Biology subjects

De Filippis, F.

Publications and source records attributed to De Filippis, F..

5 recordsLinked to original sources

bioRxiv2026

The gut bacterial community of black soldier fly larvae is a reservoir of antibiotic resistance and virulence genes

1.Antimicrobial resistance (AMR) is a serious threat to global health. Agricultural practices that have contributed greatly to AMR spread urgently require innovation to address this issue, and more broadly challenges of sustainability and environmental concern. The larvae of black soldier fly (BSFL), Hermetia illucens, are considered a promising resource for advancing sustainable and circular agri-food systems given their ability to bioconvert organic waste streams into protein-and lipid-rich biomass suitable for feed applications and the use of the rearing residues (i.e., frass) as organic fertilisers. However, despite their emerging industrial applications, the risks of antibiotic resistance spread through their use remain underexplored. To elucidate this aspect, the profiles of antibiotic resistance genes (ARGs) and virulence factors (VFs), and their occurrence on plasmids were predicted from the midgut bacterial community of BSFL. Shotgun metagenomics revealed candidate resistance genes for 26 classes of antibiotics, and virulence via 9 mechanisms (with mobility and biofilm formation as major ones), with taxa belonging to the Pseudomonadota phylum as the dominant contributors. Highly relevant to public health was the identification of genes encoding resistance to carbapenem class antibiotics in bacterial genomes and mobile plasmids. Reconstruction of metagenomes enabled more precise taxonomic resolution and revealed taxa harbouring multiple resistance and virulence genes, including a Pseudomonas species with 42 VFs and 7 ARGs. Notably, for the first time antibiotic resistant bacterial species were isolated from the gut microbiota of BSFL, validating and complementing the results obtained in silico. Together, this work represents a comprehensive profile of the BSFL midgut bacterial resistome, while also providing relevant context on virulence and mobility. Importantly, it emphasises the urgent need to adopt strategies to mitigate potential risks arising from the development of emerging technologies related to the use of insect-mediated bioconversion and derived products.

genomics↗

bioRxiv2025

A survey of bacterial and fungal communities of table olives.

Table olives are produced from a large number of olive varieties subjected to different trade preparations, resulting in a highly heterogeneous family of fermented foods. To characterise the diversity of bacterial and fungal communities and its relationship with variety, ripeness, and trade preparation, we surveyed 363 samples from 40 producers across 6 countries, combining physicochemical measurements, viable counts, and amplicon-based metagenomics. This is the largest survey of table olive microbial communities to date and includes the first culture-independent characterisation of microbial communities for several Italian PDO and non-PDO varieties, most notably Oliva di Gaeta. The contrast between alkali-treated and naturally fermented olives was the dominant structuring factor, with HALAB (Halophilic and Alkalophilic Lactic Acid Bacteria) and other halophiles enriched in alkali-treated varieties and a diverse array of Lactobacillaceae and Pseudomonadota characterising naturally fermented olives. Despite these consistent signals, striking variability was observed within the same variety and even within the same producer, driven by stochastic colonization events, house microbiota, and the widespread use of small fermentation vessels. This variability obscured variety-specific microbial signatures and prevented reliable discrimination of Italian PDO varieties from similar non-PDO counterparts using amplicon-based approaches. The ecological and taxonomic complexity documented here, encompassing bacterial and fungal genera with largely untapped starter and flavour potential, provides the foundation for the development of variety-specific microbiome-based starter cultures. HighlightsO_LIWe report a metataxonomic survey of microbial communities in 363 table olive samples C_LIO_LIAlkali treatment and natural fermentation drive distinct microbial community structures C_LIO_LIHouse microbiota and stochastic colonization generate high within-variety variability C_LIO_LIMicrobiome data provide ecological foundations for olive microbiome-based starters C_LI

microbiology↗

bioRxiv2025

Prosystemin-derived signals: bridging leaf microbiome dynamics and defense activation

