Biology subjects

Vereecke, L.

Publications and source records attributed to Vereecke, L..

10 recordsLinked to original sources

bioRxiv2026

Citrobacter rodentium infection disrupts colonic mucus barrier function via ablation of intercrypt goblet cells

The colonic mucus barrier, composed of distinct layers maintained by specialized goblet cell (GC) subtypes, forms the first line of defense against enteric pathogens. However, the individual contributions of inner (IML) and fecal (FML) mucus layers to barrier integrity, and how these layers and the GC responses are dynamically modulated during infection remain incompletely understood. Using Citrobacter rodentium infection in mice, we show that early colonization disrupts the inner mucus layer, increases mucus penetrability and drives alterations in faecal mucus layer thickness. Spatial imaging revealed progressive crypt infiltration and concurrent accumulation of pathogen clusters within the FML. Transcriptomic and functional analyses identified Spdef-dependent intercrypt goblet cells (icGCs) as essential for sustaining IML integrity and limiting epithelial access. Spdef-deficient mice exhibited delayed clearance and enhanced crypt invasion, highlighting the protective role of icGCs. Infection selectively depleted icGCs, collapsing the intercrypt mucus and creating permissive niches for colonization. Mechanistically, C. rodentium leveraged its type III secretion system, specifically the EspF effector to reprogram GC transcriptional responses, inducing metabolic stress and promoting apoptotic signatures in GCs specifically. These findings reveal a previously unrecognized virulence strategy in which EspF-driven GC remodeling compromises intercrypt mucus defenses, potentially facilitating pathogen persistence and transmission.

microbiology↗

bioRxiv2026

Comparisons among Yanomami populations reveal transitional gut microbiome configurations under urban influence

Urbanization influences gut microbiome composition and function, yet comparisons between contrasting lifestyles offer limited insight into which microbial features are most sensitive to increasing urbanization. We analyzed gut shotgun metagenomes from Yanomami participants, an Indigenous Amazonian people who maintain traditional livelihoods, across three geographically distinct populations with varying degrees of urban influence, as well as an urban Belgian cohort. Belgian and Yanomami microbiomes differed markedly in taxonomic composition and functional potential. The comparison between Bicho-Acu, the most urban-influenced Yanomami population, and Xamakorona, the least urban-exposed, revealed that although Bicho-Acu presented a broadly Yanomami-associated microbiome, it exhibited selected urban-associated features, including greater Bacteroides abundance and a higher relative abundance of genes involved in glycosaminoglycan degradation and secondary bile acid biosynthesis pathways. Furthermore, genus-level co-occurrence network connectivity showed an orderly shift across populations, declining progressively with increasing urban influence. Carbohydrate-active enzyme profiles further showed stronger non-starch-polysaccharide-associated signals in Belgium and resistant-starch-associated features in Xamakorona, suggesting distinct carbohydrate-processing strategies. Our findings support a model in which urbanization reshapes microbial composition, their ecological interactions, and metabolic capacity, with transitional configurations emerging through selective shifts across these dimensions.

microbiology↗

bioRxiv2026

Indigenous Yanomami gut microbiota protects against diet-induced metabolic dysfunction

Industrialization profoundly alters the human gut microbiota, reducing microbial diversity and eliminating taxa prevalent in non-industrialized populations. These microbiota alterations accompanying industrialization might contribute to the increasing prevalence of obesity and other chronic inflammatory diseases, yet direct experimental evidence remains lacking. We compared the gut microbiota of Indigenous Brazilian Yanomami and urban Belgian donors and transplanted these into germ-free (GF) mice subjected to high-fat diet (HFD). The Yanomami microbiota exhibited greater richness and distinct composition enriched for VANISH (Volatile and/or Associated Negatively with Industrialized Societies of Humans) taxa. Transplantation of Yanomami microbiota significantly attenuated HFD-induced metabolic dysfunction, reducing weight gain, diabetes incidence, and promoting adipose and hepatic Th2 immunity. Yanomami-derived microbial communities displayed enhanced ecological stability and enrichment for short-chain fatty acid-associated taxa and metabolic functions post-HFD. Our findings demonstrate that the microbiota from low-urbanization populations confer protection against diet-induced metabolic disease, highlighting ecological resilience and specific microbial functions as potential targets for microbiota-inspired therapeutics.

