Biology subjects

Labra, M.

Publications and source records attributed to Labra, M..

9 recordsLinked to original sources

bioRxiv2024

Data Hunters: bridging bioinformatics education and microbiome research

Vast sequencing data in public repositories offer researchers unprecedented opportunities for gaining insights through reanalysis and machine learning approaches, thereby advancing the microbiology field. However, the lack of standardized metadata poses a significant obstacle to big data reuse, necessitating advanced bioinformatics skills for curation and integration. To tackle this challenge, we organized the Data Hunters Workshop, enabling extensive human skin microbiome metadata curation through student community engagement. The Data Hunters Workshop constitutes a student-science initiative within the University of Milano-Bicocca, Italy. Integrating theoretical and hands-on phases, the workshops structure included a 6-hour lecture, covering metagenomics and metadata manipulation fundamentals, followed by an interactive practical phase designed as a learn-and-play activity. This phase was supported by in-house developed educational online and command-line resources, facilitating students acquisition of Python commands for managing microbiome metadata. Upon the workshops conclusion, its effectiveness was assessed through surveys and standardized evaluation scales. Twenty-nine students addressed the critical challenge of metagenomics metadata standardization. Workshops resources have equipped students with foundational knowledge in metagenomics and Python programming, empowering them to curate metadata from 379 amplicon-based and shotgun sequencing projects of the human skin microbiome. The collaborative endeavors of these students will ensure the construction of a curated metadata collection. The Data Hunters Workshop established a reusable model for similar educational aims, facilitating metagenomics and bioinformatics teaching and metadata curation. It bridged education and microbiome research by focusing on human skin microbiome metadata curation, ultimately striving to construct a specific collection promptly accessible to researchers.

scientific communication and education↗

bioRxiv2023

MADAME: a user-friendly bioinformatic tool for data and metadata retrieval in microbiome research

Microbiome research advancements have provided countless insights. Despite the massive amount of data currently stored in public repositories, these resources remain vastly underutilized due to the intricacy of data and metadata retrieval from these databases. However, leveraging data-driven approaches is crucial for microbiome research progress by overcoming variations between studies and identifying generalizable trends. We designed the open-access and user-friendly bioinformatic tool MADAME (MetADAta MicrobiomE) to streamline the data and metadata retrieval process. MADAME addresses the challenges posed by the public repositories current limitations, allowing users to retrieve publications associated with the accession codes of interest. Additionally, MADAME allows users to visually explore retrieved results through the generation of a comprehensive report with plots and statistics. These unique features of MADAME let users maximize their time and resources, enabling them to assess metadata suitability before pursuing data download. To showcase its diverse functionalities, we recreate several scenarios to meet the diverse requirements that researchers may have.

bioinformatics↗

bioRxiv2022

Mimicking orchids lure bees from afar with exaggerated ultraviolet signals

O_LIFlowers have many sensory traits to appeal to pollinators, including ultraviolet (UV) absorbing markings, which are well known for attracting bees at close proximity (e.g. < 1 m). While striking UV signals have been thought to attract pollinators also at greater distances of meters, how the signals impact the plant pollination success over distance remains unknown. Here we report the case of the Australian orchid Diuris brumalis, a non-rewarding species, pollinated by bees via mimicry of rewarding pea plant Daviesia decurrens. When distant from the pea plant, Diuris brumalis was hypothesized to enhance pollinator attraction by exaggerately mimicking the floral ultraviolet (UV) reflecting patterns of its model. C_LIO_LIBy experimentally modulating floral UV reflectance with a UV screening solution, we quantified the orchid pollination success at variable distance from the model plants. C_LIO_LIWe demonstrate that the deceptive orchid Diuris brumalis attracts bee pollinators by emphasizing the visual stimuli, which mimic the floral UV signalling of the rewarding model D. decurrens. Moreover, the exaggerated UV reflectance of D. brumalis flowers impacted pollinators visitation at an optimal distance from D. decurrens, and the effect decreased when orchids were too close or too far away from the model. C_LIO_LIOur findings show that salient UV flower signalling plays a functional role in visual floral mimicry, likely exploiting perceptual gaps in bee neural coding, and mediates the plant pollination success at much greater spatial scales than previously expected. C_LI

ecology↗

bioRxiv2022

Dealing with the promise of metabarcoding in mega-event biomonitoring: EXPO2015 unedited data

As human activities on our planet persist, causing widespread and irreversible environmental degradation, the need to biomonitor ecosystems has never been more pressing. These circumstances have required a renewal in monitoring techniques, encouraged by necessity to develop more rapid and accurate tools which will support timely observations of ecosystem structure and function. The World Exposition (from now EXPO2015) hosted in Milan from May to October 2015 was a global event that could be categorized as a mega-event, which can be defined as an acute environmental stressor, possibly generating biodiversity alteration and disturbance. During the six months of EXPO2015, exhibitors from more than 135 countries and 22 million visitors insisted on a 1.1 million square meters area. Faced with such a massive event, we explore the potential of DNA metabarcoding using three molecular markers to improve the understanding of anthropogenic impacts in the area, both considering air and water monitoring. Furthermore, we explore the effectiveness of the taxonomy assignment phase considering different taxonomic levels of analysis and the use of data mining approaches to predict sample origin. Unless the degree of taxa identification still remains open, our results showed that DNA metabarcoding is a powerful genomic-based tool to monitor biodiversity at the microscale, allowing us to capture exact fingerprints of specific event sites and to explore in a comprehensive manner the eukaryotic community alteration. With this work, we aim to disentangle and overcome the crucial issues related to the generalization of DNA metabarcoding in order to support future applications.

