Biology subjects

Kort, R.

Publications and source records attributed to Kort, R..

6 recordsLinked to original sources

bioRxiv2023

Bacterial vaginosis is associated with increased amylolytic activity

This study investigates the degradation of resistant -1,4-glucan by vaginal bacterial species, with a focus on Gardnerella spp., to elucidate its role in bacterial vaginosis (BV). The ability of Gardnerella vaginalis, Gardnerella swidsinskii, Gardnerella leopoldii, Gardnerella piotii, Lactobacillus iners, and Lactobacillus crispatus was assessed to metabolize an ungelatinized, labeled form of raw amylose, a degradation-resistant -1,4-glucan. The enzymatic activity of these species was evaluated in vitro, and its association with BV was examined in vaginal swabs. Gardnerella vaginalis, G. swidsinskii, and G. leopoldii demonstrated the best ability to degrade resistant -1,4-glucan in vitro. Unlike the cell-bound, S-layer-associated glycogen-degrading activity in L. crispatus, this -glucosidase activity in Gardnerella was also extracellular, but not cell-bound and not repressed by glucose. Vaginal swabs showing high rates of resistant -1,4-glucan degradation activity were associated with BV, particularly in the concurrent presence of G. leopoldii, G. swidsinskii, and G. vaginalis. These findings suggest a role of -1,4-glucan degradation in BV pathogenesis mediated by Gardnerella species. The results indicate the potential of targeting bacterial amylase activity as therapeutic strategy for BV prevention and treatment.

microbiology↗

bioRxiv2022

Multiomics characterization of the zoo-housed gorilla gut microbiome reveals loss of bacterial diversity besides abundant fungal cellulose-degrading and archaeal methanogenic activity

We carried out a comparative analysis between the bacterial microbiota composition of zoo-housed western lowland gorillas and their wild counterparts through 16S rRNA gene amplicon sequencing. In addition, we characterized the carbohydrate-active and methanogenic potential of the zoo-housed gorilla microbiome through shotgun metagenomics and RNA sequencing. The zoo-housed gorilla microbiota showed increased alpha diversity in terms of bacterial species richness and a distinct composition from that of the wild gorilla microbiota, including a loss of abundant fiber-degrading and hydrogenic Chloroflexi. Metagenomic analysis of the CAZyome indicated predominant oligosaccharide-degrading activity, while RNA sequencing revealed diverse cellulase and hemi-cellulase activities in the zoo-housed gorilla gut, contributing to a total of 268 identified carbohydrate-active enzymes. Metatranscriptome analysis revealed a substantial contribution of 38% of the transcripts from anaerobic fungi and archaea to the gorilla microbiome. This activity originates from cellulose-degrading and hydrogenic fungal species belonging to the class Neocallimastigomycetes, as well as from methylotrophic and hydrogenotrophic methanogenic archaea belonging to the classes Thermoplasmata and Methanobacteria, respectively. Our study shows the added value of RNA sequencing in a multiomics approach and highlights the contribution of eukaryotic and archaeal activities to the gut microbiome of gorillas.

microbiology↗

bioRxiv2022

Raw milk kefir: microbiota, bioactive peptides, and immune modulation.

This study aims to characterize the microbial and peptidomic composition of raw milk kefir, and to address the potential anti-allergic effects of raw milk kefir using validated research models for food allergy. Raw milk kefir was produced after incubation with a defined freeze-dried starter culture. Kefir was sampled during fermentation at seven-time intervals. For comparison, kefir was also prepared from boiled milk (100 {degrees}C; 5 sec). Peptide compositions were determined for the raw and heated milk, plus kefir end products made from these milks. In a murine food allergy model, the two kefir end products were investigated on their allergy modulating effects. In both kefirs, we identified amplicon sequence variants identical to those in the starter, matching the bacteria Lactococcus lactis, Streptococcus thermophilus, Leuconostoc and the yeast Debaromyces. In raw milk kefir, additional sequence variants of Lactococcus lactis and the yeasts Pichia and Galactomyces could be identified, which were absent in heated milk kefir. Analysis of peptide compositions in kefirs indicated that the number and intensity of peptides drastically increased after fermentation. Heating of milk negatively affected the diversity of the peptide composition in kefir. Only raw milk kefir suppressed the acute allergic skin response to the food allergen ovalbumin in sensitised mice. These effects coincided with differences in the T-cell compartment, with lower percentages of activated Th1 cells and IFNg production after treatment with kefir made from heated milk. The results of this study indicate specific properties of raw milk kefir that may contribute to its additional health benefits.

microbiology↗

bioRxiv2022

Genetic elements orchestrating Lactobacillus crispatus glycogen metabolism in the vagina

