Biology subjects

Weckx, S.

Publications and source records attributed to Weckx, S..

4 recordsLinked to original sources

bioRxiv2026

Decoding the microbiota of bors: multifunctional potential of a traditional Romanian beverage fermentation

Romanian bors, a traditional fermented wheat bran beverage, is produced through spontaneous fermentation and represents a complex microbial ecosystem. Despite its cultural importance and presumed health benefits, its microbial ecology and functional potential remain poorly characterized. The present study aimed to elucidate the microbial community structure of bors and link it to functional traits relevant to fermentation performance and food functionality by integrating culture-independent sequencing with culture-dependent isolation and functional characterization. A total of 32 bors samples (12 commercial and 20 homemade) were analyzed. Amplicon-based sequencing revealed a microbiome dominated by lactic acid bacteria (LAB), with lactobacilli accounting for the majority of the bacterial communities and Lactobacillus amylolyticus being identified as the most prevalent and abundant species. The yeast communities were mainly composed of fermentative taxa, including Pichia kudriavzevii and Kluyveromyces marxianus. Lactobacillus amylolyticus and P. kudriavzevii were also the most frequently isolated species among bacteria and yeasts, respectively. These results highlighted a strong adaptation of the microbial isolates to starch-rich cereal substrates and underscored the central role of these microorganisms in wheat bran fermentation for bors production. Whereas the sequencing-based analyses showed no significant differences in overall diversity between the commercial and homemade bors samples, the cultivation-based results indicated a higher bacterial richness in the commercial products. Notably, the culture-dependent method captured substantially fewer taxa, highlighting the complementary nature of the two approaches. Of a total of 101 bacterial strains (88 LAB and 13 acetic acid bacteria) isolated, many exhibited rapid growth and strong acidification capacity, reaching pH values below 4.5 within 12 h. A functional screening revealed that 21 % of these strains displayed -amylase activity, 65 % phytase activity, and 50 % {beta}-glucosidase activity, highlighting their capacity to metabolize cereal substrates and enhance the nutrient availability of bors. All strains showed antibacterial activity against at least one indicator bacterium tested, with a universal inhibition of Listeria monocytogenes. Overall, Romanian bors harbored a lactic acid bacteria-dominated core microbiome with a significant functional diversity. These findings underscored its potential as a rich source of functional and technologically important strains for application in starter and protective culture development.

microbiology↗

bioRxiv2025

Unraveling yeast diversity in food fermentation using ITS1-2 amplicon-based metabarcoding

A detailed characterization of the microbial ecosystem involved in the production processes of fermented foods is essential. Although fermented foods are an important part of the human diet and have seen an increasing interest nowadays, some challenges still need to be solved. Specifically, yeast identification through culture-independent methodologies is still limited to the genus level. Unlike for bacterial species identifications, long-read sequencing technologies have barely been used for yeast species identification, and, to the best of the authors knowledge, it has not been validated with mock communities reflecting food fermentation processes yet. Therefore, in the current study, we present an amplicon-based metabarcoding approach targeting the full-length internal transcribed spacer (ITS) region comprising the ITS1, 5.8S rRNA gene, and ITS2 using the PacBio HiFi sequencing platform. This method was validated using mock communities composed of yeast species involved in sourdough, lambic beer, and cocoa fermentation processes. Accurate species-level identification was achieved for most of the species. However, special attention should be given to Saccharomyces-rich niches, as accurate species-level identification for this genus is still challenging. Furthermore, underestimation of the relative abundance of species with short ITS regions, such as Pichia and Brettanomyces, occurred. In addition, the method was successfully applied to describe the yeast diversity present in two sourdough and two lambic beer samples. Overall, the current method provides an unprecedented way of determining the species-level yeast composition of complex ecosystems present in fermented food products. ImportanceTo date, species-level identification of common yeasts present in food fermentation ecosystems has been difficult, if not impossible, when using short-read sequencing methods. However, species-level identification is essential when evaluating and describing the characteristics of fermented food microbiomes. The current study reports on the development and validation of an amplicon-based metabarcoding approach combined with long-read PacBio HiFi sequencing targeting the full ITS region, comprising the ITS1 and ITS2 regions as well as the 5.8S rRNA gene. The described methodology enables species-level identification of the most common yeasts present in food fermentation ecosystems. This new methodology is of importance for all researchers in the field of fermented foods. By extension, researchers in other fields of microbiology can find inspiration in this paper.

microbiology↗

bioRxiv2025

Rising together: Exploring Sourdough Fermentation Diversity through Co-design in the HealthFerm Citizen Science Initiative

Fermented foods are culturally significant and increasingly recognized for their potential health benefits, yet scientific data on household fermentation practices remain limited. We launched a co-designed citizen science (CS) initiative within the HealthFerm project to collect sourdough fermentation data across Europe. Over 1000 participants from 33 countries registered, with 671 samples submitted, enabling large-scale analysis of fermentation practices, motivations, and sourdough characteristics. Participants also completed standardized at-home experiments and sensory evaluations, generating a dataset linking baking habits with physicochemical and sensory profiles. Distinct patterns emerged: professional bakers used older, more frequently refreshed starters and fermented at higher temperatures. Ingredient choices and motivations varied by country, shaped by perceived health benefits. Beyond data collection, this initiative established a microbial biobank and harmonized metadata resource, while offering practical insights into co- design, logistics, and public engagement. The resulting framework provides a transferable model for participatory research in microbiology and food systems science.

scientific communication and education↗

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↗