A Comparative Pan-Genome Perspective of Niche-Adaptable Cell-Surface Protein Phenotypes in Lactobacillus rhamnosus

Lactobacillus rhamnosus is a ubiquitously adaptable Gram-positive bacterium and as a typical commensal can be recovered from various microbe-accessible bodily orifices and cavities. Then again, other isolates are food-borne, with some of these having been long associated with naturally fermented cheeses and yogurts. Additionally, because of perceived health benefits to humans and animals, numerous L. rhamnosus strains have been selected for use as so-called probiotics and are often taken in the form of dietary supplements and functional foods. At the genome level, it is anticipated that certain genetic variances will have provided the niche-related phenotypes that augment the flexible adaptiveness of this species, thus enabling its strains to grow and survive in their respective host environments. For this present study, we considered it functionally informative to examine and catalogue the genotype-phenotype variation existing at the cell surface between different L. rhamnosus strains, with the presumption that this might be relatable to habitat preferences and ecological adaptability. Here, we conducted a pan-genomic study involving 13 genomes from L. rhamnosus isolates with various origins. In using a benchmark strain (gut-adapted L. rhamnosus GG) for our pan-genome comparison, we had focused our efforts on a detailed examination and description of gene products for certain functionally relevant surface-exposed proteins, each of which in effect might also play a part in niche adaptability among the other strains. Perhaps most significantly of the surface protein loci we had analyzed, it would appear that the spaCBA operon (known to encode SpaCBA-called pili having a mucoadhesive phenotype) is a genomic rarity and an uncommon occurrence in L. rhamnosus. However, for any of the so-piliated L. rhamnosus strains, they will likely possess an increased niche-specific fitness, which functionally might presumably be manifested by a protracted transient colonization of the gut mucosa or some similar microhabitat.

鼠李糖乳杆菌（Lactobacillus rhamnosus）是一种广泛适应性极强的革兰氏阳性菌，作为典型共生菌，可从各类微生物可定植的人体腔道与腔体中分离得到。此外，部分分离株为食源性菌株，其中一些长期与天然发酵奶酪、酸奶相关联。鉴于其对人类和动物具有潜在健康益处，众多鼠李糖乳杆菌菌株已被筛选为所谓的益生菌（probiotics），常以膳食补充剂和功能食品的形式被摄入。在基因组层面，据推测特定遗传变异赋予了该物种生态位相关的表型，强化了其灵活适应性，使得各菌株能够在对应的宿主环境中生长存活。针对本研究，我们认为对不同鼠李糖乳杆菌菌株细胞表面存在的基因型-表型变异进行检测与编目具有功能研究价值，并推测该变异或与菌株的生境偏好及生态适应性相关。本研究针对13株不同来源的鼠李糖乳杆菌分离株开展了泛基因组（pan-genomic）研究。本研究以肠道适应性鼠李糖乳杆菌GG（Lactobacillus rhamnosus GG）作为泛基因组比较的参考菌株，重点对若干功能相关的表面暴露蛋白的基因产物进行了详细分析与描述——这类蛋白理论上也可能参与其他菌株的生态位适应过程。在所分析的表面蛋白基因座中，最为关键的发现或许是：spaCBA操纵子（spaCBA operon，已知其编码具有黏膜黏附表型的SpaCBA类菌毛（pili））在鼠李糖乳杆菌中属于基因组罕见事件，出现频率较低。不过，任何携带这类菌毛的鼠李糖乳杆菌菌株，其生态位特异性适合度大概率会有所提升，该功能或可通过延长肠黏膜或类似微生境中的瞬时定植时长等方式得以体现。