microbiology↗

bioRxiv2026

Mixed acid fermentation products from Lachnospira eligens counteract myotube atrophy

IntroductionAcute myeloid leukemia (AML) is a hematological malignancy associated with muscle wasting. As the relative abundance of Lachnospira eligens was reduced in patients with AML compared to healthy individuals and correlated positively with muscle strength, we hypothesized that L. eligens positively impacts the muscle through the production of small metabolites reaching the systemic circulation. MethodsL. eligens levels were analyzed in two additional independent cohorts. Six L. eligens isolates were characterized through whole-genome sequencing to select clinically relevant strains. The composition of their culture supernatant was analyzed by metabolomics. The impact of L. eligens supernatant on dexamethasone- and interleukin-6-atrophied murine myotubes was assessed. Bioactive metabolites and their production mechanism were identified using among others bioactivity-guided fractionation. The underlying mechanism was also explored on the host side through myotubes transcriptome analysis and metabolic flux analysis. The relevance of bioactive metabolites and their production mechanism was evaluated through clinical data and samples analyses and in a mouse model of leukemia. ResultsThe levels of L. eligens are reduced in independent cohorts of patients with AML and its supernatant counteracts myotube atrophy. This anti-atrophic effect, conserved between strains of the same species, depends on the occurrence of mixed acid fermentation (MAF) in anoxic culture conditions and the presence of its acid end-products acetate, formate and D-lactate. Consistent with those results, blood levels of acetate are decreased and the relative abundance of fecal bacteria capable of performing aerobic respiration is increased in patients with AML. However, bacterial supernatant failed to prevent muscle atrophy and weakness in leukemic mice, likely due to insufficient sustained elevation of acid end-products in the blood. ConclusionThis work reveals the anti-atrophic effect of MAF end-products on myotubes and suggests the importance of considering gut electron acceptor levels (e.g. O2) in disorders affecting muscle health. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC="FIGDIR/small/729780v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@112529eorg.highwire.dtl.DTLVardef@1ee1929org.highwire.dtl.DTLVardef@b5f389org.highwire.dtl.DTLVardef@187bc40_HPS_FORMAT_FIGEXP M_FIG Mixed acid fermentation products from Lachnospira eligens counteract myotube atrophy. Our study suggests that gut anaerobiosis is disrupted in treatment-naive patients with acute myeloid leukemia (AML), leading to decreased circulating acetate levels and a reduced relative abundance of L. eligens, which significantly correlated with muscle strength. In line with this framework, in vitro experiments demonstrate that the culture supernatant of L. eligens, which contains mixed acid fermentation (MAF) end-products such as acetate, effectively counteracts C2C12 myotube atrophy in the presence of pro-atrophying stimuli. Further mechanistic experiments indicate a causal role for MAF end-products in this anti-atrophying effect. Created with BioRender.com. Legend: solid frames: experimental results; dashed frames: hypothetical conclusions derived from results; black solid arrow: established correlation; black dashed arrows: hypothetical causation. C_FIG

microbiology↗

bioRxiv2024

VSIG4-Expressing Macrophages Contribute To Anti-Parasitic And Anti-Metastatic Responses In The Peritoneal Cavity

