Biology subjects

Bruno, A.

Publications and source records attributed to Bruno, A..

16 recordsLinked to original sources

bioRxiv2026

Widespread SARS-CoV-2 infection in free-ranging Neotropical bats suggests repeated human-to-bat spillback

Bats harbor exceptional coronavirus diversity and are considered ancestral sources of several human pathogens. As SARS-CoV-2 transitioned from pandemic emergence to global endemicity in humans, concern has shifted from wildlife-to-human spillover toward reverse zoonosis. However, infection of free-ranging bat populations under natural conditions has not previously been demonstrated. Here, we report widespread detection of SARS-CoV-2 RNA in wild Neotropical bats sampled across Andean and Amazonian ecosystems of Southern Ecuador. RT-qPCR screening of 126 individuals, representing nine taxa, detected SARS-CoV-2 RNA in 34.12% of bats across multiple sites. Partial to near-complete viral genomes recovered from five individuals showed >99% nucleotide identity to contemporary human SARS-CoV-2 lineages and clustered within multiple global phylogenetic clades. Mixed-effects modeling revealed pronounced species-level heterogeneity, a positive association between elevation and infection probability, and higher infection probability in females compared with males. The close phylogenetic affinity of bat-derived genomes to circulating human variants and their distribution across multiple lineages suggest repeated anthropogenic spillback rather than sustained bat-specific circulation. These results expand current understanding of the ecological footprint of the COVID-19 pandemic and highlight the importance of integrating wildlife surveillance into long-term One Health strategies for emerging infectious diseases.

microbiology↗

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↗

bioRxiv2024

Binocular combination in the autonomic nervous system

Pupil diameters are regulated by the autonomic nervous system, which combines light signals across the eyes independently of the visual cortex. Distinct classes of retinal photoreceptor are involved in this process, with cones and rods driving the initial constriction and intrinsically photosensitive retinal ganglion cells main-taining diameter over prolonged time periods. We investigated binocular combination by targeting different photoreceptor pathways using a novel binocular multiprimary system to modulate the input spectra via silent substitution. At the first harmonic of the modulation frequency, luminance and S-cone responses showed strong binocular facilitation, and weak interocular suppression. Melanopsin responses were invariant to the number of eyes stimulated. The L-M pathway involved binocular inhibition, whereby responses to binocular stimulation were weaker than for monocular stimulation. The second harmonic involved strong interocular suppression in all pathways, but with some evidence of binocular facilitation. Our results are consistent with a computational model of binocular signal combination (implemented in a Bayesian hierarchical framework), in which the weight of interocular suppression differs across pathways. We also find pathway differences in response phase, consistent with different lag times for phototransduction. These results provide evidence that binocular interactions in the pupillary pathway differ across photoreceptor-directed modulations and across harmonic components of the response.

neuroscience↗

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↗

bioRxiv2023

Measuring the perception and metacognition of time

The ability of humans to identify and reproduce short time intervals (in the region of a second) may be affected by many factors ranging from the gender of the individual observer, through the attentional state, to the precise spatiotemporal structure of the stimulus. The relative roles of these very different factors are a challenge to describe and define; several methodological approaches have been used to achieve this to varying degrees of success. Here we describe a new paradigm affording not only a first-order measurement of the perceived duration of an interval but also a second-order metacognitive judgement of perceived time. This approach, we argue, expands the form of the data generally collected in duration-judgements and allows more detailed comparison of psychophysical behaviour to the underlying theory. We also describe a measurement model which provides estimates of the variability of the temporal estimates and the metacognitive judgments allowing comparison to an ideal observer. We fit the model to data collected for judgements of 750ms (bisecting 1500ms) and 1500ms (bisecting 3000ms) intervals across three stimulus modalities (Visual, Audio & Audiovisual). This enhanced form of data on a given interval judgement and the ability to track its progression on a trial-by-trial basis offers a way of looking at the different roles that subject-based, task-based and stimulus-based factors have on the perception of time.

neuroscience↗

bioRxiv2023

A purely visual adaptation to motion can differentiate between perceptual timing and interval timing

