(Marie Skłodowska-Curie Actions MSCA) The current global biodiversity crisis requires rapid, inexpensive and reliable methods of detecting the main threats to species’ survival: pathogens, habitat change, and loss of genetic diversity1. Equally crucial are solutions for stemming biodiversity loss: we lack vital models that determine how these threats interact, which would help prioritise conservation efforts. Recently, CRI-CG has discovered for one species of frog over a relatively small geographic area that eDNA extracted from water samples captures more genetic diversity than analyses using tissue samples (UNESCO-funded project ACQUAVIVA). The same eDNA can be used to detect amphibian pathogens. NIPMAP will apply this knowledge in an innovative way by: i) optimizing this eDNA approach to estimate mtDNA diversity in four amphibian taxa (two caudates, two anurans) and pathogen diversity (principal pathogens: Bd, Bsal, Rv) across the eastern Italian Alps; ii) using these data to inform individual-based and spatially explicit simulations of host movements and pathogen transmission37; iii) integrating parameters from i-ii with skin microbiota and other health indices, as well as iv) environmental variables at each sample site, to generate correlative models (e.g. GLMMs and SDMs) and potential distribution maps to direct conservation management decisions. We will also pilot two innovative eDNA protocols: one to measure nuclear DNA diversity (to measure current gene flow and dispersal rates) and one to understand microbiota function using metatranscriptomics. These interdisciplinary tools will be integrated into a workflow that will be applicable to animal taxa anywhere on the planet.

(MIUR PRIN) Obiettivo generale del progetto è lo studio della co-evoluzione genomico della popolazione umano della Val Rendena e la razza bovina Rendena. Questo progetto è una continuazione della collaborazione a lungo termine sulla genomica della Razza Rendena con UNIPV e UNICATT (vedi progetto di dottorato RENDENAGEN).

Attività FEM:
Partecipazione all'interpretazione dei risultati dal punto di vista genomico, storico e antropologico; stesura pubblicazioni scientifiche; disseminazione dei risultati al pubblico.

(Ministero della Salute) L’echinococcosi alveolare e le infezioni da Hantavirus sono zoonosi che costituiscono un serio problema sanitario in Europa. In entrambi i casi, si tratta di zoonosi gravi, con una letalità variabile ma non trascurabile. Ciò che le accomuna è il fatto che il loro ciclo biologico è legato ad alcuni piccoli roditori selvatici, che per Echinococcus multilocularis costituiscono gli ospiti intermedi e per Hantavirus il serbatoio naturale. La stretta relazione con tali specie, comuni ma tipicamente elusive e poco conosciute, rende complesso indagare la distribuzione e l’ecologia di questi patogeni, e a maggior ragione valutare il rischio di infezione per l’uomo. Risulta pertanto strategica un’indagine strutturata su questi ospiti, in particolare Apodemus flavicollis e Myodes glareolus, generalmente considerati il principale serbatoio per gli Hantavirus, e Arvicola amphibius, che recenti studi suggeriscono rilevante nell’eco-epidemiologia di E. multilocularis.

Attività FEM:

• WP4, Task 4.1: Genetica di popolazione di Arvicola amphibius anche in relazione alla presenza e prevalenza di E. multilocularis;
• WP1 Progettazione campionamento;
• WP3 Epidemiologia;
• WP5 Analisi del rischio.

(Horizon Europe MSCA Postdoctoral Fellowships 2022)  The biodiversity hypothesis asserts there is a link between the diversity of environmental and host-associated microbes and ‘civilization diseases', such as asthma and allergies, the result of immune dysfunction and chronic inflammation. Using a well-studied rodent model, the bank vole, SOIL2GUT will test for the first time whether exposure to natural communities of soil microbes during development can improve individual health by promoting microbiota function at the host-microbiota interface (ileum and colon mucous layers) and reduce the risk of immune-related diseases. SOIL2GUT will take advantage of tissue samples generated by an ongoing intervention experiment, promoting the 3Rs policy, but also providing a unique opportunity for ‘omics integration (metataxonomics + MTX). Innovatively, this project will focus on the function of gut flora (not merely taxonomical characterization), in both bacteria and fungi (the latter is particularly unusual), using recent developments in metatranscriptonomics (MTX) to explore functional activity, and combining metadata and metatranscriptomes in statistical models to identify critical factors determining health. Since 68% of the human population will be urbanized by 2050, SOIL2GUT will contribute significantly to the WHO OneHealth framework. This project will also provide data that can be used to plan urban greenspaces, enhance rewilding interventions and improve domestic and zoo animal wellbeing. The researcher will build on his previous experiences and solid publications as a PhD/postdoc, receiving advanced personalized training in bioinformatics and soft skills, including writing grant applications for expanding to other tissues (lung, skin), and rendering him highly employable. In exchange, the researcher will bring methods for measuring individual health and immune gene expression to the hosting lab, among others. A synergy of expertise in microbiota research is envisaged, leading to future collaborative endeavors.

Keywords:

microbial ecology, ecosystem microbiota, metatranscriptomics, wild rodent model, conservation 'omics