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Probiotic bacteria harbor effector molecules that confer health benefits, but also adaptation factors that enable them to persist in the gastrointestinal tract of the consumer. To study these adaptation factors, an antibiotic-resistant derivative of the probiotic model organism Lactobacillus plantarum WCFS1 was repeatedly exposed to the mouse digestive tract by three consecutive rounds of (re)feeding of the longest persisting colonies. This exposure to the murine intestine allowed the isolation of intestine-adapted derivatives of the original strain that displayed prolonged digestive tract residence time. Re-sequencing of the genomes of these adapted derivatives revealed single nucleotide polymorphisms as well as a single nucleotide insertion in comparison with the genome of the original WCFS1 strain. Detailed in silico analysis of the identified genomic modifications pinpointed that alterations in the coding regions of genes encoding cell envelope associated functions and energy metabolism appeared to be beneficial for the gastrointestinal tract survival of L. plantarum WCFS1. This work demonstrates the feasibility of experimental evolution for the enhancement of the gastrointestinal residence time of probiotic strains, while full-genome resequencing of the adapted isolates provided clues towards the bacterial functions involved. Enhanced gastrointestinal residence is industrially relevant because it enhances the efficacy of the delivery of viable probiotics in situ.
Worldwide, coral reefs are rapidly declining due to increased sea water temperatures and other environmental stresses (Figure 1). To counter the extinction of major coral reef building species on the island of Bonaire, the non-profit organization Reef Renewal Foundation Bonaire is restoring degraded reef sites using corals that are grown in local nurseries. In these nurseries, corals are propagated on artificial trees using fragmentation. After 6-8 months of growth in the nursery, the corals are transplanted to degraded reef sites around the island. Over the years more than 21.000 corals have been outplanted to reef restoration sites in this way. These corals show high survivorship under natural reef conditions but remain under threat by environmental disturbances, such as increased water temperatures, diseases, and competition with macroalgae. A promising intervention to increase reef persistence and resilience is to manipulate the coral-associated microbiome. At present, the composition of the microbiome in nursery-reared and outplanted corals on Bonaire is unknown. The aim of the current project is to identify and isolate naturally occurring beneficial bacteria that may stimulate the resilience of these corals. Our key objectives are: 1) to assess the presence of functionally beneficial bacteria in corals in nursery and restoration sites on Bonaire using metagenomic screening. 2) to design culture strategies to isolate these functionally beneficial bacteria. In the future, a selection of these beneficial bacteria can be applied to the corals to increase their resilience against environmental disturbances.