Glycogen in the female lower reproductive tract is a major carbon source for vaginal colonization and acidification by common vaginal Lactobacillus species, such as Lactobacillus crispatus. Previously we identified the pullulanase gene pulA in Lactobacillus crispatus, correlating with its ability to autonomously utilize glycogen for growth. Here we further characterize genetic variation and differential regulation of pulA affecting the presence of its gene product on the outer surface layer. We show that alpha-glucan degrading activity dissipates when Lactobacilllus crispatus is grown on glucose, maltose and maltotriose, in agreement with carbon catabolite repression elements flanking the pulA gene. Proteome analysis of the S-layer confirmed that the pullulanase protein is highly abundant in an S-layer enriched fraction, but not in a strain with a defective pullulanase variant or in a pullulanase-sufficient strain grown on glucose. In addition, we provide evidence that Lactobacillus crispatus pulA mutants are relevant in vivo, as they are commonly observed in metagenome datasets of human vaginal microbial communities. Analysis of the largest publicly available human vaginal metagenome dataset indicates that 15 out of 272 samples, containing a Lactobacillus crispatus pulA gene, contain a defective variant of this gene. Another 23 out of 272 samples show large deletions or transposon insertions. Taken together, these results demonstrate that both environmental as well as genetic factors explain variation of Lactobacillus crispatus alpha-glucosidases in the vaginal environment.

microbiology↗

bioRxiv2021

Different resource allocation in a Bacillus subtilis population displaying bimodal motility

To cope with sudden changes in their environment, bacteria can use a bet-hedging strategy by dividing the population into cells with different properties. This so-called bimodal or bistable cellular differentiation is generally controlled by positive feedback regulation of transcriptional activators. Due to the continuous increase in cell volume, it is difficult for these activators to reach an activation threshold concentration when cells are growing exponentially. This is one reason why bimodal differentiation is primarily observed from the onset of the stationary phase when exponential growth ceases. An exception is the bimodal induction of motility in Bacillus subtilis, which occurs early during exponential growth. Several mechanisms have been put forward to explain this, including double negative-feedback regulation and the stability of the mRNA molecules involved. In this study, we used fluorescence-assisted cell sorting to compare the transcriptome of motile and non-motile cells and noted that expression of ribosomal genes is lower in motile cells. This was confirmed using an unstable GFP reporter fused to the strong ribosomal rpsD promoter. We propose that the reduction in ribosomal gene expression in motile cells is the result of a diversion of cellular resources to the synthesis of the chemotaxis and motility systems. In agreement, single-cell microscopic analysis showed that motile cells are slightly shorter than non-motile cells, an indication of slower growth. We speculate that this growth rate reduction can contribute to the bimodal induction of motility during exponential growth. IMPORTANCETo cope with sudden environmental changes, bacteria can use a bet-hedging strategy and generate different types of cells within a population, so called bimodal differentiation. For example, a Bacillus subtilis culture can contain both motile and non-motile cells. In this study we compared the gene expression between motile and non-motile cells. It appeared that motile cells express less ribosomes. To confirm this, we constructed a ribosomal promoter fusion that enabled us to measure expression of this promoter in individual cells. This reporter fusion confirmed our initial finding. The re-allocation of cellular resources from ribosome synthesis towards synthesis of the motility apparatus results in a reduction in growth. Interestingly, this growth reduction has been shown to stimulate bimodal differentiation.

microbiology↗

bioRxiv2018

Comparative genomics of human Lactobacillus crispatus isolates reveals genes for glycosylation and glycogen degradation: Implications for in vivo dominance of the vaginal microbiota

BackgroundA vaginal microbiota dominated by lactobacilli (particularly Lactobacillus crispatus) is associated with vaginal health, whereas a vaginal microbiota not dominated by lactobacilli is considered dysbiotic. Here we investigated whether L. crispatus strains isolated from the vaginal tract of women with Lactobacillus-dominated vaginal microbiota (LVM) are pheno- or genotypically distinct from L. crispatus strains isolated from vaginal samples with dysbiotic vaginal microbiota (DVM).\n\nResultsWe studied 33 L. crispatus strains (n=16 from LVM; n=17 from DVM). Comparison of these two groups of strains showed that, although strain differences existed, both groups were heterofermentative, produced similar amounts of organic acids, inhibited Neisseria gonorrhoeae growth and did not produce biofilms. Comparative genomics analyses of 28 strains (n=12 LVM; n=16 DVM) revealed a novel, 3-fragmented glycosyltransferase gene that was more prevalent among strains isolated from DVM. Most L. crispatus strains showed growth on glycogen-supplemented growth media. Strains that showed less efficient (n=6) or no (n=1) growth on glycogen all carried N-terminal deletions (respectively, 29 and 37 amino acid-deletions) in a putative pullulanase type I gene.\n\nDiscussionL. crispatus strains isolated from LVM were not phenotypically distinct from L. crispatus strains isolated from DVM, however, the finding that the latter were more likely to carry a 3-fragmented glycosyltransferase gene may indicate a role for cell surface glycoconjugates, which may shape vaginal microbiota-host interactions. Furthermore, the observation that variation in the pullulanase type I gene associated with growth on glycogen discourages previous claims that L. crispatus cannot directly utilize glycogen.

microbiology↗