Impact of Different Microbial Biostimulants and Salt Stress on the Endophytome of the Edible Part of Lettuce and Tomato Plants

The human gut microbiota plays a critical role in health throughout life. While fruits and vegetables are well-known sources of nutrients and prebiotics, recent studies suggest they may also contribute viable microorganisms to the gut microbiome, particularly when consumed raw. However, the impact of agricultural practices-such as the use of microbial biostimulants or exposure to salt stress-on the composition of the edible plant microbiome remains poorly understood. In this study, we performed a comprehensive metataxonomic analysis of the endophytic microbiome in the edible tissues (leaves or fruits) of lettuce (<i>Lactuca sativa</i>) and tomato (<i>Solanum lycopersicum</i>), cultivated under standard conditions with or without microbial biostimulants and salt stress. Our results show that microbial biostimulants-<i>Priestia megaterium</i> (PGPB) and <i>Rhizophagus irregularis</i> (AMF)-as well as moderate salt stress, significantly reshape the composition and diversity of endophytes in both crops. Notably, the PGPB and NaCl treatments enhanced the abundance of bacterial genera such as <i>Pantoea</i>, <i>Stenotrophomonas</i>, and <i>Massilia</i>, which are associated with plant health and may have probiotic potential. Salt stress also increased alpha-diversity indices and favored the presence of <i>Firmicutes</i> and <i>Bacteroidota</i>, phyla commonly linked to a healthy human gut microbiome. Agronomic inputs used in organic and conventional farming, such as microbial biostimulants or controlled salt exposure, may represent novel strategies to enhance the microbial quality of fresh produce and promote gut microbial diversity through diet.