It is unclear whether our brain extracts and processes time information using a single centralized mechanism or through a network of distributed mechanisms, which are specific for modality and time range. Visual adaptation has previously been used to investigate the mechanisms underlying time perception for millisecond intervals. Here, we investigated whether a well-known duration aftereffect induced by motion adaptation in the sub-second range (referred to as perceptual timing), also occurs in the supra-second range (called interval timing), which is more accessible to cognitive control. Participants judged the relative duration of two intervals after spatially localized adaptation to drifting motion. Adaptation substantially compressed the apparent duration of a 600 ms stimulus in the adapted location, whereas it had a much weaker effect on a 1200 ms interval. Discrimination thresholds after adaptation improved slightly relative to baseline, implying that the duration effect cannot be ascribed to changes in attention or to noisier estimates. A novel computational model of duration perception can explain these results, and also bidirectional shifts of perceived duration after adaptation reported in other studies. We suggest that we can use adaptation to visual motion as a tool to investigate the mechanisms underlying time perception at different time scales.

neuroscience↗

bioRxiv2023

Different rules for binocular combination of luminance flicker in cortical and subcortical pathways

1How does the human brain combine information across the eyes? It has been known for many years that cortical normalisation mechanisms implement ocularity invariance: equalising neural responses to spatial patterns presented either monocularly or binocularly. Here we used a novel combination of electrophysiology, psychophysics, pupillometry and computational modelling to ask whether this invariance also holds for flickering luminance stimuli with no spatial contrast. We find dramatic violations of ocularity invariance for these stimuli, both in cortex and also in the subcortical pathways that govern pupil diameter. Specifically, we find substantial binocular facilitation in both pathways with the effect being strongest in cortex. Near-linear binocular additivity (instead of ocularity invariance) was also found using a perceptual luminance matching task. Ocularity invariance is therefore not a ubiquitous feature of visual processing, and the brain appears to repurpose a generic normalisation algorithm for different visual functions by adjusting the amount of interocular suppression.

neuroscience↗

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

IL-1α secreted by subcapsular sinus macrophages promotes melanoma metastasis in the sentinel lymph node by upregulating STAT3 signaling in the tumor.

During melanoma metastasization, tumor cells originated in the skin migrate via lymphatic vessels to the sentinel lymph node (sLN) in a process that facilitates their spread across the body. Here, we characterized the innate inflammatory responses to melanoma metastasis in the sLN. For this purpose, we confirmed the migration of fluorescent metastatic melanoma cells to the sLN and we characterized the inflammatory response in the metastatic microenvironment. We found that macrophages located in the subcapsular sinus (SSM), produce pro-tumoral IL-1 after recognition of tumor antigens. Moreover, we confirmed that the administration of an anti-IL-1 depleting antibody reduced metastasis. Conversely, the administration of recombinant IL-1 accelerated the lymphatic spreading of the tumor. Additionally, the elimination of the macrophages significantly reduced the progression of the metastatic spread. To understand the mechanism of action of IL-1 in the context of the lymph node microenvironment, we applied single-cell RNA sequencing to dissected metastases obtained from animals treated with an anti-IL-1 blocking antibody. Amongst the different pathways affected, we identified STAT3 as one of the main targets of IL-1 signaling in metastatic cells. Moreover, we found that the anti-IL-1 anti-tumoral effect was not mediated by lymphocytes, as IL-1R1 KO mice did not show any improvement in metastasis growth. Finally, we found a synergistic anti-metastatic effect of the combination of IL-1 blocking and the STAT3 inhibitor (STAT3i) stattic. In summary, we described a new mechanism by which SSM support melanoma metastasis, highlighting a new target for immunotherapy.

immunology↗

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

A polyphenol-rich extract of Olive Mill Wastewater Enhances cancer chemotherapy effects while mitigating cardiac toxicity.

