A5033724811- Probiotics and Fermented Foods
- Gut microbiota and health
- Genomics and Phylogenetic Studies
- Oral microbiology and periodontitis research
- Microbial Metabolites in Food Biotechnology
- Evolution and Genetic Dynamics
- Microbial Metabolic Engineering and Bioproduction
- Bacterial Genetics and Biotechnology
- Reproductive tract infections research
- Bacteriophages and microbial interactions
- Microbial Community Ecology and Physiology
- Gene Regulatory Network Analysis
- Dermatology and Skin Diseases
- Cancer Genomics and Diagnostics
- Bacterial biofilms and quorum sensing
- Metabolomics and Mass Spectrometry Studies
- Anaerobic Digestion and Biogas Production
- CRISPR and Genetic Engineering
- Viral gastroenteritis research and epidemiology
- Acne and Rosacea Treatments and Effects
- Polyamine Metabolism and Applications
- Neurological diseases and metabolism
- Antimicrobial Peptides and Activities
- Mycorrhizal Fungi and Plant Interactions
- Wastewater Treatment and Nitrogen Removal
European Molecular Biology Laboratory
2023
University of Antwerp
2016-2022
Sichuan Agricultural University
2020
Vrije Universiteit Brussel
2016-2019
KU Leuven
2017
The genus Lactobacillus comprises 261 species (at March 2020) that are extremely diverse at phenotypic, ecological and genotypic levels. This study evaluated the taxonomy of Lactobacillaceae Leuconostocaceae on basis whole genome sequences. Parameters were included core phylogeny, (conserved) pairwise average amino acid identity, clade-specific signature genes, physiological criteria ecology organisms. Based this polyphasic approach, we propose reclassification into 25 genera including...
To improve our understanding of upper respiratory tract (URT) diseases and the underlying microbial pathogenesis, a better characterisation healthy URT microbiome is crucial. In this first large-scale study, we obtained more insight in adults. Hereto, collected paired nasal nasopharyngeal swabs from 100 participants citizen-science project. High throughput 16S rRNA gene V4 amplicon sequencing was performed samples were processed using DADA2 algorithm. This allowed us to identify bacterial...
While specific mutations allow organisms to adapt stressful environments, most changes in an organism's DNA negatively impact fitness. The mutation rate is therefore strictly regulated and often considered a slowly-evolving parameter. In contrast, we demonstrate unexpected flexibility cellular rates as response selective pressure. We show that hypermutation independently evolves when different Escherichia coli cultures high ethanol stress. Furthermore, hypermutator states are transitory...
Tailored skin microbiome modulation approaches with probiotics are highly challenging. Here, we show that lactobacilli underestimated members of the microbiota. We select specific strains nomadic for their functional applicability on and capacity to inhibit growth inflammation by pathobionts. The formulated as microcapsules topical formulations tested in patients mild-to-moderate acne. selected able reduce inflammatory lesions a pilot placebo-controlled study. Daily application 8 weeks is...
The closely related species of the Lactobacillus casei group are extensively studied because their applications in food fermentations and as probiotics. Our results show that many strains this incorrectly classified reclassifying them to most type strain improves functional predictive power taxonomy. In addition, our findings may spark increased interest L. species. We find after reclassification, only 10 genomes remain . These some interesting properties. First, they all appear be catalase...
ABSTRACT Spontaneous vegetable fermentations, with their rich flavors and postulated health benefits, are regaining popularity. However, microbiology is still poorly understood, therefore raising concerns about food safety. In addition, such spontaneous fermentations form interesting cases of man-made microbial ecosystems. Here, samples from 38 carrot juice were collected through a citizen science initiative, in addition to three laboratory fermentations. Culturing showed that...
There are more than 200 published species within the Lactobacillus genus complex (LGC), majority of which have sequenced type strain genomes available. Although genome-based delimitation cutoffs accepted as gold standard by community, these seldom actually checked for new or already species. In addition, availability genome data is revealing inconsistencies in species-level classification many strains. We constructed a de novo taxonomy LGC based on 2,459 publicly available genomes, using 94%...
