Periodic Reporting for period 4 - Lacto-Be (Advancing Lactobacillus’ beneficial potential)
Reporting period: 2024-09-01 to 2025-02-28
Lacto-Be aimed to address a fundamental question in microbiology: how do beneficial bacteria, particularly lactobacilli, evolve and adapt to the diverse environments they inhabit? Despite their crucial roles in human health, food fermentation, and ecosystems, the evolutionary dynamics and functional adaptations of these microbes remained largely unexplored. This knowledge gap is significant, as lactobacilli help maintain a healthy human microbiome, especially in the vaginal environment, enhance food safety and nutrition of fermented foods, and support plant and insect ecosystems. Understanding how these bacteria adapt and function can lead to innovations in health, nutrition, and sustainable agriculture.
To tackle this challenge, Lacto-Be integrated and developed cutting-edge genomics, microbiology, and citizen science to study lactobacilli across three habitats: the female reproductive tract, fermented foods, and the natural environment.
All three research lines used citizen science to study lactobacilli. For the female reproductive tract, samples from over 3,300 Belgian women revealed a healthy core of co-occurring taxa and were influenced by environmental factors. In vegetable fermentation, systematic dominance of lactic acid bacteria species was shown in this habitat, with variations depending on internal and external factors. Sampling of pollinators and plants revealed the importance of Apilactobacillus and related taxa in insects. These efforts led to the creation of a unique biobank of over 680 lactobacilli strains, a valuable resource for future research and the discovery of novel species from all three habitats.
A key technological achievement was the development of SCARAP, a tool to construct a comprehensive pangenome enabling the identification of key adaptive traits in each habitat. In the vagina, lactobacilli showed adaptations including acid tolerance, glycogen metabolism, and cross-feeding. In fermented foods, local strains dominated due to better pH tolerance, carbohydrate metabolism, osmotolerance, and carotenoid biosynthesis. In pollinators and plants, carotenoids were linked to UV protection, while specific sugar preferences supported adaptation.
Lacto-Be further explored the beneficial properties of selected strains, including antipathogenic activity and host-supporting functions. One major discovery was the production unique antimicrobials in vaginal lactobacilli, with patenting in progress.
In conclusion, Lacto-Be significantly advanced our understanding of lactobacilli, from their evolution and ecological roles to their potential in health, food, and biotechnology. It delivered powerful tools, rich datasets, and a unique strain collection that will support future scientific discovery and societal innovation.
To tackle this challenge, Lacto-Be integrated and developed cutting-edge genomics, microbiology, and citizen science to study lactobacilli across three habitats: the female reproductive tract, fermented foods, and the natural environment.
All three research lines used citizen science to study lactobacilli. For the female reproductive tract, samples from over 3,300 Belgian women revealed a healthy core of co-occurring taxa and were influenced by environmental factors. In vegetable fermentation, systematic dominance of lactic acid bacteria species was shown in this habitat, with variations depending on internal and external factors. Sampling of pollinators and plants revealed the importance of Apilactobacillus and related taxa in insects. These efforts led to the creation of a unique biobank of over 680 lactobacilli strains, a valuable resource for future research and the discovery of novel species from all three habitats.
A key technological achievement was the development of SCARAP, a tool to construct a comprehensive pangenome enabling the identification of key adaptive traits in each habitat. In the vagina, lactobacilli showed adaptations including acid tolerance, glycogen metabolism, and cross-feeding. In fermented foods, local strains dominated due to better pH tolerance, carbohydrate metabolism, osmotolerance, and carotenoid biosynthesis. In pollinators and plants, carotenoids were linked to UV protection, while specific sugar preferences supported adaptation.
Lacto-Be further explored the beneficial properties of selected strains, including antipathogenic activity and host-supporting functions. One major discovery was the production unique antimicrobials in vaginal lactobacilli, with patenting in progress.
In conclusion, Lacto-Be significantly advanced our understanding of lactobacilli, from their evolution and ecological roles to their potential in health, food, and biotechnology. It delivered powerful tools, rich datasets, and a unique strain collection that will support future scientific discovery and societal innovation.
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.
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.
The Lacto-Be project has delivered several key breakthroughs that have advanced the field of microbiome research and opened new directions for research and application.
A major achievement the international revision of the classification system for lactobacilli. This widely cited work has reshaped how scientists understand and describe these bacteria, enabling more accurate microbiome research and safer applications in food and health.
Equally impactful was the project’s citizen science approach, highlighting the Isala initiative. Far beyond a sample collection effort, Isala became a global platform for engagement. The involvement of thousands of women led to insights into microbial cooperation and inspired similar initiatives in over a dozen countries. These “Isala sisterhood” initiatives are now using the tools developed by Lacto-Be to explore local microbial diversity and health-promoting properties.
Together, these achievements have pushed the boundaries of what we know about lactobacilli and their potential, and they continue to inspire new research and applications in health, food, and microbiome science.
A major achievement the international revision of the classification system for lactobacilli. This widely cited work has reshaped how scientists understand and describe these bacteria, enabling more accurate microbiome research and safer applications in food and health.
Equally impactful was the project’s citizen science approach, highlighting the Isala initiative. Far beyond a sample collection effort, Isala became a global platform for engagement. The involvement of thousands of women led to insights into microbial cooperation and inspired similar initiatives in over a dozen countries. These “Isala sisterhood” initiatives are now using the tools developed by Lacto-Be to explore local microbial diversity and health-promoting properties.
Together, these achievements have pushed the boundaries of what we know about lactobacilli and their potential, and they continue to inspire new research and applications in health, food, and microbiome science.