Biology subjects

Boekhorst, J.

Publications and source records attributed to Boekhorst, J..

7 recordsLinked to original sources

bioRxiv2025

IL-26 from ILCs regulates early-life gut epithelial homeostasis by shaping microbiota composition

Animals host symbiotic microbial communities that shape gut health. However, how the host immune system and microbiota interact to regulate epithelial homeostasis, particularly during early development, remains unclear. Human interleukin-26 (IL-26) is associated with gut inflammation and has intrinsic bactericidal activity in vitro, yet its in vivo functions are largely unknown, primarily due to its absence in rodents. To examine the role of IL-26 in early life, we used zebrafish and found that gut epithelial cells in il26-/- larvae exhibited increased proliferation and DNA damage, faster turnover, and an altered abundance of cell populations. This epithelial dysregulation occurred independently of the IL-26 canonical receptor and resulted from dysbiosis in il26-/-. Moreover, IL-26 bactericidal activity was conserved in zebrafish. Our findings suggest that IL-26 directly regulates microbiota composition through this property. We further identified innate lymphoid cells (ILCs) as the primary source of IL-26 at this developmental stage. These findings establish IL-26 as a central player in a regulatory circuit linking the microbiota, ILCs, and intestinal epithelial cells to maintain gut homeostasis during early life.

immunology↗

bioRxiv2025

Genome-Wide Identification of Conditionally Essential Genes Supporting Streptococcus suis Growth in Serum and Cerebrospinal Fluid

Streptococcus suis is a major cause of sepsis and meningitis in pigs, and zoonosis through the emergence of disease-associated lineages. The ability of S. suis to adapt and survive in host environments, such as blood and cerebrospinal fluid (CSF), is important for pathogenesis. Here, we used Tn-Seq coupled with Nanopore sequencing to identify conditionally essential genes for growth of S. suis P1/7 in active porcine serum (APS) and CSF derived from choroid plexus organoids (Zhao et al., 2025). Through comparative fitness analyses we identified 33 conditionally essential genes (CEGs) supporting growth in APS and 25 CEGs in CSF, highlighting the importance of pathways involved in amino acid transport, nucleotide metabolism, and cell envelope integrity. Notably, the LiaFSR regulatory system and multiple ABC transporters were important for proliferation. We also identified several genes of unknown function as essential for growth, pointing to previously unrecognized genetic factors involved in S. suis adaptation during infection. These findings provide new insights into the genetic requirements for S. suis survival in host-like environments and a deeper understanding of its ability to adapt to distinct physiological niches.

microbiology↗

bioRxiv2025

Interleukin-22 in enteroendocrine cells controls early-life gut motility through interactions with the microbiota

The gut microbiota, immune system, and enteric nervous system tightly interact to regulate adult gut physiology. Yet the mechanisms establishing gut physiology during development remain unknown. Here, we report that in developing zebrafish, enteroendocrine cells produce IL-22 in response to microbial signals before lymphocytes populate the gut. In larvae, IL-22 is crucial to set gut microbiota composition, and ghrelin hormone expression to promote gut motility. IL-22 developmental function depends on its ability to modulate gut microbiota, as bacterial transfer from wild-type zebrafish restored gut motility in il22-/- by reestablishing ghrelin hormone expression. Additionally, IL-22-deficient mice show impaired gut motility and reduced ghrelin expression in early life, indicating a conserved function. Altogether, we identify a circuit where enteroendocrine cells regulate gut function via cytokine control of the microbiota, showing how gut physiology is set prior to immune system maturation.

immunology↗

bioRxiv2024

Differences in maternal diet fiber content influence patterns of gene expression and chromatin accessibility in fetuses and piglets

This study investigates the impact of maternal gestation diets with varying fiber contents on gene expression and chromatin accessibility in fetuses and piglets fed a low fiber diet post weaning. High-fiber maternal diets, enriched with sugar beet pulp or pea internal fiber, were compared to a low-fiber maternal diet to evaluate their effects on liver and muscle tissues. The findings demonstrate that maternal high-fiber diets significantly alter the chromatin accessibility, predicted transcription factor activity and transcriptional landscape in both fetuses and piglets. A gene set enrichment analysis revealed over-expression of gene ontology terms related to metabolic processes and under-expression of those linked to immune responses in piglets from sows given the high-fiber diets during gestation. This suggests better metabolic health and immune tolerance of the fetus and offspring, in line with the documented epigenetic effects of short chain fatty acids on immune and metabolic pathways. A deconvolution analysis of the bulk RNA-seq data was performed using cell-type specific markers from a single cell transcriptome atlas of adult pigs. These results confirmed that the transcriptomic and chromatin accessibility data do not reflect different cell type compositions between maternal diet groups but rather phenotypic changes triggered by the critical role of maternal nutrition in shaping the epigenetic and transcriptional environment of fetus and offspring. Our findings have implications for improving animal health and productivity as well as broader implications for human health, suggesting that optimizing maternal diet with high-fiber content could enhance metabolic health and immune function in the formative years after birth and potentially to adulthood.

