Lacto-Be investigated how lactobacilli provide benefits across diverse habitats through three integrated research lines: the female reproductive tract, fermented foods, pollinators and phyllosphere. The project combined advanced genomics, microbiology, and large-scale citizen science to uncover the evolutionary, ecological, and functional mechanisms behind their success.
The first research line focused on the female reproductive tract. Despite the challenges of the COVID-19 pandemic, over 3,300 women provided vaginal swabs in the citizen science initiative, Isala (isala.be/en),for microbiome culturomics, and metabolomics analyses. A novel embedding approach revealed a continuum of microbiome types, moving beyond classical community state types. Strong associations were found between microbiome composition and lifestyle and environmental factors.
In the second research line, 16S rRNA amplicon sequencing of over 400 citizen science samples from vegetable fermentations including sauerkraut, carrot juice (Ferme Pekes), and kimchi (Sonmat), showed the dominance of Leuconostoc and other lactic acid bacteria and revealed substrate dependent variation. Additionally, autochthonous strains perform better, possibly due to enhanced pH tolerance, carbohydrate metabolism, osmotolerance, and carotenoid biosynthesis.
The third research line focused on pollinators and the phyllosphere. Samples from bees and plants were collected through citizen science (Sabofleur), identifying Apilactobacillus and related taxa as dominant. These strains exhibited adaptations such as C30 carotenoid production, supporting oxidative stress resistance and UV protection, as well as specific sugar preferences aiding survival in nectar-rich environments.
Across all research lines, Lacto-Be has generated a wealth of exploitable resources, including a biobank of over 680 lactobacilli strains from diverse habitats and a comprehensive pangenome of all sequenced Lactobacillales constructed with SCARAP, a scalable pangenome construction tool. These resources support future applications in probiotic development, antimicrobial compound discovery, and microbial ecology. Various strains were screened for beneficial properties, including antipathogenic activity and host-supporting functions, with patenting in process. Notably, a Limosilactobacillus reuteri strain was identified that overproduces vitamin B2, with potential for nutritional and therapeutic use.
Dissemination and public engagement were also central to the project. The Isala project became a flagship example of inclusive citizen science, empowering women to contribute to microbiome research. Its publication in Nature Microbiology has become highly cited, reflecting its impact. The team delivered numerous lectures for both scientists and laymen and participated in numerous science festivals, public talks, and media outreach events. A major highlight was the release of the documentary “The Wonder Down Under,” which tells the story of the Isala project and the science behind the vaginal microbiome. The film is currently screened at public events, with a trailer online available.
In conclusion, the Lacto-Be project has delivered on its objectives providing new insights into how lactobacilli adapt and function across diverse environments. It produced valuable scientific insights, biological resources, and tools that will drive future innovation in health, food, and microbial ecology. Its strong emphasis on citizen science helped bridge the gap between microbiology and society.
