Biology subjects

Gil, F.

Publications and source records attributed to Gil, F..

4 recordsLinked to original sources

bioRxiv2026

Gut complement C1q and C3 interact with Clostridioides difficile spores via CdeM and contribute to pathogenesis.

Clostridioides difficile infection (CDI) is characterized by toxin-mediated epithelial injury, intestinal inflammation, and a high frequency of disease recurrence. Although complement components are produced locally within the gastrointestinal tract, their contribution to C. difficile pathogenesis remains poorly understood. Here, we investigated the interaction of the complement proteins C1q and C3 with C. difficile spores and their contribution to spore-host interactions and disease outcome. We found that C1q and C3 are accessible within the healthy ileal mucosa and that TcdB intoxication differentially remodels their spatial availability, decreasing accessible C1q while increasing accessible C3 at higher toxin concentrations. C. difficile spores associated with both complement components in vivo and directly interacted with purified human C1q and C3 in vitro, with immunogold electron microscopy localizing these interactions to the outer exosporium. Although the collagen-like BclA proteins modulated complement binding under some conditions, they were not required for C1q or C3 association. Far-Western analysis coupled to mass spectrometry identified the exosporium proteins CotE and CdeM as candidate complement-interacting proteins, and purified CdeM inclusion bodies directly associated with both C1q and C3. Exposure of spores to human serum promoted their interaction with intestinal epithelial cells, whereas depletion of either C1q or C3 markedly reduced spore internalization and reconstitution with the corresponding purified protein partially restored entry. C3-derived species, including C3dg, were selectively associated with spores but not vegetative cells, without reducing spore viability. Finally, C1q deficiency did not alter the initial onset of CDI but accelerated recovery and markedly attenuated recurrent disease following vancomycin treatment. Together, these findings identify intestinal complement as a previously unrecognized component of the C. difficile spore-host interface and reveal C1q and C3 as modulators of spore epithelial entry, persistence, and recurrent disease.

microbiology↗

bioRxiv2026

Distinctive spore architecture and developmental biology of Turicibacter sanguinis reveal unexpected diversity among gut spore formers

Sporulation is a widespread but incompletely characterized trait among gut commensals, where it underpins microbial persistence, transmission, and ecological resilience. Most insights into spore biology derive from Bacilli and Clostridia, yet little is known about sporulation in phylogenetically distant gut-associated lineages. Turicibacter sanguinis, a strict anaerobe linked to host serotonin metabolism, lipid homeostasis, and neurodegenerative disease, represents one such understudied taxon. Here, we integrate ultrastructural, physiological, and comparative genomic analyses to define the sporulation and germination program of T. sanguinis. We show that T. sanguinis forms heat-resistant spores with a canonical core-cortex-coat architecture but displays previously undescribed features including a dual-layered outer envelope and bimodal electron-dense coat morphotypes. Developmental stages of sporulation follow canonical stages of Bacillus- and Clostridium-like sporulation while genomic analyses reveal a hybrid regulatory architecture combining Clostridial-type Spo0A initiation with Bacillus-like late-stage sigma factor control. Germination assays and genomic signatures further indicate a nutrient-responsive, Bacillus-like pathway involving Ger-family receptors, SpoVA-mediated Ca-DPA release, and CwlJ- and SleM-type cortex hydrolases. Together, these findings identify T. sanguinis as a distinct spore-forming lineage within the human gut microbiota and expand the known diversity of sporulation strategies across the Firmicutes.

microbiology↗

bioRxiv2025

Capturing global pet dog gut microbial diversity and hundreds of near-finished bacterial genomes by using long-read metagenomics in a Shanghai cohort

Pet dogs are considered part of the family, and understanding their gut microbiomes can provide insights into both animal and household health. Most comprehensive studies, however, relied on short-read sequencing, resulting in fragmented MAGs that miss mobile elements, antimicrobial-resistance genes, and ribosomal genes. Here, we applied deep long-read metagenomics (polished with short-reads) to fecal samples from 51 urban pet dogs in Shanghai, generating 2,676 MAGs--representing 320 bacterial species--, of which [~]72% achieved near-finished quality, often improving on the corresponding reference public genome. Comparisons with external datasets showed that our Shanghai-based MAG catalog is representative of pet dogs worldwide (median read mapping of >90%). Moreover, we recovered circular extrachromosomal elements, including those linked to antimicrobial resistance, which were also detected in external dog gut datasets. In conclusion, we provide a high-quality reference resource and demonstrate the power of deep long-read metagenomics to resolve microbial diversity in complex host-associated microbiomes.

microbiology↗

bioRxiv2025

Clostridioides difficile major toxins remodel the intestinal epithelia, affecting spore adherence/internalization into intestinal tissue and their association with gut vitronectin.

The most common cause of healthcare-associated diarrhea and colitis in the U.S., is Clostridioides difficile, a spore-forming pathogen. Two toxins, TcdA and TcdB, are major virulence factors essential for disease manifestations, while C. difficile spores are essential for disease transmission and recurrence. Both toxins cause major damage to the epithelial barrier, trigger massive inflammation, and reshape the microbiome and metabolic composition, facilitating C. difficile colonization. C. difficile spores, essential for transmission and recurrence of the disease, persist adhered and internalized in the intestinal epithelia. Studies have suggested that toxin-neutralization in combination with antibiotic during CDI treatment in humans significantly reduces disease recurrence, suggesting a link between toxin-mediated damage and spore persistence. Here, we show that TcdA/TcdB-intoxication of intestinal epithelial Caco-2 cells leads to remodeling of accessible levels of fibronectin (Fn) and vitronectin (Vn) and their cognate alpha-integrin subunits. While TcdB-intoxication of intestinal tissue had no impact in accessible levels of Fn and Vn, but significantly increased levels of intracellular Vn. We observed that Fn and Vn released to the supernatant readily bind to C. difficile spores in vitro, while TcdB-intoxication of intestinal tissue led to increased association of C. difficile spores with gut Vn. Toxin-intoxication of the intestinal tissue also contributes to increased adherence and internalization of C. difficile spores. However, TcdB-intoxicated ligated loops infected of mice treated with Bezlotoxumanb (monoclonal anti- TcdB antibodies) did not prevent TcdB-mediated increased spore adherence and internalization into intestinal tissue. This study highlights the importance of studying the impact of C. difficile toxins of host tissues has in C. difficile interaction with host surfaces that may contribute to increased persistence and disease recurrence.

microbiology↗