Biology subjects

Lebeer, S.

Publications and source records attributed to Lebeer, S..

15 recordsLinked to original sources

bioRxiv2026

Exopolysaccharides of Lactobacillus crispatus mediate key balancing interactions with the vaginal mucosa

Lactobacillus crispatus is a dominant member of the healthy vaginal microbiota, yet the mechanisms by which it modulates host immunity remain poorly defined, in part due to the lack of tractable in vivo models. Here, we integrate bacterial genetics, in vitro epithelial systems, human-derived data and proteomic approach (Olink) to uncover a critical role for L. crispatus exopolysaccharides (EPS) in shaping the bacteria-vagina interactions. Comparative genomics identified a conserved EPS biosynthetic locus, with the priming glycosyltransferase gene epsE emerging as a regulatory node, in line with its distinct expression in human vaginal samples. Functional disruption of epsE abrogated L. crispatus EPS production and revealed its role for immune modulation. In human vaginal epithelial monolayers, EPS presence enhanced immune-regulatory (LAP TGF-beta-1) and anti-inflammatory (CST5) responses, whereas its absence triggered elevated pro-inflammatory cytokines (IL-1{beta}, IL-6, IL-8) and matrix metalloproteinase (MMP-10). In a 3D vaginal organotypic model, EPS increased chemokines (CXCL5, CXCL6) linked to immune surveillance and the presence of the markers was validated in vaginal samples of healthy volunteers. These findings position EPS as a key immunomodulatory structure of L. crispatus, advancing our mechanistic understanding of host-commensal interactions and informing microbiome-based strategies to promote vaginal health.

microbiology↗

bioRxiv2025

Vitamin B2 Production by Vaginal Lactobacilli Promotes Symbiosis

The human vaginal microbiome, particularly with lactobacilli as the main inhabitants, plays a key role in maintaining womens health. While lactic acid-mediated pathogen exclusion is well known, broader metabolic functions of vaginal lactobacilli remain underexplored. In this study, we analyzed the vaginal microbiome and metabolome of 258 healthy women from the Isala program. Using targeted metabolomics analysis, we detected a high prevalence with strong interpersonal differences of most B-vitamins, their precursors, and vitamin A in the vaginal microenvironment. Riboflavin (B2) and biotin (B7) showed strong associations with Lactobacillus crispatus and Limosilactobacillus sp. Comparative genomics, phenotypic assays, and in vivo metatranscriptomic data (VIRGO2) collectively confirmed riboflavin biosynthesis by these taxa. Using a riboflavin overproducing Lim. reuteri as a functional model, we showed that microbially derived riboflavin and its pathway intermediates are transported across the vaginal epithelium and modulate host redox balance, cytokine production, and activation of mucosal-associated invariant T (MAIT) cells via induction of MR1 (Major histocompatibility complex, class I-related protein receptor), revealing a potential immunometabolic interface between the vaginal microbiota and its host.

microbiology↗

bioRxiv2025

From Diversity to Dominance: How Salt and CO2 Shape LAB-dominated Ecosystems in Vegetable Fermentations

Research on microbial ecosystems is often challenging due to high diversity of microbial taxa present and the complexity of controlling environmental variables. To address these challenges, fermented foods are simpler and more reproducible model ecosystems, where both community composition and environmental factors can be more precisely controlled and manipulated. In this study, we focused on fermented vegetables which are typically dominated by lactic acid bacteria (LAB). It is not completely understood why lactic acid bacteria (LAB) consistently drive the spontaneous fermentation of vegetables such as cabbage and carrots and how variables such as vegetable substrates, salt addition, and carbon dioxide levels can impact microbial community dynamics. Here, we explored the temporal microbial dynamics in standardized fermentations of 11 different vegetables (including beetroot, bell pepper, cabbage, carrot, cucumber, fennel, green asparagus, leek, parsnip, sunroot, and tomato), revealing a consistent dominance of Leuconostoc and other LAB. Additionally, we investigated the impact of varying salt concentrations, demonstrating that lower salt levels resulted in a delayed appearance of the typically dominant LAB community, while simultaneously revealing a higher abundance of Weissella and various Enterobacterales taxa. These effects imposed by reduced salt concentrations were mitigated by CO2 injection, which reverted the enhanced Enterobacterales levels and increased the overall abundance of Lactobacillales. This study demonstrates how targeted manipulation of environmental parameters, such as salinity and gas composition, can be used to uncover ecological principles governing microbial succession and community assembly in reproducible fermentation-based model ecosystems. ImportanceUnderstanding the ecological principles that shape microbial community assembly is essential for advancing our knowledge of microbial ecosystems. Fermented vegetables, increasingly popular among the general population, provide tractable and reproducible model systems to study microbial succession under controlled environmental conditions. By systematically manipulating variables such as vegetable type, salinity and gas composition, we uncovered the effect of these factors on the microbial dynamics throughout the fermentation. These insights not only contribute to a better understanding of the microbial ecology of these man-made food systems but also suggest directions for novel strategies to optimize fermentation processes for producing faster, safer, and more flavorful foods.

