Can gut microbiota analysis be beneficial for ex-situ and in-situ conservation of threatened animal species?

Ex-situ conservation and the in-situ conservation of natural habitats are the tools to conserve biodiversity. Habitats and ecosystems have been becoming altered by human activities and a growing number of species requires form of management to ensure their survival. Conservation queries become more complex and urgent. Developing scientifically based and innovative approaches to ex-situ conservation is necessary. Recent studies underline importance of gut microbiome in animal health with implications for animal conservation and management. Animal and human studies have demonstrated that environmental factors can impact gut microbiome composition. Within this scenario, the present work focused on species belonging to different taxa, reptiles and mammals: Aldabrachelys gigantea, the giant tortoise of the Seychelles islands and Indri indri, the greatest leaving lemur of Madagascar. The Seychelles giant tortoise is vulnerable species with declining population, whereas the indri is a critically endangered species that could reach the extinction within 25 years. Both need research to help them to survive. Tortoises live for very long time and to observe how they can afford the environmental changes is very difficult. Indris, instead, are able to survive only in a small area of the Madagascar forest, with a very strong link between the species’ survival and the environment. The obtained results underline importance of environmental factors, both in-situ and ex-situ, for species conservation. Microbiome could help the organisms to respond on a short timescale and cope with, environmental changes. However, species with long generation time might not be able to adapt to fast changes but bacteria with a short generation time can adapt on a shorter timescale allowing the host to cope with fluctuating environment. Gut microbiome plays an important role in an animal’s health and has the potential to improve the management of individuals under human care for conservation purposes.

Beyond pollinator reward: steps forward and knowledge gaps on the role of floral nectar in plant-animal interactions.

The work done within the framework of my PhD project has been carried out between November 2019 and January 2023 at the Department of Biological, Geological and Environmental Sciences of the University of Bologna, under the supervision of Prof. Marta Galloni and PhD Gherardo Bogo. A period of three months was spent at the Natural History Museum of Rijeka, under the supervision of Prof. Boštjan Surina. The main aim of the thesis was to investigate further the so-called pollinator manipulation hypothesis, which states that when a floral visitor gets in contact with a specific nectar chemistry, the latter affects its behavior of visit on flowers, with potential repercussions on the plant reproductive fitness. To the purpose, the topic was tackled by means of three main approaches: field studies, laboratory assessments, and bibliographic reviews. This research project contributes to two main aspects. First, when insects encounter nectar-like concentrations of a plethora of secondary metabolites in their food-environment, various aspects of their behavior relevant to flower visitation can be affected. In addition, the results I gained confirm that the combination of field studies and laboratory assessments allows to get more realistic pictures of a given phenomenon than the single approaches. Second, reviewing the existent literature in the field of nectar ecology has highlighted how crucial is to establish the origin of nectar biogenic amines to either confirm or reject the multiple speculations made on the role of nectar microbes in shaping plant-animal interactions.

Modelling, simulations and monitoring for sustainable plant and animal production systems through precision technique

Protected crop production is a modern and innovative approach to cultivating plants in a controlled environment to optimize growth, yield, and quality. This method involves using structures such as greenhouses or tunnels to create a sheltered environment. These productive solutions are characterized by a careful regulation of variables like temperature, humidity, light, and ventilation, which collectively contribute to creating an optimal microclimate for plant growth. Heating, cooling, and ventilation systems are used to maintain optimal conditions for plant growth, regardless of external weather fluctuations. Protected crop production plays a crucial role in addressing challenges posed by climate variability, population growth, and food security. Similarly, animal husbandry involves providing adequate nutrition, housing, medical care and environmental conditions to ensure animal welfare. Then, sustainability is a critical consideration in all forms of agriculture, including protected crop and animal production. Sustainability in animal production refers to the practice of producing animal products in a way that minimizes negative impacts on the environment, promotes animal welfare, and ensures the long-term viability of the industry. Then, the research activities performed during the PhD can be inserted exactly in the field of Precision Agriculture and Livestock farming. Here the focus is on the computational fluid dynamic (CFD) approach and environmental assessment applied to improve yield, resource efficiency, environmental sustainability, and cost savings. It represents a significant shift from traditional farming methods to a more technology-driven, data-driven, and environmentally conscious approach to crop and animal production. On one side, CFD is powerful and precise techniques of computer modeling and simulation of airflows and thermo-hygrometric parameters, that has been applied to optimize the growth environment of crops and the efficiency of ventilation in pig barns. On the other side, the sustainability aspect has been investigated and researched in terms of Life Cycle Assessment analyses.

New insights into vaginal environment during pregnancy: a multi-omics approach

The present thesis aims to provide a thorough comprehension of the vaginal ecosystem of pregnant women and enhance the knowledge of pregnancy pathophysiology. The first study emphasized the importance of limiting protein intake from animal sources, consuming carbohydrates, and avoiding starting pregnancy overweight to maintain a healthy vaginal environment characterized by lactobacilli and related metabolites. In the second paper, a reduction in bacterial diversity, an increase in Lactobacillus abundance, and a decrease in bacterial vaginosis-related genera were observed during pregnancy. Lactobacillus abundance correlated with higher levels of lactate, sarcosine, and amino acids, while bacterial vaginosis-related genera were associated with amines, formate, acetate, alcohols, and short-chain fatty acids. An association between intrapartum antibiotic prophylaxis for Group B Streptococcus and higher vaginal abundance of Prevotella was found. Moreover, women experiencing a first-trimester miscarriage displayed a higher abundance of Fusobacterium. The third study explored the presence of macrolides and tetracyclines resistance genes in the vaginal environment, highlighting that different vaginal microbiota types were associated with distinct resistance profiles. Lactobacilli-dominated ecosystems showed fewer or no resistance genes, while women with increased bacterial vaginosis-related genera were positive for resistance genes. The last two papers aimed to identify potential biomarkers of vaginal health or disease status. The fourth paper showed that positivity for Torquetenovirus decreased from the first to the third trimester, being more prevalent in women with higher vaginal leukocyte counts. Torquetenovirus-positive samples showed higher levels of cytokines, propionate, and cadaverine. Lactobacillus species decreased in Torquetenovirus-positive samples, while Sneathia and Shuttleworthia increased. The last work pointed out the association between clade 2 of Gardnerella vaginalis and bacterial vaginosis. Moreover, as the number of simultaneously detected G. vaginalis clades increased, bacterial vaginosis-associated bacteria also tended to increase. Additionally, sialidase gene levels negatively correlated with Lactobacillus and positively correlated with Gardnerella, Atopobium, Prevotella, Megasphaera, and Sneathia.