BackgroundCardiovascular toxicities still remain one of the most undesirable side effects in cancer patients receiving chemotherapy, and cardiotoxicity has been detected associated with many therapeutic regimens. A number of mechanisms are reported for these effects, some of which are related to inflammation, oxygen radical generation, mitochondrial damage. Extra-virgin olive oil (EVOO) is rich in cancer preventive polyphenols endowed with anti-inflammatory, antioxidant activities which could exert protective effects on the heart cells. One very interesting derivative of EVOO preparation is represented by purified extract form waste waters. Here, we investigated the anti-cancer activity when combined with chemotherapeutics as well as potential cardioprotective activities of a polyphenol-rich extract from waste product of the EVOO, named A009. Methods and ResultsMice bearing prostate cancer (PCa) xenografts were treated with cisplatin with and without A009. Tumor cell growth was reduced by cis and by A009 and further hindered by the combination. The effects of the A009 extract on cardiovascular toxicities was investigated in vivo. Hearts of mice were analyzed, and the mitochondria were studied by transmission electron microscopy. A protection activity by A009 was observed. To confirm the in vivo data obtained with cisplatin therapy, tumor cell lines and rat cardiomyocytes were treated with cisplatin in vitro with and without A009. A009 enhanced cisplatin and 5FU reduced cancer cell growth while did not further affect co-treated rat cardiomyocytes. Another frequently used chemotherapeutic agent 5-fluorouracil (5FU), was also tested in this assay a similar effects were observed. The cardioprotective effects of the A009 extract towards 5 FU chemotherapy were further investigated in a second system of in vitro cultures, on cardiomyocytes freshly isolated from mice pups. These cells were treated with 5-fluorouracil and A009. Wastewater extract mitigated toxicity of the fluorpyrimidine. ConclusionsIn vivo, we found synergisms of A009 and cisplatin in prostate cancer treatment. Hearts of mice xenografted with PCa cell lines and receiving co-treatments of A009 extracts along with cisplatin had reduced mitochondria damage compared to chemotherapy alone, indicating a cardioprotective role. A009 in vitro was additive to cisplatin and 5FU to reduce cancer cell growth while did not further affect rat cardiomyocytes cell cultures treated with cisplatin and 5FU. The A009 extract also rescued the proliferation rate of neonatal murine cardiomyocytes treated with 5-Fluorouracil. Our study demonstrates that the polyphenol rich purified A009 extracts enhances the effect of chemotherapy in vitro and in vivo but mitigates effects on heart and heart cells. It could therefore represent a potential candidate for cardiovascular prevention in patients undergoing cancer chemotherapy.

cancer biology↗

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↗

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

Prostate cancer peripheral blood NK cells show enhanced CD9, CD49a, CXCR4, CXCL8, MMP-9 production, and secrete monocyte-recruiting and polarizing factors