microbiology↗

bioRxiv2025

T cell-microbiome associations captured through T cell receptor convergence analysis

The gut microbiome modulates mucosal immunity, yet how specific bacterial taxa shape the diversity and specificity of T cell receptor (TCR) repertoires remains poorly understood. Existing approaches emphasize single-species effects or broad immune features, without pinpointing which microbes drive specific T cell clonotypes. We present AIRRWAS, a computational framework that integrates TCR-microbiome interaction analysis with targeted in vitro validation to detect genus-level TCR convergence. Applied to three independent cohorts, AIRRWAS identified reproducible associations between convergent TCR clusters and 21 bacterial genera spanning core commensals, probiotics and taxa with immunomodulatory roles. Predicted clonotypes were enriched within the TCR-microbiome interaction network and preferentially activated by genus-matched stimuli, eliciting different functional T cell responses. These findings demonstrate that distinct repertoires can share genus-specific TCR motifs, enabling detection of shared immune signatures. AIRRWAS can map these TCR- microbiome interactions, laying the groundwork for biomarker discovery immune monitoring and the development of microbiome-targeted therapies.

bioinformatics↗

bioRxiv2025

First-void urine and cervicovaginal brushes as sampling devices for vaginal microbiome studies: a proof-of-concept study

This proof-of-concept study compares first-void urine (FVU) and cervicovaginal brushes to vaginal swabs for microbiome profiling in ten women. FVU and brushes provided comparable results in most cases, though storage conditions influenced microbial composition, especially for FVU. Despite limitations in sample size and diversity in participants, findings support these methods potential for self-sampling in womens health research, emphasizing the need for optimized techniques to improve vaginal microbiome profiling.

microbiology↗

bioRxiv2025

The female intimate microbiome space

Despite its importance in health, the female skin microbiome remains understudied. In this study we explored microbial dispersal across intimate body sites, including the vagina, groins, breast and mouth. Microbial similarity correlated with physical proximity, suggesting dispersal influenced by hygiene or sexual activity. Notably, lactobacilli were unexpectedly abundant on breast skin. These findings highlight the need for research into microbiome dynamics and their implications for womens health.

microbiology↗

bioRxiv2024

Bridging immunotypes and enterotypes using a systems immunology approach

Unveiling the systemic effects of disease and health requires an holistic approach that has mainly revolved around well established, directly determinable molecular relationships such as the protein synthesis cascade and epigenetic mechanisms. In this study, involving 394 individuals, we found direct linkage of branches spanning human biological functions often not studied in conjunction, using clinical data, gut microbial abundances, blood immune cell repertoires, blood transcriptomic and blood T cell receptor data. Contrary to current paradigms, we demonstrate that immunotypes and enterotypes are orthogonal, likely fulfilling distinct roles in maintaining homeostasis, only bridged via the blood transcriptome. We also identified two distinct inflammatory profiles: the first driven by interferon signalling and the other characterised by non-viral, NF-kB and IL-6 markers. Lastly, we present compelling data showing strong associations of the Ruminococcaceae and Christensenellaceae bacteria with a healthy immunotype and transcriptomic pattern, highlighting their potential role in immune health. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=194 HEIGHT=200 SRC="FIGDIR/small/625344v1_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@c6b5eorg.highwire.dtl.DTLVardef@15d0c3forg.highwire.dtl.DTLVardef@1cf29eeorg.highwire.dtl.DTLVardef@1c9ff8d_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2024

Lacticaseibacillus rhamnosus GG in a chewable colonizes the nose and facilitates local immune benefits in allergic rhinoconjunctivitis patients

