Biology subjects

Biagi, E.

Publications and source records attributed to Biagi, E..

4 recordsLinked to original sources

bioRxiv2025

Sequence alignment with k-bounded matching statistics

Finding high-quality local alignments between a query sequence and sequences contained in a large genomic database is a fundamental problem in computational genomics, at the core of thousands of biological analysis pipelines. Here, we describe a novel algorithm for approximate local alignment search based on the so-called k-bounded matching statistics of the query sequence with respect to an indexed database of sequences. We compute the k-bounded matching statistics, which capture the longest common suffix lengths of consecutive k-mer matches between query and target sequences, using the spectral Burrows-Wheeler transform, a data structure that enables computationally efficient queries. We show that our method is as fast and as accurate as state-of-the-art tools in several bacterial genomics tasks. Our method is available as a set of three kbo Rust packages that provide a command-line interface, a graphical user interface that runs in a browser without server-side processing, and a core library that can be accessed by other tools.

bioinformatics↗

bioRxiv2024

Finimizers: Variable-length bounded-frequency minimizers for k-mer sets

The minimizer of a k-mer is the smallest m-mer inside the k-mer according to some order relation < of the m-mers. Minimizers are often used as keys in hash tables in indexing tasks in metagenomics and pangenomics. The main weakness of minimizer-based indexing is the possibility of very frequently occurring minimzers, which can slow query times down significantly. Popular minimizer alignment tools employ various and often wild heuristics as workarounds, typically by ignoring frequent minimizers or blacklisting commonly occurring patterns, to the detriment of other metrics (e.g., alignment recall, space usage, or code complexity). In this paper, we introduce frequency-bounded minimizers, which we call finimizers, for indexing sets of k-mers. The idea is to use an order relation < for minimizer comparison that depends on the frequency of the minimizers within the indexed k-mers. With finimizers, the length m of the m-mers is not fixed, but is allowed to vary depending on the context, so that the length can increase to bring the frequency down below a user-specified threshold t. Setting a maximum frequency solves the issue of very frequent minimizers and gives us a worstcase guarantee for the query time. We show how to implement a particular finimizer scheme efficiently using the Spectral Burrows-Wheeler Transform (SBWT) (Alanko et al., Proc. SIAM ACDA, 2023) augmented with longest common suffix information. In experiments, we explore in detail the special case in which we set t = 1. This choice simplifies the index structure and makes the scheme completely parameter-free apart from the choice of k. A prototype implementation of this scheme exhibits k-mer localization times close to, and often faster than, stateof-the-art minimizer-based schemes. The code is available at https://github.com/ElenaBiagi/Finito.

bioinformatics↗

bioRxiv2020

Particulate Matter emission sources and meteorological parameters combine to shape the airborne microbiome communities in the Ligurian coast, Italy

Here we explore how the chemical composition of particulate matter (PM) and meteorological conditions combine in shaping the air microbiome in a heavily inhabited industrial urban settlement. During the observation time, the air microbiome was highly dynamic, fluctuating between different compositional states, likely resulting from the aerosolization of different microbiomes emission sources. This dynamic process depends on the combination of local meteorological parameters and particle emission sources, which may affect the prevalent aerosolized microbiomes. In particular, we showed that, in the investigated area, industrial emissions and winds blowing from the inlands combine with an airborne microbiome that includes faecal microbiomes components, suggesting multiple citizens exposure to both chemicals and microorganisms of faecal origin, as related to landscape exploitation and population density. In conclusion, our findings support the need to include monitoring of the air microbiome compositional structure as a relevant factor for the final assessment of local air quality.

ecology↗

bioRxiv2018

Gut microbiome response to a modern Paleolithic diet in a Western lifestyle context

The progressive reduction of gut microbiome (GM) biodiversity along human evolutionary history has been found to be particularly exacerbated in Western urban compared to traditional rural populations, and supposed to contribute to the increasing incidence of chronic non-communicable diseases. Together with sanitation, antibiotics and C-section, the Western diets, low in microbiota-accessible carbohydrates (MACs) while rich in industrialized and processed foods, are considered one of the leading causes of this shrinkage. However, significant questions remain unanswered, especially whether high-MAC low-processed diets may be sufficient to recover GM diversity in Western urban populations. Here, we profiled the GM structure of urban Italian subjects adhering to the modern Paleolithic diet (MPD), a dietary pattern featured by high consumption of MACs and low-to-zero intake of refined sugars and processed foods, and compared data with other Italian individuals following a Mediterranean Diet (MD), as well as worldwide traditional hunter-gatherer populations from previous publications. Notwithstanding a strong geography effect on the GM structure, our results show an unexpectedly high degree of GM biodiversity in MPD subjects, which well approximates that of traditional populations. Increasing the consumption of MACs at the expense of refined sugars, and minimizing the intake of processed foods, both hallmarks of the MPD, could be the key to rewild the Western microbiota, counteracting the loss of GM diversity and thus restoring evolutionarily important functionality to our gut for improved human health.

microbiology↗