Functional Screening of Human Small Intestinal Lactobacilli Reveals Strain-Specific Modulation of Epithelial Immune and Hormonal Responses

The human small intestine (SI) microbiome is a dynamic ecosystem that engages in complex interactions with the host, including those mediated by diet, hormones, and immune systems. However, the cultivation and characterization of small intestinal microbial therapeutics have yet to be developed. One reason for their limited progress may be that previous microbes were derived from other environments, including food, stool, and breast milk, rather than directly from their native environment, the human SI. Therefore, we investigated the human SI as a relevant source and vital target for the development of future microbial therapeutics for SI diseases. We isolated 10 unique Lactobacillaceae isolates from six different species from samples spanning the upper gastrointestinal tract of five organ donors. We performed whole-genome sequencing analysis and assessed the viability of isolates after numerous GI-like stresses. Next, we examined the ability of the isolates to stimulate enteric hormone secretion, modulate pro-inflammatory cytokines, and influence the replication of a live, attenuated oral rotavirus vaccine strain. We observed that SI Lactobacillaceae strains can survive GI-related stresses like other commercialized lactobacilli. Certain isolates were able to promote secretion of the hormones secretin and oxytocin from ex-vivo adult tissue and human infant intestinal organoids. In addition, we found strains that were able to modulate TNF secretion from the human monocytoid line THP-1. Finally, we found that L. rhamnosus strain 103 (Lr 103) significantly promoted antiviral IFN-{lambda} secretion via TLR3 by secreted RNA in infant organoids. Lr 103, restricted rotavirus vaccine strain replication in infant organoids. ImportanceThe impact of the microbiome on human health and disease has highlighted the potential of using microorganisms to prevent and treat human disease. The small intestine has been dramatically under sampled in regard to the intestinal microbiome. Here we isolate several novel organisms from the small intestine and focus on new isolates from lactic acid bacteria that are currently used as probiotics. We find that individual isolates have the ability to impact gut hormone secretion and modulate the immune system. Our work demonstrates the human SI as a relevant source of potential microbial therapeutics through the isolation of novel strains and their modulation of host physiology in preclinical models.