Current treatments fall short in managing allergic rhinitis (AR), emphasizing the need for additional strategies. Beneficial bacteria application shows promise in AR, however most studies focus on oral probiotic administration without monitoring the applied strains in the upper respiratory tract (URT) and their local effects. In this randomized, double-blind, placebo-controlled trial, the probiotic Lacticaseibacillus rhamnosus GG was administered via chewable tablets in seasonal AR patients, randomized to probiotic (n=33) or placebo (n=31) groups. Per-protocol analysis of the URT microbiome, immune markers and AR symptoms was performed. L. rhamnosus GG trafficked from chewables to the oropharynx (77%, p=0.02) and nasopharynx (41%, p<0.0001). Control of self-reported AR symptoms via validated questionnaires under grass pollen exposure was observed after two weeks of probiotic administration and not upon placebo. A local decrease in salivary interleukin-4 (p < 0.05) and nasal IL-13 (p < 0.0001) was observed in the probiotic group. These data indicate that L. rhamnosus GG chewables can target the URT and exert local effects on key allergy cytokines after temporal probiotic engraftment. ImportanceAllergic rhinitis (AR) or hay fever is a highly prevalent condition, impacting nearly half the population in some countries. Supplementation of beneficial bacteria or probiotics has gained increasing attention in AR, and a key innovative way to do this is direct administration to the upper airways. Our study shows for the first time that the model probiotic strain Lacticaseibacillus rhamnosus GG can traffic to the nose in AR patients when administered via a slow-releasing chewable tablet. This trafficking is associated with local benefits in the airways, including on grass pollen-induced nasal symptoms and allergy-related cytokines.

microbiology↗

bioRxiv2024

Standardising a microbiome pipeline for body fluid identification from complex crime scene stains

BackgroundRecent advances in next-generation sequencing have opened up new possibilities for utilizing the human microbiome in various fields, including forensics. Researchers have capitalized on the site-specific microbial communities found in different parts of the body to identify body fluids from biological evidence. Despite promising results, microbiome-based methods have not yet been fully integrated into forensic practice due to the lack of standardized protocols and systematic testing of methods on forensically relevant samples. Our study addresses critical decisions in establishing these protocols, focusing on bioinformatics choices and the use of machine learning to present microbiome results in court for forensically relevant and challenging samples. ResultsWe propose using Operational Taxonomic Units (OTUs) for read data processing and creating heterogeneous training datasets for training a random forest classifier. Our classifier incorporates six forensically relevant classes: saliva, semen, hand skin, penile skin, urine, and vaginal/menstrual fluid. Across these classes, our classifier achieved a high weighted average F1 score of 0.89. Systematic testing on mixed-source samples and underwear revealed reliable detection of at least one component of the mixture and the identification of vaginal fluid from underwear substrates. Additionally, when investigating the sexually shared microbiome (sexome) of heterosexual couples, our classifier shows promising results for the inference of sexual activity. ConclusionIn our study, we recommend the use of a novel random forest classifier trained on a heterogenous dataset for obtaining predictions from samples mimicking forensic evidence. We also highlight the potential of the sexome for assessing the nature of sexual activities in forensic investigations, while delineating areas that warrant further research. Furthermore, we underscore key considerations when presenting machine learning results for classifying mixed-source samples.

bioinformatics↗

bioRxiv2023

Resource-efficient nitrogen removal from source separated urine with partial nitritation/anammox in a membrane aerated biofilm reactor