Peritoneal tissue-resident macrophages, also referred to as large peritoneal macrophages (LPMs), play an important role as gatekeepers of peritoneal homeostasis by providing a first line of defense against pathogenic threats. About a third of the LPMs express the surface receptor V-set and Immunoglobulin domain containing 4 (VSIG4), but it is unclear to what extent these cells differ from their VSIG4-negative counterparts and perform dedicated functions. Here, we demonstrate that VSIG4+ LPMs, in contrast to VSIG4- LPMs, are in majority derived from embryonal precursors and their occurrence is to a large extent independent from sex and microbiota. Although their transcriptome and surface proteome are indistinguishable from VSIG4- LPMs at steady-state, VSIG4+ LPMs are superior in phagocytosing Gram-positive bacteria and colorectal carcinoma (CRC) cells. In-house generated anti-VSIG4 nanobody constructs that are antibody-dependent cell-mediated cytotoxicity (ADCC)-enabled allowed a selective elimination of the VSIG4+ LPM subset without affecting the overall LPM content of the peritoneal cavity. This strategy uncovered a role for VSIG4+ LPMs in lowering the first peak of parasitemia in a Trypanosoma brucei brucei infection model and in reducing the outgrowth of CRC cells in the peritoneal cavity, a prime metastatic site in CRC patients. Altogether, our data uncover a protective role for VSIG4+ LPMs in infectious and oncological diseases in the peritoneal cavity.

immunology↗

bioRxiv2024

Neonatal microbiota colonization drives maturation of primary and secondary goblet cell mediated protection in the pre-weaning colon

In the distal colon, mucus secreting goblet cells primarily confer protection from luminal microorganisms via generation of a sterile inner mucus layer barrier structure. Bacteria-sensing sentinel goblet cells provide a secondary defensive mechanism that orchestrates mucus secretion in response to microbes that breach the mucus barrier. Previous reports have identified mucus barrier deficiencies in adult germ-free mice, thus implicating a fundamental role for the microbiota in programming mucus barrier generation. In this study, we have investigated the natural neonatal development of the mucus barrier and sentinel goblet cell-dependent secretory responses upon postnatal colonization. Combined in vivo and ex vivo analyses of pre- and post-weaning colonic mucus barrier and sentinel goblet cell maturation demonstrated a sequential microbiota-dependent development of these primary and secondary goblet cell-intrinsic protective functions, with dynamic changes in mucus processing dependent on innate immune signalling via MyD88, and development of functional sentinel goblet cells dependent on the NADPH/Dual oxidase family member Duox2. Our findings therefore identify new mechanisms of microbiota-goblet cell regulatory interaction and highlight the critical importance of the pre-weaning period for the normal development of colonic barrier function.

immunology↗

bioRxiv2023

GDF15 mediates inflammation-associated bone loss through a brain-bone axis

Metabolic mediators play an important role in regulating chronic inflammation in the body. Here we report an unexpected role for GDF15 (Growth Differentiation Factor 15), a central mediator of food intake, in inflammation-associated bone loss. GDF15 serum levels were found to be elevated in arthritis patients and inversely correlated with bone density. Despite being associated with inflammation, we found that GDF15 itself does not cause, nor contribute to, clinical or histopathological arthritis. Rather, under inflammatory conditions, GDF15 mediates trabecular bone loss through its receptor GFRAL, which is exclusively expressed in the hindbrain. GDF15-GFRAL binding results in {beta}-adrenergic activation of MALPs (Marrow Adipocytic Lineage Precursors) in the bone marrow, which stimulate osteoclasts and trigger bone loss. These data suggest a metabolic mediator-controlled brain-bone axis in inflammation, through which bone loss is induced in a contextual rather than general manner. These findings may lead to more specific therapeutic interventions to protect bone.

