Rodent and human malaria parasites cause dysbiosis in the host gut microbiome, but whether Plasmodium species affecting birds cause dysbiosis in their hosts is currently unknown. Here we used a model of avian malaria infection to test whether parasite infection modulates the bird microbiome. To this aim, bird fecal microbiomes were characterized at different time points after infection of canaries with the avian malaria parasite Plasmodium homocircumflexum. Avian malaria caused no significant changes in the alpha and beta diversity of the microbiome in infected birds. In contrast, we discovered changes in the composition and abundance of several taxa. Co-occurrence networks were used to characterize the assembly of the microbiome and trajectories of microbiome structural states progression were found to be different between infected and uninfected birds. Prediction of functional profiles in bacterial communities using PICRUSt2 showed infection by P. homocircumflexum to be associated with the presence of specific degradation and biosynthesis metabolic pathways, which were not found in healthy birds. Some of the metabolic pathways with decreased abundance in the infected group had significant increase in the later stage of infection. The results showed that avian malaria parasites affect bacterial community assembly in the host gut microbiome. Microbiome modulation by malaria parasites could have deleterious consequences for the host bird. Knowing the intricacies of bird-malaria-microbiota interactions may prove helpful in determining key microbial players and informing interventions to improve animal health.

Avian malaria infection has been known to affect host microbiota, but the impact of Plasmodium infection on the colonization resistance in bird gut microbiota remains unexplored. This study investigated the dynamics of Plasmodium relictum infection in canaries, aiming to explore the hypothesis that microbiota modulation by P. relictum would reduce colonization resistance. Canaries were infected with P. relictum, while a control group was maintained. The results revealed the presence of P. relictum in the blood of all infected canaries. Analysis of the host microbiota showed no significant differences in alpha diversity metrics between infected and control groups. However, significant differences in beta diversity indicated alterations in the microbial taxa composition of infected birds. Differential abundance analysis identified specific taxa with varying prevalence between infected and control groups at different time points. Network analysis demonstrated a decrease in correlations and revealed that P. relictum infection compromised the bird microbiota’s ability to resist the removal of taxa but did not affect network robustness with the addition of new nodes. These findings suggest that P. relictum infection reduces gut microbiota stability and has an impact on colonization resistance. Understanding these interactions is crucial for developing strategies to enhance colonization resistance and maintain host health in the face of parasitic infections.

Studies on the microbiota of ticks have promoted hypotheses about the combined effects of the bacterial community, its functional contributions to the tick’s physiology or probable competition effects with some tick-borne pathogens. However, knowledge on the origin of the microbiota of newly hatched larvae is missing. This study aimed to elucidate the source(s) of the microbiota in unfed tick larvae, addressing the composition of the “core microbiota” and the best ways to decontaminate eggs for microbiota studies. We applied laboratory degree bleach washes and/or ultraviolet light treatments on engorged Rhipicephalus australis females and/or their eggs. No significant effects of these treatments on the reproductive parameters of females and the hatching rates of eggs were observed. However, the different treatments did show striking effects on the composition of the microbiota. The results indicated that bleach washes disrupted the internal tick microbiota in females, implying that bleach may have entered the tick and subsequently affected the microbiota. Furthermore, the analyses of results demonstrated that the ovary is a main source of tick microbiota, while the contribution of Gené’s organ (a part of the female reproductive system that secretes a protective wax coat onto tick eggs) or the male’s spermatophore requires further investigation. Further studies are needed to identify best practice protocols for the decontamination of ticks for microbiota studies. Graphical Abstract

Xylella fastidiosa is a vector-borne plant vascular bacterial pathogen that causes several economically important diseases, including Pierce’s disease (PD) in grapevine and olive quick decline syndrome (OQDS) in olive trees, among others

Ticks, particularly Ixodes ricinus , are significant vectors of pathogens such as Borrelia spp. and tick‐borne encephalitis virus (TBEV), which cause Lyme borreliosis (LB) and tick‐borne encephalitis (TBE), respectively. Understanding how these pathogens interact within the tick microbiome is essential for developing vector control strategies. This study investigates the impact of Borrelia afzelii and TBEV, as well as their coinfection, on the microbiota composition and structure of I. ricinus nymphs. Using a network‐based approach, we analyzed the microbial communities of ticks exposed to infected or coinfected mice. DNA extracted from newly molted nymphs was sequenced for the bacterial 16S rRNA gene, and microbial diversity metrics (alpha and beta diversity) were calculated. Our results showed that TBEV infection increased microbiome diversity compared to the uninfected and Borrelia groups. Co‐occurrence network analyses revealed that while microbial structures remained consistent across conditions, TBEV‐infected networks exhibited higher robustness to perturbations, indicating a stabilizing effect on the tick microbiome. Furthermore, the hierarchical position and associations of Borrelia varied significantly depending on the infection scenario, highlighting its adaptive role within the tick microbiota. The study demonstrates that pathogen presence alters tick microbial dynamics, with TBEV enhancing stability, suggesting virus‐mediated modifications of the microbiome. These findings advance our understanding of pathogen–tick–microbiome interactions and provide insights into the ecological mechanisms underlying pathogen coexistence within ticks. This research underscores the importance of microbial networks in ticks and offers new perspectives for targeted approaches in managing tick‐borne diseases.

Modulation du microbiote des vecteurs pour le contrôle des pathogènes vectoriels: Le cheptel corse, composé d'ovins, de caprins, de porcins et de bovins, est principalement élevé dans des systèmes d'élevage extensifs. Les interactions fréquentes entre le bétail, la faune sauvage et les populations humaines favorisent donc la circulation des tiques et des micro-organismes transmis par les tiques. Une forte prévalence de bactéries transmises par les tiques des familles Rickettsiaceae et Anaplasmataceae a été signalée chez les chèvres (Anaplasma ovis), les moutons (A. ovis), les bovins (Anaplasma marginale, Anaplasma phagocytophilum et Ehrlichia minasensis) et les tiques (Rickettsia spp.) en Corse. Certaines de ces bactéries (par exemple, A. phagocytophilum et Rickettsia sp.) sont zoonotiques et pathogènes pour l'homme. Actuellement, il n'existe pas de mesures préventives pour le contrôle des tiques et des maladies transmises par les tiques. Le microbiome des tiques est un ensemble très complexe de micro-organismes en interaction qui ont un impact sur la physiologie des tiques et leur compétence vectorielle. Récemment, nous avons montré que les vaccins anti-microbiote des tiques peuvent produire une mortalité élevée chez celles-ci pendant leur alimentation. Les vaccins anti-microbiotiques peuvent également moduler le microbiome des tiques et peuvent donc être utilisés comme outil de contrôle de la transmission des pathogènes transmis par les tiques. Dans ce projet, nous utiliserons le séquençage de nouvelle génération des amplicons 16S pour étudier la diversité taxonomique et fonctionnelle du microbiome de Rhipicephalus bursa et Hyalomma marginatum, les principales tiques vectrices de pathogènes chez le bétail en Corse. En utilisant les réseaux de co-occurrence et la détection à haut débit des pathogènes, nous identifierons ensuite les bactéries clés interagissant avec les pathogènes détectés transmis par les tiques. Les bactéries clés de voûte seront utilisées pour formuler des vaccins anti-microbiotiques afin de bloquer l'acquisition et/ou la transmission des pathogènes.