Source separation and decentralized urine treatment can cut costs in centralized wastewater treatment by diverting 80% of the nitrogen load in sewage. One promising approach for nitrogen removal in this context is partial nitritation/anammox (PN/A), reducing the aeration demand by 67% and organics dosage by 100% compared to nitrification/denitrification. Whilst previous studies with suspended biomass have encountered stability issues during PN/A treatment of urine, a PN/A biofilm was hypothesized to be more resilient. Its use for urine treatment was pioneered here for maximum rates and efficiencies in the energy efficient membrane-aerated biofilm reactor (MABR). Nitrogen removal rates of 1.0 g N L-1 d-1 and removal efficiencies of 80-95% were achieved during a 335-day stable operation at 28{degrees}C on stabilized (pH>11), diluted urine (10%). A balance between N2 and NO3 - formation was observed whilst optimizing the supply of O2 and was rate limiting for the conversion towards N2. Short-term operation on less- and undiluted urine yielded N removal rates of 0.6-0.8 g N L-1 d-1 and removal efficiencies of 93% on 66% urine and 85% on undiluted urine. Metataxonomic analysis and fluorescence in-situ hybridization confirmed the presence of biofilms consisting of nitrifiers (Nitrosomonas, Nitrospira) at the membrane side and anammox bacteria ("Candidatus Brocadia") at the anoxic bulk side. The findings suggest that a biofilm approach to PN/A treatment of urine overcomes stability issues, and a PN/A-MABR has significant potential for resource efficient decentralized treatment. In human long-duration deep-space missions, this gravity-independent technology could produce N2 to compensate artificial atmosphere losses whilst facilitating water recovery from urine. [GRAPHICAL ABSTRACT, COLOR] O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=101 SRC="FIGDIR/small/572732v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@1680b0corg.highwire.dtl.DTLVardef@1ad822dorg.highwire.dtl.DTLVardef@3d5c4borg.highwire.dtl.DTLVardef@764841_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2022

Compost Teas: market survey and microbial analysis

Compost teas (CTs) are fermented watery compost extracts that can be made with a wide variety of organic ingredients. These extracts are applied on plants to promote plant growth and increase protection against pathogens. Several studies have shown that the live micro-organisms present in these teas play an important role in plant protection. Still, our knowledge on the identity and functionality of bacterial communities in CTs remains limited. Moreover, CTs are a heterogeneous group, as various combinations of ingredients, fermentation parameters and application guidelines are possible and little is known on the current practices in commercially available products. Consequently, also the microbial communities in these commercially available CTs are unknown. Here, we surveyed 68 CTs on ingredients, claims and guidelines regarding preparation and application. This revealed that most products were sold in dried form which needed to be rehydrated by the customers. Moreover, kelp, humic acid, sugar and molasses, were common ingredients. Additionally, we investigated the bacterial communities of eight products, covering different ingredients and preparations, using sequencing and culture-based techniques. Bacterial communities were remarkably similar at genus level, with Pseudomonas, Massilia, Comamonas, Chryseobacterium, Brevundimonas and Acinetobacter as most prevalent genera. The genus Pseudomonas was more abundant in CTs that were prepared without aeration. Moreover, differences between liquid and dry products revealed the importance of formulation to secure the viability of the desired microbes. This study has given insight in common practices in CTs on the market, their microbial composition, and highlighted several discrepancies with current literature. ImportanceCompost teas are fermented watery compost extracts which are used in professional and amateur horticulture to promote plant growth and suppress plant diseases. Beneficial microbes present in these extracts are suggested to play an important role in the mode of action. However, little is known on the identity and functionality of the bacteria in compost teas. Moreover, compost teas are a heterogeneous group of products that can be made with numerous combinations of ingredient and fermentation parameters and little is known on current practices in products available on the market. Therefore, we surveyed these practices in 68 commercial products and for a subset of these, we explored their bacterial communities using both culture dependent and independent techniques. This study has unveiled the common practices on the market, their microbial communities, and highlighted several discrepancies between commercial practices and scientific research.

microbiology↗

bioRxiv2022

Live biotherapeutic throat spray for respiratory virus inhibition and interferon pathway induction

Respiratory viruses such as influenza viruses, respiratory syncytial virus (RSV), and coronaviruses initiate infection at the mucosal surfaces of the upper respiratory tract (URT), where the resident respiratory microbiome has an important gatekeeper function. In contrast to gut-targeting administration of beneficial bacteria against respiratory viral disease, topical URT administration of probiotics is currently underexplored, especially for the prevention and/or treatment of viral infections. Here, we report the selection and formulation of a broad-acting throat spray with live lactobacilli which induce interferon regulatory pathways and are able to inhibit respiratory viruses. Rational selection of Lactobacillaceae strains was based on safety, applicability, and potential antiviral and immunostimulatory efficacy in the URT. Three strains, Lacticaseibacillus casei AMBR2, Lacticaseibacillus rhamnosus GG and Lactiplantibacillus plantarum WCFS1 significantly reduced the cytopathogenic effects of RSV, influenza A/H1N1 and B viruses, and HCoV-229E coronavirus in co-culture models with bacteria, virus and host cells. Subsequently, these strains were formulated in a throat spray and human monocytes were employed to confirm the formulation process did not reduce the interferon regulatory pathway-inducing capacity. Administration of the throat spray in healthy volunteers revealed that the lactobacilli were capable of temporary colonization of the throat in a metabolically active form.

