Data_Sheet_1_Comparative Genomics of Lactiplantibacillus plantarum: Insights Into Probiotic Markers in Strains Isolated From the Human Gastrointestinal Tract and Fermented Foods.docx

Lactiplantibacillus (Lpb.) plantarum is a versatile species commonly found in a wide variety of ecological niches including dairy products and vegetables, while it may also occur as a natural inhabitant of the human gastrointestinal tract. Although Lpb. plantarum strains have been suggested to exert beneficial properties on their host, the precise mechanisms underlying these microbe–host interactions are still obscure. In this context, the genome-scale in silico analysis of putative probiotic bacteria represents a bottom–up approach to identify probiotic biomarkers, predict desirable functional properties, and identify potentially detrimental antibiotic resistance genes. In this study, we characterized the bacterial genomes of three Lpb. plantarum strains isolated from three distinct environments [strain IMC513 (from the human GIT), C904 (from table olives), and LT52 (from raw-milk cheese)]. A whole-genome sequencing was performed combining Illumina short reads with Oxford Nanopore long reads. The phylogenomic analyses suggested the highest relatedness between IMC513 and C904 strains which were both clade 4 strains, with LT52 positioned within clade 5 within the Lpb. plantarum species. The comparative genome analysis performed across several Lpb. plantarum representatives highlighted the genes involved in the key metabolic pathways as well as those encoding potential probiotic features in these new isolates. In particular, our strains varied significantly in genes encoding exopolysaccharide biosynthesis and in contrast to strains IMC513 and C904, the LT52 strain does not encode a Mannose-binding adhesion protein. The LT52 strain is also deficient in genes encoding complete pentose phosphate and the Embden–Meyerhof pathways. Finally, analyses using the CARD and ResFinder databases revealed that none of the strains encode known antibiotic resistance loci. Ultimately, the results provide better insights into the probiotic potential and safety of these three strains and indicate avenues for further mechanistic studies using these isolates.

乳酸植物杆菌（Lpb. plantarum）是一种适应性广泛的菌种，广泛分布于多种生态位中，包括乳制品和蔬菜，同时它也可能是人类胃肠道中的自然栖息者。尽管有研究表明，Lpb. plantarum 菌株对其宿主具有有益的特性，但这些微生物与宿主之间相互作用的确切机制仍然扑朔迷离。在此背景下，对假定的益生菌进行基因组规模的虚拟分析，是一种自下而上的方法，旨在识别益生菌生物标志物，预测理想的功能特性，以及鉴定潜在的具有抗生素耐药性的基因。在本研究中，我们鉴定了从三个不同环境中分离的三种 Lpb. plantarum 菌株的细菌基因组[菌株 IMC513（来自人类胃肠道），C904（来自橄榄），和 LT52（来自生乳奶酪）]。通过结合 Illumina 短读长和 Oxford Nanopore 长读长进行全基因组测序。系统发育基因组分析表明，IMC513 和 C904 菌株之间具有最高的相关性，它们都是第四类菌株，而 LT52 菌株位于 Lpb. plantarum 物种中的第五类。在多个 Lpb. plantarum 代表菌株之间进行的比较基因组分析突出了参与关键代谢途径的基因以及编码这些新分离菌株中潜在益生菌特征的基因。特别是，我们的菌株在编码外多糖生物合成的基因上存在显著差异，与菌株 IMC513 和 C904 不同，LT52 菌株不编码甘露糖结合的粘附蛋白。LT52 菌株在编码完整的戊糖磷酸途径和艾姆登-迈耶霍夫途径的基因上也存在缺陷。最后，使用 CARD 和 ResFinder 数据库的分析显示，这些菌株中均未编码已知的抗生素耐药性位点。最终，这些结果为这些三种菌株的益生菌潜力和安全性提供了更深入的见解，并为使用这些分离菌株进行进一步机制研究指明了方向。