Biology subjects

Casiraghi, M.

Publications and source records attributed to Casiraghi, M..

5 recordsLinked to original sources

bioRxiv2021

SKIOME Project: a curated collection of skin microbiome datasets enriched with study-related metadata

Large amounts of data from microbiome-related studies have been (and are currently being) deposited on international public databases. These datasets represent a valuable resource for the microbiome research community and could serve future researchers interested in integrating multiple datasets into powerful meta-analyses. However, this huge amount of data lacks harmonization and is far from being completely exploited in its full potential to build a foundation that places microbiome research at the nexus of many subdisciplines within and beyond biology. Thus, urges the need for data accessibility and reusability, according to FAIR (Findable, Accessible, Interoperable, and Reusable) principles, as supported by National Microbiome Data Collaborative and FAIR Microbiome. To tackle the challenge of accelerating discovery and advances in skin microbiome research, we collected, integrated and organized existing microbiome data resources from human skin 16S rRNA amplicon sequencing experiments. We generated a comprehensive collection of datasets, enriched in metadata, and organized this information into data frames ready to be integrated into microbiome research projects and advanced post-processing analysis, such as data science applications (e.g. machine learning). Furthermore, we have created a data retrieval and curation framework built on three different stages to maximize the retrieval of datasets and metadata associated with them. Lastly, we highlighted some caveats regarding metadata retrieval and suggested ways to improve future metadata submissions. Overall, our work resulted in a curated skin microbiome datasets collection accompanied by a state-of-the-art analysis of the last 10 years of the skin microbiome field.

bioinformatics↗

bioRxiv2021

Newly developed ad hoc molecular assays shows how eDNA can witness and anticipate the monk seal recolonization of central Mediterranean

The monk seal Monachus monachus is the most endangered pinniped worldwide and the only one found in the Mediterranean, where its distribution and abundance have suffered a drastic decline in the last few decades. Data on its status are scattered due to both its rarity and evasiveness, and records are biased towards occasional, mostly coastal, encounters. Nowadays molecular techniques allow us to detect and quantify minute amounts of DNA traces released in the environment (eDNA) by any organism. We present three qPCR-assays targeting the monk seal mitogenome. The assays were soundly tested on an extensive and diversified sample set (n=73), including positive controls from Madeira breeding population collected during the peak of abundance, and two opportunistic Mediterranean eDNA-sample collections (offshore/coastal) from on-going projects. Monk seal DNA was detected in 47.2% and 66.7% of the samples collected in the Tyrrhenian from a ferry platform (2018-2019) and in the Pelagie archipelago -Strait of Sicily- (2020) respectively, anticipating (up to 2 year) visual observations occurred subsequently in proximity of the sampled areas. In the Tyrrhenian, detection occurrence increased between 2018 and 2019. Monk seal DNA recoveries were commoner in night-time ferry-samples, suggesting nocturnal predatory activity in pelagic waters. The proposed technique provides a non-invasive and yet highly-sensitive tool for defining the monk seal actual distribution and home range, its recovery rate and pinpoint coastal/offshore localities where prioritizing conservation, research, citizen science and education initiatives.

molecular biology↗

bioRxiv2021

EFFECTS OF LAND-USE INTENSIFICATION AND ENVIRONMENTAL STRESSORS ON INTRASPECIFIC FUNCTIONAL TRAITS VARIABILITY IN BUMBLEBEES

The way urbanization shapes the intraspecific variation of pollinator functional traits is little understood. However, this topic is relevant for investigating ecosystem services and pollinator health. Here, we studied how urbanization affects the functional traits of workers in two bumblebee species (Bombus terrestris and B. pascuorum) sampled in 37 sites along a gradient of urbanization in North Italy (an area of 1800 km2 including the metropolitan context of Milan and other surrounding capital districts). Namely, we investigated the role played by land-use composition, configuration, temperature, flower resource abundance, and air pollutants on the variation of traits related to flight performance (i.e., body size, wing shape and size fluctuating asymmetry). These traits are relevant because they are commonly used as indicators of stress during insect development. The functional traits of the two bumblebees responded idiosyncratically to urbanization. Urban temperatures were associated with smaller wing sizes in B. pascuorum and with more accentuated fluctuating asymmetry of wing size in B. terrestris. Moreover, flower abundance correlated with bigger wings in B. terrestris and with less asymmetric wing sizes in B. pascuorum. Other traits did not vary significantly and other urban variables played minor effects. These patterns highlight that environmental stressors linked to urbanization negatively impact traits related to flight performance and development stability of these species with possible consequences on the pollination service they provide. Overall, this study found species-specific variation patterns in syntopic taxa, expanding our understanding about the effects of anthropic disturbance in shaping relevant functional traits of pollinator model species.

ecology↗

bioRxiv2020

ExTaxsI: an exploration tool of biodiversity molecular data

BackgroundThe increasing availability of multi omics data is leading to continually revise estimates of existing biodiversity data. In particular, the molecular data enable to characterize novel species yet unknown and to increase the information linked to those already observed with new genomic data. For this reason, the management and visualization of existing molecular data, and their related metadata, through the implementation of easy to use IT tools have become a key point for the development of future research. The more users are able to access biodiversity related information, the greater the ability of the scientific community to expand the knowledge in this area. ResultsIn our research we have focused on the development of ExTaxsI (Exploring Taxonomies Information), an IT tool able to retrieve biodiversity data stored in NCBI databases and provide a simple and explorable visualization. Through the three case studies presented here, we have shown how an efficient organization of the data already present can lead to obtaining new information that is fundamental as a starting point for new research. Our approach was also able to highlight the limits in the distribution data availability, a key factor to consider in the experimental design phase of broad spectrum studies, such as metagenomics. ConclusionsExTaxI can easily produce explorable visualization of molecular data and its metadata, with the aim to help researchers to improve experimental designs and highlight the main gaps in the coverage of available data.

bioinformatics↗

bioRxiv2020

Italian Odonates in the Pandora's Box: A Comprehensive DNA Barcoding Inventory Shows Taxonomic Warnings at the Holarctic Scale

The Odonata are considered among the most endangered freshwater faunal taxa. Their DNA-based monitoring relies on validated reference datasets that are often lacking or do not cover important biogeographical centres of diversification. This study presents the results of a DNA barcoding campaign on Odonata, based on the standard 658 bp 5 end region of the mitochondrial COI gene, involving the collection of 812 specimens (409 of which barcoded) from peninsular Italy and its main islands (328 localities), belonging to all the 88 species (31 Zygoptera and 57 Anisoptera) known from the country. Additional BOLD and GenBank data from Holarctic samples expanded the dataset to 1294 DNA barcodes. A multi-approach species delimitation analysis involving two distance (OT and ABGD) and four tree-based (PTP, MPTP, GMYC, bGMYC) methods were used to explore these data. Of the 88 investigated morphospecies, 75 (85%) unequivocally corresponded to distinct Molecular Operational Units, whereas the remaining ones were classified as warnings (i.e., showing a mismatch between morphospecies assignment and DNA-based species delimitation). These results are in contrast with other DNA barcoding studies on Odonata showing up to 95% of identification success. The species causing warnings were grouped in three categories depending on if they showed low, high, or mixed genetic divergence patterns. The analysis of haplotype networks revealed unexpected intraspecific complexity at the Italian, Palearctic, and Holarctic scale, possibly indicating the occurrence of cryptic species. Overall, this study provides new insights into the taxonomy of odonates and a valuable basis for future DNA and eDNA-based monitoring studies.

zoology↗