molecular biology↗

bioRxiv2021

City climate and landscape structure shape pollinators, nectar and transported pollen along a gradient of urbanization

O_LIUrbanization gradients influence both landscape and climate and provide opportunity for understanding how species, especially plants and pollinators, respond to artificially driven environmental transitions. C_LIO_LIHere, we investigated several aspects of pollination along an urbanization gradient in landscape and climate. We quantified wild hoverfly and bee abundances with trapping, standing crop of nectar with spectrophotometer, and the pollen transported by flower-visitors with DNA-metabarcoding, in 40 independent sites from seminatural to built-up areas in Northern Italy. C_LIO_LILinear and nonlinear relationships were detected along the urbanization gradient. Pollinator abundances increased until 22% of impervious surface, dropping by 34% after that, and it also decreased with green patch distance and urban park size. Thus, suburban landscapes host more pollinators than highly cemented or seminatural areas. Moreover, pollinators diminished by up to 45% in areas with low temperature seasonality: urbanized areas likely posing thermic stress. Furthermore, the sugar mass available in nectar increased by 91% with impervious cover, indicating that city nectars were less consumed or flowers more productive. Furthermore, the species richness of pollen decreased by 32% in highly urbanized areas, and with a high incidence of exotic plants, hinting for anthropized plant communities. C_LIO_LISynthesis and applications. Urbanization influences pollinator abundances, nectar resources and transported pollen. Pollinators are negatively affected by a thermally harsh climate in highly urbanized areas with isolated green areas and large parks. Suburban landscapes demonstrated the highest pollinator presence. In the city core, flowers contained more nectary sugar, while pollinators collected pollen from a small number of plants, mainly exotic. These findings highlight the influence of urban landscape structure and climate on pollinators and plants, showing that cities are heterogenous realities. Patterns from this study will serve as basis for pollinator-friendly planning and management of urban landscapes. C_LI

ecology↗

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

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

Tasting the differences: microbiota analysis of different insect-based novel food

Traceability, quality and safety of edible insects are important both for the producers and the consumers. Today, alongside the burst of edible insects in western countries, we are facing a gap of knowledge of insect microbiota associated with the microbial ecosystems of insect-based products. Recent studies suggest that the insect microbiota can vary between insect species and that can be shaped by additional factors, such as rearing conditions. Also, the production processes of raw materials (i.e. insect flour) into final food products can affect the insect microbiota too. This has consequences for the evaluation of food safety and food traceability. In this context, High-Throughput DNA Sequencing (HTS) techniques can give insight into the carryover of insect microbiota into final food products. In this study, we investigated the microbiota composition of insect-based commercial food products, applying HTS techniques coupled with bioinformatic analysis. The aim of this work was to analyse the microbiota variability of different categories of insect-based products made of A. domesticus (house cricket), T. molitor (mealworm beetle), and A. diaperinus (lesser mealworm or litter beetle), including commercial raw materials and processed food items, purchased via e-commerce from different companies. Our data revealed that samples cluster per insect species based on microbiota profile and preliminary results suggested that a small number of prevalent bacteria formed a "core microbiota" characterizing the products depending on the insect, suggesting that a resident microbiota is conserved. This microbial signature can be recognized despite the different food processing levels, rearing conditions selling companies. We showed that differences exist when comparing raw vs processed food made of the same insect, or similar products produced by different companies as well, laying the groundwork for further analyses. These results support the application of HTS analysis for studying the composition of processed insect food in a wider perspective, for food traceability and food quality control.

microbiology↗

bioRxiv2019

Does a strong reduction of colony workforce affect the foraging strategy of a social pollinator?

The way pollinators gather resources may play a key role for buffering their population declines. Social pollinators like bumblebees could adjust their foraging after significant workforce reductions to keep provisions to the colony optimal, especially in terms of pollen quality, diversity, and quantity. To test what effects a workforce reduction causes on the foraging for pollen, colonies of the bumblebee Bombus terrestris were experimentally manipulated in field by removing half the number of workers. The pollen pellets of the workers were taxonomically identified with DNA metabarcoding, a ROC approach was used to filter out underrepresented OTUs, and video cameras and network analyses were employed to investigate foraging strategies and behaviour. The results suggested that the plant diversity in the pollen pellets was high but plant identity and pollen quantity traits were influenced mainly by plant phenology. During the experiment, although the treated colonies increased foraging effort in relation to control nests, only minor changes in the diet breadth and in the other node-level and network-level indices were observed after workforce removal. Therefore, a consistency in the bumblebees feeding strategies emerges despite the lowered workforce, which questions the ability of social pollinators to adjust their foraging in the field.

ecology↗