microbiology↗

bioRxiv2019

Comparative genome analysis of Lactobacillus mudanjiangensis, an understudied member of the Lactobacillus plantarum group

The genus Lactobacillus is known to be extremely diverse and consists of different phylogenetic groups that show a diversity roughly equal to the expected diversity of a typical bacterial genus. One of the most prominent phylogenetic groups within this genus is the Lactobacillus plantarum group which contains the understudied Lactobacillus mudanjiangensis species. Before this study, only one L. mudanjiangensis strain, DSM 28402T, was described but without whole-genome analysis. In this study, three strains classified as L. mudanjiangensis, were isolated from three different carrot juice fermentations and their whole-genome sequence was determined, together with the genome sequence of the type strain. The genomes of all four strains were compared with publicly available L. plantarum group genome sequences. This analysis showed that L. mudanjiangensis harbored the second largest genome size and gene count of the whole L. plantarum group. In addition, all members of this species showed the presence of a gene coding for a putative cellulose-degrading enzyme. Finally, three of the four L. mudanjiangensis strains studied showed the presence of pili on scanning electron microscopy (SEM) images, which were linked to conjugative gene regions, coded on plasmids in at least two of the strains studied. Author summaryLactobacillus mudanjiangensis is an understudied species within the Lactobacillus plantarum group. Since its first description, no other studies have reported its isolation. Here, we present the first four genome sequences of this species, which include the genome sequence of the type strain and three new L. mudanjiangensis strains isolated from fermented carrot juice. The genomes of all four strains were compared with publicly available L. plantarum group genome sequences. We found that this species harbored the second largest genome size and gene count of the whole L. plantarum group. Furthermore, we present the first scanning electron microscopy (SEM) images of L. mudanjiangensis, which showed the formation of pili in three strains that we linked to genes related to conjugation. Finally, we found the presence of a unique putative cellulose-degrading enzyme, opening the door for different industrial applications of these Lactobacillus strains.

microbiology↗

bioRxiv2019

A genome-based species taxonomy of the Lactobacillus Genus Complex

BackgroundThere are over 200 published species within the Lactobacillus Genus Complex (LGC), the majority of which have sequenced type strain genomes available. Although gold standard, genome-based species delimitation cutoffs are accepted by the community, they are seldom checked against currently available genome data. In addition, there are many species-level misclassification issues within the LGC. We constructed a de novo species taxonomy for the LGC based on 2,459 publicly available, decent-quality genomes and using a 94% core nucleotide identity threshold. We reconciled these de novo species with published species and subspecies names by (i) identifying genomes of type strains in our dataset and (ii) performing comparisons based on 16S rRNA sequence identity against type strains. ResultsWe found that genomes within the LGC could be divided into 239 clusters (de novo species) that were discontinuous and exclusive. Comparison of these de novo species to published species lead to the identification of ten sets of published species that can be merged and one species that can be split. Further, we found at least eight genome clusters that constitute new species. Finally, we were able to accurately classify 98 unclassified genomes and reclassify 74 wrongly classified genomes. ConclusionsThe current state of LGC species taxonomy is largely consistent with genome data, but there are some inconsistencies as well as genome misclassifications. These inconsistencies should be resolved to evolve towards a meaningful taxonomy where species have a consistent size in terms of sequence divergence.

bioinformatics↗

bioRxiv2018

Topical cream with live lactobacilli modulates the skin microbiome and reduce acne symptoms

The skin is home to an important part of our commensal microbiota, despite it being a cool, acidic and desiccated environment. Tailored microbiome modulation approaches with, for example probiotics, are highly challenging for this body site. Here we show by next-generating sequencing that Lactobacillus taxa -especially those known to be dominant in the human vagina- are underestimated members of the skin microbiota. Specific Lactobacillus strains were selected in the lab and formulated in a viable form in an oil in water-based topical cream. Facial application by patients with mild-to-moderate acne symptoms was able to reduce inflammatory lesions and comedone formation. This was associated with a temporary modulation of the skin microbiome, including a reduction in relative abundance of staphylococci and an increase in lactobacilli. Skin microbiome modulation by addition of carefully formulated lactobacilli seems to be new therapeutic option to reduce antibiotic use for common acne symptoms.

clinical trials↗