Biology subjects

Correa-Fiz, F.

Publications and source records attributed to Correa-Fiz, F..

6 recordsLinked to original sources

bioRxiv2026

First outbreak of Lumpy Skin disease in Catalonia, Spain, 2025-2026

Lumpy skin disease (LSD) is an emerging cattle disease caused by lumpy skin disease virus (LSDV), with major impacts on the industry, being classified as a Category A disease. Although it was historically confined to Africa, LSD has expanded into the Middle East, Asia and Europe. Here, we report two LSDV genomes from the first outbreak detected in Catalonia, Spain, in October 2025. The genomes were assembled from high-throughput sequencing data generated from two homogenized skin nodules. Comparative phylogenetic analyses were performed using all available complete LSDV genomes and rpo30 gene sequences. These analyses placed the LSDV isolates detected in Catalonia within clade 1.2, closely related to the isolates recently reported in Sardinia, Italy. Our findings also support a connection between recent south-western Europe and central African strains, possibly through northern Africa, and highlight the need for more complete genomes to clarify the origin and connections among recent LSDV outbreaks.

genomics↗

bioRxiv2026

Genome-scale metabolic model atlas of the zoonotic pathogen Streptococcus suis

Streptococcus suis is a Gram-positive bacterium with a dual role as a commensal member of the porcine nasal microbiota and a pathogen causing systemic disease in pigs and humans. Mounting evidence suggests that metabolism is a key driver of S. suis pathogenicity. Given the species high genetic variability, we hypothesize that differences in metabolic networks could explain the diverse pathogenic phenotypes observed across different strains. To test this, we generated an atlas of over 3000 strain-specific and automatically curated genome-scale metabolic models that cover the breadth of pathogenic and commensal S. suis lineages. Using this model atlas, we performed the first species-level examination of metabolic traits in S. suis. Our simulations, supported by experimental validation, revealed three key insights. First, while metabolic traits are broadly conserved in S. suis, there are nevertheless lineage-dependent differences in amino acid auxotrophies and carbon utilization patterns that point towards distinct in vivo niches. Second, most strains are predicted to grow in different plausible in vivo environments regardless of their virulence phenotype, suggesting that metabolism is a weak barrier to systemic infection. Third, by systematically predicting reaction essentiality in more than 15 million reaction-strain-condition combinations, we identify a subset of 17 reactions, largely in nucleotide metabolism, that are conditionally essential in vivo and may serve as new targets for the development of new antimicrobials or vaccines. Overall, this study provides a valuable new resource for broadly examining S. suis metabolism and its role in pathogenicity.

Systems Biology↗

bioRxiv2024

In vitro metabolic interaction network of a rationally designed nasal microbiota community

Mounting evidence suggests that metabolite exchange between microbiota members is a key driver of microbiota composition. However, we still know little about the metabolic interaction networks that occur within many microbiota. This is particularly true for the nasal microbiota, and current efforts towards this end are hampered by a lack of microbial consortia that would enable the mapping of metabolic interactions between nasal microbiota members under in vitro conditions. To tackle these issues, we developed the Porcine Nasal Consortium (PNC8), a rationally designed microbial consortium of eight strains representing the most in vivo abundant genera in the nasal microbiota of healthy piglets. We used this consortium to systematically examine the metabolic capabilities of nasal microbiota members, as well as the metabolic interactions occurring between them. We found that PNC8 strains differ substantially in their metabolic pathway repertoire and ability to grow across various in vitro conditions. Nevertheless, spent-media experiments revealed that most metabolic interactions between PNC8 strains are negative, and exometabolomics data pointed to co-depletion of sugars as a key driver of this interaction network. Finally, direct co-cultivation experiments showed that, as a result of this largely negative metabolic interaction network, competition is common among pairs of PNC8 strains and leads to a complex competition hierarchy in which only few strains are able to consistently outcompete all others. Overall, this work provides a valuable resource for studying the nasal microbiota under experimentally tractable in vitro conditions and is a key step towards mapping its metabolic interaction network.

systems biology↗

bioRxiv2024

Porcine Nasal Organoids as a model to study the interactions between the swine nasal microbiota and the host

Interactions between the nasal epithelium, commensal nasal microbiota, and respiratory pathogens play a key role in respiratory infections. Currently there is a lack of experimental models to study such interactions under defined in vitro conditions. Here, we developed a Porcine Nasal Organoid (PNO) system from nasal tissue of pigs as well as from cytological brushes. PNOs exhibited similar structure and cell types than the nasal mucosa, as evaluated by immunostaining. PNOs were inoculated with porcine commensal strains of Moraxella pluranimalium, Rothia nasimurium and the pathobiont Glaesserella parasuis for examining host-commensal-pathogen interactions. All strains adhered to the PNOs, although at different levels. M. pluranimalium and G. parasuis strains stimulated the production of proinflammatory cytokines, whereas R. nasimurium induced the production of IFN{gamma} and diminished the proinflammatory effect of the other strains. Overall, PNOs mimic the in vivo nasal mucosa and can be useful to perform host-microbe interaction studies. In briefInteractions between nasal epithelium, commensal nasal microbiota, and respiratory pathogens play a key role in respiratory infections. We developed porcine nasal organoids to mimic the nasal mucosa and use as a model to study those interactions. Additionally, this development supports the reduction of the number of animals for animal experimentation. HighlightsO_LIFirst generation of Porcine Nasal Organoids (PNOs) from nasal turbinates and swabs C_LIO_LIPNOs recapitulate features of in vivo tissue and maintain self-renewal capacity C_LIO_LIHost-microbe interactions can be studied using the PNO system C_LIO_LIRothia nasimurium inhibits the inflammation induced by other bacteria C_LI

microbiology↗

bioRxiv2023

Gut-associated microbes are present and active in the pig nasal cavity

BackgroundThe nasal microbiota is a key contributor to animal health, and characterizing the nasal microbiota composition is an important step towards elucidating the role of its different members. Efforts to characterize the nasal microbiota composition of domestic pigs and other farm animals frequently report the presence of bacteria that are typically found in the gut, including many anaerobes from the Bacteroidales and Clostridiales orders. However, the in vivo role of these gut-microbiota associated taxa is currently unclear. Here, we tackled this issue by examining the prevalence, origin, and activity of these taxa in the nasal microbiota of piglets. ResultsFirst, analysis of the nasal microbiota of farm piglets sampled in this study, as well as various publicly available data sets, revealed that gut-microbiota associated taxa indeed constitute a substantial fraction of the pig nasal microbiota that is highly variable across individual animals. Second, comparison of herd-matched nasal and rectal samples at amplicon sequencing variant (ASV) level showed that these taxa are largely shared in the nasal and rectal microbiota, suggesting a common origin driven presumably by the transfer of fecal matter. Third, surgical sampling of the inner nasal tract showed that gut-microbiota associated taxa are found throughout the nasal cavity, indicating that these taxa do not stem from contaminations introduced during sampling with conventional nasal swabs. Finally, analysis of cDNA from the 16S rRNA gene in these nasal samples indicated that gut-microbiota associated taxa are indeed active in the pig nasal cavity. ConclusionThis study shows that gut-microbiota associated taxa are not only present, but also active, in the nasal cavity of domestic pigs, and paves the way for future efforts to elucidate the in vivo function of these taxa within the nasal microbiota.

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↗