genomics↗

bioRxiv2023

A comparison of bioinformatics pipelines for compositional analysis of the human gut microbiome

Investigating the impact of gut microbiome on human health is a rapidly growing area of research. A significant limiting factor in the progress in this field is the lack of consistency between study results, which hampers the correct biological interpretation of findings. One of the reasons is variation of the applied bioinformatics analysis pipelines. This study aimed to compare five frequently used bioinformatics pipelines (NG-Tax 1.0, NG-Tax 2.0, QIIME, QIIME2 and mothur) for the analysis of 16S rRNA marker gene sequencing data and determine whether and how the analytical methods affect the downstream statistical analysis results. Based on publicly available case-control analysis of ADHD and two mock communities, we show that the choice of bioinformatic pipeline does not only impact the analysis of 16S rRNA gene sequencing data but consequently also the downstream association results. The differences were observed in obtained number of ASVs/OTUs (range: 1,958 - 20,140), number of unclassified ASVs/OTUs (range: 210 - 8,092) or number of genera (range: 176 - 343). Also, the case versus control comparison resulted in different results across the pipelines. Based on our results we recommend: i) QIIME1 and mothur when interested in rare and/or low-abundant taxa, ii) NG-Tax1 or NG-Tax2 when favouring stringent artefact filtering, iii) QIIME2 for a balance between two abovementioned points, and iv) to use at least two pipelines to assess robustness of the results. This work illustrates the strengths and limitations of frequently used microbial bioinformatics pipelines in the context of biological conclusions of case-control comparisons. With this, we hope to contribute to "best practice" approaches for microbiome analysis, promoting methodological consistency and replication of microbial findings. Author SummaryStudies increasingly demonstrate the relevance of gut microbiota in understanding human health and disease. However, the lack of consistency between study results is a significant limiting factor of progress in this field. The reasons for this include variation in study design, sample size, bacterial DNA extraction and sequencing method, bioinformatics analysis pipeline and statistical analysis methodology. This paper focuses on the variation generated by bioinformatics pipelines. A choice of a bioinformatic pipeline can influence the assessment of microbial diversity. However, it is unclear to what extent and how the results and conclusion of a case-control study can be influenced. Therefore, we compared the results of a case-control study across different pipelines (applying default settings) while using the same dataset. Our results indicate a lack of consistency across the pipelines. We show that the choice of bioinformatic pipeline not only affects the analysis results of 16S rRNA gene sequencing data from the gut microbiome, but also the associated conclusions for the case-control study. This means different conclusions would be drawn from the same data analysed with different bioinformatic pipeline.

bioinformatics↗

bioRxiv2022

Transcriptomics in serum and culture medium reveal shared and differential gene regulation in pathogenic and commensal Streptococcus suis

Streptococcus suis colonizes the upper respiratory tract of healthy pigs at high abundance but can also cause opportunistic respiratory and systemic disease. Disease-associated S. suis reference strains are well studied, but less is known about commensal lineages. It is not known what mechanisms enable some S. suis lineages to cause disease while others persist as commensal colonizers, or to what extent gene expression in disease-associated and commensal lineages diverge. In this study we compared the transcriptomes of 21 S. suis strains grown in active porcine serum and Todd-Hewitt yeast broth. These strains included both commensal and pathogenic strains, including several strains of sequence type (ST) 1, which is responsible for most cases of human disease and considered the most pathogenic S. suis lineage. We sampled the strains during their exponential growth phase and mapped RNA-sequencing reads to the corresponding strain genomes. We found that the transcriptomes of pathogenic and commensal strains with large genomic divergence were unexpectedly conserved when grown in active porcine serum, but that regulation and expression of key pathways varied. Notably, we observed strong variation of expression across media of genes involved in capsule production in pathogens, and of the agmatine deiminase system in commensals. ST1 strains displayed large differences in gene expression between the two media compared to strains from other clades. Their capacity to regulate gene expression across different environmental conditions may be key to their success as zoonotic pathogens.

microbiology↗

bioRxiv2022

Streptococcus suis infection on European farms is associated with an altered tonsil microbiome and resistome

Streptococcus suis is a Gram-positive opportunistic pathogen causing systemic disease in piglets around weaning age. The factors predisposing to disease are not known. We hypothesised that the tonsillar microbiota might influence disease risk via colonisation resistance and/or co-infections. We conducted a cross-sectional case-control study within outbreak farms complemented by selective longitudinal sampling and comparison with control farms without disease occurrence. We found a small but significant difference in tonsil microbiota composition between case and control piglets (n=45+45). Variants of putative commensal taxa, including Rothia nasimurium, were reduced in abundance in case piglets compared to asymptomatic controls. Case piglets had higher relative abundances of Fusobacterium gastrosuis, Bacteroides heparinolyticus, and uncultured Prevotella and Alloprevotella species. Despite case-control pairs receiving equal antimicrobial treatment, case piglets had higher abundance of antimicrobial resistance genes (ARGs) conferring resistance to antimicrobial classes used to treat S. suis. This might be an adaption of disease-associated strains to frequent antimicrobial treatment.

microbiology↗