Abstract Vulvovaginal candidosis (VVC) is a common condition with severe symptoms and high recurrence rates. Probiotic lactobacilli are explored as alternatives to azole treatments. Although the vaginal microbiota generally not depleted in during VVC, studies indicate that functionality antimicrobial activity of impaired. We selected three strains from Lactobacillus genus complex ( L. rhamnosus GG, pentosus KCA1 plantarum WCFS1) based on vitro evaluation formulated them gel for application....
Lactobacillus represents a versatile bacterial genus, which can adapt to wide variety of ecological niches, including human body sites such as the intestinal and urogenital tract. In this study, complete genome sequence vaginal probiotic rhamnosus GR-1 was determined compared other L. strains at genomic phenotypic level. The strain originally isolated from female urethra, assessed with GG feces sample healthy male, LC705 dairy product. A key difference is absence in spaCBA locus required for...
While bacterial vaginosis (BV) is a well-known type of vaginal dysbiosis, aerobic vaginitis (AV) an inflammatory condition that remains understudied and under-recognised. It predisposes women to serious complications including urogenital infections pregnancy problems. Here, we investigated the community in AV explore its possible role pathogenesis. We collected lavage fluid samples (n = 58) classified by wet-mount microscopy as suffering from or BV included asymptomatic reference group...
Summary 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 this body site. Here we show by next-generating sequencing that Lactobacillus taxa -especially those known be dominant in the human vagina- underestimated members microbiota. Specific strains were selected lab formulated viable form oil water-based topical cream....
Comparing the nasal microbiome of healthy individuals and chronic rhinosinusitis (CRS) patients revealed Dolosigranulum pigrum as a species clearly associated with health, although isolates obtained from are scarce. In this study, we explored properties understudied lactic acid bacterium by integrating comparative genomics, habitat mining, cultivation, functional characterization interaction capacities. Mining 10.000 samples Earth Microbiome Project 17 types that is mainly human cavity. D....
A laboratory-scale sequencing batch reactor (SBR) was operated for 450 days to assess aerobic granule formation when treating brewery/bottling plant wastewater by consistent application of a feast/famine regime. The experiment divided into three major periods according the different operational conditions: (I) no pH control and strong fluctuations in organic loading rate (OLR) (1.18 ± 0.25 kgCOD·(m3·day)-1), (II) aeration strategy reduce OLR (1.45 0.65 kgCOD·(m3·day)-1) (III) stable (1.42...
Abstract Multi‐omics analyses are used in microbiome studies to understand molecular changes microbial communities exposed different conditions. However, it is not always clear how much each omics data type contributes our understanding and whether they concordant with other. Here, we map the response of a synthetic community 32 human gut bacteria three non‐antibiotic drugs by using five layers (16S rRNA gene profiling, metagenomics, metatranscriptomics, metaproteomics metabolomics). We find...
Farmers face difficulties in redeeming their investment larger litter sizes since this comes with heterogenicity, lower resilience and risk of higher mortality. Dietary oligosaccharides, given to the sow, proved beneficial for offspring's performance. However, giving oligosaccharides suckling piglet is poorly explored. Therefore, field trial studied effect dietary short-chain fructo-oligosaccharides (scFOS; 1g/day; drenched) supplementation low (LBW, quartile), normal (NBW, two intermediate...
The genus Lactobacillus is known to be extremely diverse and consists of different phylogenetic groups that show a diversity roughly equal the expected typical bacterial genus. One most prominent within this plantarum group, which contains understudied mudanjiangensis species. Before study, only one L. strain, DSM 28402 T , had been described, but without whole-genome analysis. In three strains classified as were isolated from carrot juice fermentations their sequence was determined,...
While an increasing number of beneficial microbiome members is characterized for the human gut and vagina, microbes are underexplored upper respiratory tract (URT). In this study, we demonstrate that taxa from Lactobacillus genus might have a role as keystone species in healthy URT. Several URT-specific isolates were cultured, characterized, further explored their genetic functional properties related to adaptation Catalase genes found identified taxa, which unique feature within mostly...