ABSTRACTBackground Natural killer (NK) cells are effector lymphocytes of the innate immunity. Two major NK cell subsets are mostly present in the peripheral blood (pNKs): the cytotoxic CD56dimCD16+ NK cell subset (90-95% of pNKs), and the low cytotoxic, highly cytokine-producing CD56brightCD16-/low NK cell subset (5-10% of pNKs). It has been demonstrated that NK cells in peripheral blood of patients with several tumors are altered. We have shown that in NSCLC and colon cancer, tumor associated circulating NK (pTA-NK) and tumor infiltrating NK (TI-NK) are skewed towards the CD56brightCD16-/low phenotype. We have detected the production of pro-inflammatory and pro-angiogenic cytokines and chemokines. Other groups are reporting similar observations. There is still a lack of knowledge concerning the phenotype of pNK cells in prostate cancer (PCa). Here, we phenotypically and functionally characterized peripheral blood NK (pNK) from PCa patients (PCa pTA-NKs) and investigated their production of soluble factors, with endothelial cells and macrophage stimulatory action.Methods NK cell subset distribution was investigated in the peripheral blood of PCa patients, by multicolor flow cytometry (FC) for surface antigens expression. Protein arrays were performed to characterize the secretome on FACS-sorted pNK cells. Secreted products from FACS-sorted PCa TA-NKs were used to characterize their production of pro-inflammatory molecules. Secreted products from FACS-sorted PCa pTA-NKs were also used to stimulate endothelial cells and monocytes and macrophages, determining their ability to recruit and polarize them. Alterations of endothelial cells and monocytes, following exposure to secreted products from FACS-sorted PCa pTA-NKs, was assessed by RT-PCR. To confirm these observations, secreted products from 3 different PCa (PC-3, DU-145, LNCaP) cell lines were used to assess their effects on human NK cell polarization, by multicolor flow cytometry.Results Circulating NK cells from prostate cancer patients have been studied before, mostly for their impaired lytic functions. However, here we are the first to report that circulating pNK cells from PCa patients acquire a CD56brightCD9+CD49a+CXCR4+ phenotype with pro-inflammatory properties. We observed a similar polarization of heathy-donor derived pNK cells exposed to secreted products of three different PCa cell lines. Increased production of CXCL8, CXCR4, MMP-9, pro-inflammatory and reduced production of TNFα, IFNγ and Granzyme-B was detected. PCa TA-NKs released factors able to support angiogenesis in vitro and increased the expression of CXCL8, ICAM-1 and VCAM-1 mRNA in endothelial cells, confirming a pro-inflammatory signature. Secretome analysis revealed the ability of PCa pTA-NKs to release pro-angiogenic cytokines/chemokines involved in monocyte recruitment and M2-like polarization. In experimental setting, secreted products from PCa pTA-NKs can recruit THP-1 monocyte and polarize THP-1-differentiated macrophage towards CD206/Arginase1/IL-10/CXCL8-expressing M2-like/TAMs.Conclusions Our results show that PCa pTA-NKs are effector cells able to produce pro-inflammatory angiogenesis factors able to stimulate endothelial cells, attract monocytes and polarize macrophage to an M2-like type. Our data provides a rationale for the possible use of pNK profiling in clinical studies on PCaGraphical Abstract: Representative cartoon illustrating the pro-angiogenic features of PCa pTA-NKs.A) direct effects of PCa pTA-NKs in supporting angiogenesis by interacting with endothelial cells. B) Proposed model for PCa pTA-NK pro-angiogenic activities via macrophage recruitment and polarization.Competing Interest StatementThe authors have declared no competing interest.ABBREVIATIONSADCCAntibody Dependent Cellular CytotoxicityADKAdenocarcinomaANGAngiogeninANGIOP1Angiopoietin 1ANOVAAnalysis of VarianceCCLChemokine Ligand (C-C motif)cDNAcomplementary DNACMConditioned MediaCRPCCastration Resistant Prostate CancerCXCLChemokine Ligand (C-X-C motif)DNAM-1DNAX accessory molecule 1dNK cellsdecidual Natural Killer cellsEBMEndothelial cell Basal MediumEGMEndothelial cell Growth MediumFACSFluorescence-Activated Cell SortingFBSFetal Bovine SerumFCFlow CytometryFSCForward ScatterGAPDHGlyceraldehyde-3-Phosphate DehydrogenaseGM-CSFGranulocyte-Macrophage Colony-Stimulating FactorHBVHepatitis B VirusHCHealthy ControlHCVHepatitis C VirusHIVHuman Immunodeficiency VirusHUVECHuman Umbilical Vein Endothelial CellICAMInter Cellular Adhesion Molecule-1IFN-γ = Interferon γIHCImmuno Histo ChemistryIL-Interleukin-I-TACInterferon-inducible T-cell Alpha ChemoattractantmAbsmonoclonal AntibodiesMCP-1/CCL2Monocyte Chemoattractant Protein-1MMPsMatrix Metallo ProteinasesMNCsMono Nuclear CellsNKNatural KillerNKG2DNatural Killer receptor Group 2 DNSCLCNon-Small Cell Lung CancerPAIPlasminogen Activator InhibitorPBPeripheral Blood cellsPBMCsperipheral Blood Mononuclear CellsPCaProstate CancerPD-L1Programmed Death receptor Ligand 1PGE2Prostaglandin E2PlGFPlacental Growth FactorPMAPhorbol Merystate AcetateP/SPenicillin / StreptomycinPTA-NKsProstate Tumor Associated Natural Killer cellsRANTESRegulated upon Activation, Normal T Cell Expressed and Presumably SecretedSSCSide ScatterSTATSignal Transducer and Activator of TranscriptionTAMsTumor Associated MacrophagesTGFβTransforming Growth Factor-βTIMPTissue Inhibitor of Metallo-ProteinaseTMETumor MicroenvironmentTNF αTumor Necrosis Factor-αTregT Regulatory CellsuPARurokinase-type Plasminogen Activator ReceptorVCAMVascular Cellular Adhesion Molecule-1VEGFVascular Endothelial Growth FactorVEGFRVascular Endothelial Growth Factor ReceptorView Full Text

cancer biology↗

bioRxiv2020

BoardION: real-time monitoring of Oxford Nanopore Technologies devices

SummaryOne of the main advantages of the Oxford Nanopore Technology (ONT) is the possibility of sequencing in real time. However, the ONT sequencing interface is not sufficient to explore the quality of sequencing data in depth and existing tools do not take full advantage of real-time data streaming. We present BoardION, an interactive web application, dedicated to sequencing platforms, for real-time monitoring of all ONT sequencing devices (MinION, Mk1C, GridION and PromethION). BoardION allows users to easily explore sequencing metrics and optimize the quantity and the quality of the generated data during the experiment. It also enables the comparison of several flowcells to evaluate the library preparation protocols or the quality of input samples. AvailabilitySource code and a Docker image are available at http://www.genoscope.cns.fr/boardion/ Contactstefan.engelen@genoscope.cns.fr

bioinformatics↗

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↗