肠道微生物，是下一代益生菌的候选菌。随着益生菌现在被用于临床治疗，需要考虑到它们的安全性和副作用。因此，全面了解不同prausnitzii菌株的遗传多样性、功能特征和潜在风险是十分必要的。在本研究中，我们收集了84f的遗传信息。对Prausnitzii菌株进行多视角的泛基因组分析。基于单拷贝基因、16S rRNA序列和泛基因组组成，对不同菌株进行系统发育分析，发现菌株间存在遗传多样性。在泛基因组蛋白中，我们发现辅助簇对prausnitzii菌株主要遗传功能的贡献大于核心簇和特定簇。F. prausnitzii的功能注释表明，只有极少数蛋白质与人类疾病有关，不存在编码有害产物的次级代谢基因簇。同时，在prausnitzii中检测到完整的脂肪酸代谢。此外，我们检测了抗生素耐药基因、毒力因子和致病基因等有害元素，并提出了益生菌潜在风险指数（PPRI）和益生菌潜在风险评分（PPRS），将84株菌株分为低、中、高风险组。最终筛选出15株低危菌株，优先进行临床应用。毫无疑问，我们的研究结果提供了对F. prausnitzii的全面认识和洞察，PPRI和PPRS可以用于总体评价益生菌的潜在风险，并指导益生菌在临床应用中的应用。
Faecalibacterium prausnitzii is a beneficial human gut microbe and a candidate for next-generation probiotics. With probiotics now being used in clinical treatments, concerns about their safety and side effects need to be considered. Therefore, it is essential to obtain a comprehensive understanding of the genetic diversity, functional characteristics, and potential risks of different F. prausnitzii strains. In this study, we collected the genetic information of 84 F . prausnitzii strains to conduct a pan-genome analysis with multiple perspectives. Based on single-copy genes and the sequences of 16S rRNA and the compositions of the pan-genome, different phylogenetic analyses of F. prausnitzii strains were performed, which showed the genetic diversity among them. Among the proteins of the pan-genome, we found that the accessory clusters made a greater contribution to the primary genetic functions of F. prausnitzii strains than the core and specific clusters. The functional annotations of F. prausnitzii showed that only a very small number of proteins were related to human diseases and there were no secondary metabolic gene clusters encoding harmful products. At the same time, complete fatty acid metabolism was detected in F. prausnitzii. In addition, we detected harmful elements, including antibiotic resistance genes, virulence factors, and pathogenic genes, and proposed the probiotic potential risk index (PPRI) and probiotic potential risk score (PPRS) to classify these 84 strains into low-, medium-, and high-risk groups. Finally, 15 strains were identified as low-risk strains and prioritized for clinical application. Undoubtedly, our results provide a comprehensive understanding and insight into F. prausnitzii, and PPRI and PPRS can be applied to evaluate the potential risks of probiotics in general and to guide the application of probiotics in clinical application.