immunology↗

bioRxiv2023

Myeloid A20 is critical for type-2 immune mediated helminth resistance

Protective immunity against intestinal helminths requires induction of robust Type-2 immunity orchestrated by various cellular and soluble effectors which promote goblet cell hyperplasia, mucus production, epithelial proliferation and smooth muscle contractions to expel worms and reestablish immune homeostasis. Conversely, defects in type-2 immunity result in ineffective helminth clearance, persistent infection and chronic inflammation. We identify A20 as an essential myeloid factor for the induction of type-2 immune responses against the intestinal parasite Trichuris muris. Myeloid cell-specific loss of A20 in mice (A20myel-KO) results in chronic Trichuris muris infection and intestinal inflammation. Myeloid A20 deficient mice are not able to induce anti-helmith type-2 immune responses while instead mount detrimental Th1/Th17 polarized immune responses. Antibody-mediated neutralization of the type-1 cytokines IFN{gamma}, IL18 and IL12 prevents Th1/Th17 polarization and reestablishes Type-2 mediated protective immunity against Trichuris muris in A20myel-KO mice. In contrast, the strong Th1/Th17 biased immunity in A20myel-KO mice offers protection against Salmonella infection. We hereby identify A20 as an essential myeloid factor to initiate approriate adaptive immunity in response to infection, and to induce a balanced type-2 immune response against the intestinal parasite Trichuris muris. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/556360v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@632052org.highwire.dtl.DTLVardef@1def1f2org.highwire.dtl.DTLVardef@1de8459org.highwire.dtl.DTLVardef@1c316ff_HPS_FORMAT_FIGEXP M_FIG C_FIG Graphical abstractThe clearance of gastrointestinal helmiths depends on type-2 immunity. Helminths interact with and damage intestinal tissue, which leads to the release of intracellular DAMPs and cytokines such as TSLP and IL33, and IL25 produced by epithelial cells. These factors may activate myeloid cells and ILCs, which further activate T and B cells to mount effective Th2 responses and the secretion of IL4, IL5 and IL13 cytokines, as well as helminth-specific IgG1 immunoglobulins, leading to effective expulsion of the helminths. Deletion of A20 in the myeloid cells leads to enhanced secretion of type-1 cytokines, including IL12, IL18 and IFN{gamma}, which impede type-2 immune-mediated helminth clearance and promotes chronic intestinal inflammation.

immunology↗

bioRxiv2023

Colibactin-induced genotoxicity and colorectal cancer exacerbation critically depends on adhesin-mediated epithelial binding

Various bacteria are suggested to contribute to colorectal cancer (CRC) development, including pks+ E. coli which produce the genotoxin colibactin that induces characteristic mutational signatures in host epithelial cells. It remains unclear how the highly unstable colibactin molecule is able to access host epithelial cells and its DNA to cause harm. Using the microbiota-dependent ZEB2-transgenic mouse model of invasive CRC, we found that pks+ E. coli drives CRC exacerbation and tissue invasion in a colibactin-dependent manner. Using isogenic mutant strains, we further demonstrate that CRC exacerbation critically depends on expression of the E. coli type-1 pilus adhesin FimH and the F9-pilus adhesin FmlH. Blocking bacterial adhesion using a pharmacological FimH inhibitor attenuates colibactin-mediated genotoxicity and CRC exacerbation. Together, we show that the oncogenic potential of pks+ E. coli critically depends on bacterial adhesion to host epithelial cells and is critically mediated by specific bacterial adhesins. Adhesin-mediated epithelial binding subsequently allows production of the genotoxin colibactin in close proximity to host epithelial cells, which promotes DNA damage and drives CRC development. These findings present promising therapeutic avenues for the development of anti-adhesive therapies aiming at mitigating colibactin-induced DNA damage and inhibiting the initiation and progression of CRC, particularly in individuals at risk for developing CRC.

cancer biology↗

bioRxiv2023

Sterile triggers drive joint inflammation in TNF and IL-1beta dependent mouse arthritis models

Arthritis is the most common extra-intestinal complication in inflammatory bowel disease (IBD). Conversely, arthritis patients are at risk for developing IBD and often display subclinical gut inflammation. These observations suggest a shared disease etiology, commonly termed the gut-joint-axis. The clinical association between gut and joint inflammation is further supported by the success of common therapeutic strategies and microbiota dysbiosis in both conditions. Most data however support a correlative relationship between gut & joint inflammation, while causative evidence is lacking. Using two independent transgenic mouse arthritis models, either TNF or IL1{beta} dependent, we demonstrate that arthritis develops independently of the microbiota and intestinal inflammation, since both lines develop full-blown articular inflammation under germ-free conditions. In contrast, TNF-driven gut inflammation is fully rescued in germ-free conditions indicating that the microbiota is driving TNF-induced gut inflammation. Together, our study demonstrates that, although common inflammatory pathways may drive both gut and joint inflammation, the molecular triggers initiating such pathways are distinct in these tissues.

immunology↗