AbstractThe use of plant-derived peptides as resistance inducers provides innovative and potentially environmentally friendly methods to safeguard crop health. Although their use is increasing rapidly, their broader impact, particularly on plant-associated microbiomes, remains underexplored. This study investigated the influence of a promising immunomodulatory peptide derived from the tomato defense protein prosystemin on the tomato phyllosphere microbiome. We applied the peptide via foliar spray biweekly to simulate common agricultural practices from the planting stage to two months post-germination. Using a shotgun metagenomics approach combined with qPCR, we identified bacterial communities of high abundance (up to 4.6 log10 bacterial 16S rRNA copies) and high diversity, mainly comprising Actino-, Alphaproteo- and Gammaproteobacteria, on all tomato leaves. The peptide treatment led to a significant and targeted shift in the bacterial community, characterized by reduced diversity and network complexity and species loss, i.e., Streptomyces. The enrichment was predominantly observed in bacterial genera such as Acinetobacter, Sphingobium, Sphingomonas, Brevundimonas, and Massilia, which are typically associated with improved plant growth and stress resilience. Intriguingly, shifts in both taxonomic and functional profile upon peptide application aligned with patterns typically observed during plant defense activation, involving jasmonic acid and related secondary metabolites. Members of the Sphingomonadaceae family, particularly Sphingobium yanoikuyae, have emerged as potential drivers of such microbial dynamics, likely adapting to plant upregulated defenses and potentially supporting its resilient phenotype. Overall, in addition to its well-established role in combating tomato pests and necrotrophic fungi, the prosystemin-derived peptide paves the way for disentangling peptide-induced resistance and its interplay with the plant microbiota.

plant biology↗

bioRxiv2019

Global Genetic Cartography of Urban Metagenomes andAnti-Microbial Resistance

We have created a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities across 3 years. This is the first systematic, worldwide study cataloging the urban microbial ecosystem. We identify taxonomically-defined microorganisms collected across three years. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics AMR markers, and novel genetic elements, including 10,928 viral, 1302 bacteria, and 2 archaea novel species. We identify 4,424 species of urban microorganisms and a consistent "core" of 31 species found in nearly all samples that is largely distinct from any human commensal microbiome. Profiles of AMR genes show geographic variation in type and density. Together, these results constitute a high-resolution, global metagenomic atlas, which enables the discovery of new genetic components, highlights potential forensic applications, and provides an essential first draft of the global AMR burden of the worlds cities.

microbiology↗

bioRxiv2019

The Prevotella copri complex comprises four distinct clades that are underrepresented in Westernised populations

Prevotella copri is a common inhabitant of the human gut. Interest in P. copri has gathered pace due to conflicting reports on whether it is beneficial or detrimental to health. In a cross-continent meta-analysis exploiting >6,500 available metagenomes supported by new isolate sequencing and recovery of high-quality genomes from metagenomes, we obtained >1,000 P. copri genomes. This 100-fold increase over existing isolate genomes allowed the genetic and global population structure of P. copri to be explored at an unprecedented depth. We demonstrate P. copri is not a monotypic species, but encompasses four distinct clades (>10% inter-clade vs. <4% intra-clade average single nucleotide variants) for which we propose the name P. copri complex, comprising clades A, B, C and D. We show the complex is near ubiquitous in non-Westernised populations (95.4% versus 29.6% in Westernised populations), where all four clades are typically co-present within an individual (61.6% of the cases), in contrast to Westernised populations (4.6%). Genomic analysis of the complex reveals substantial and complementary functional diversity, including the potential for utilisation of complex carbohydrates, suggestive that multi-generational dietary modifications may be a driver for the reduced P. copri prevalence in Westernised populations. Analysis of ancient stool microbiomes highlights a similar pattern of P. copri presence consistent with modern non-Westernised populations, allowing us to estimate the time of clade delineation to pre-date human migratory waves out of Africa. Our analysis reveals P. copri to be far more diverse than previously appreciated and this diversity appears to be underrepresented in Western-lifestyle populations.

microbiology↗