Biology subjects

Zuccotti, G.

Publications and source records attributed to Zuccotti, G..

4 recordsLinked to original sources

bioRxiv2025

A Simple and Cost-Effective Protocol for Enriching 'Ca. Saccharimonadia' from Human Saliva to Enable Efficient Genome Sequencing

Background"Candidatus Saccharimonadia", a lineage within the Candidate Phyla Radiation (CPR), is characterized by small cell size, reduced genomes, and an epibiotic lifestyle dependent on bacterial hosts. Despite their presence in diverse environments, including the human oral microbiota, their role in human health remains largely unexplored. Observational studies have linked increased "Ca. Saccharimonadia" abundance in human saliva with inflammatory conditions such as periodontitis and inflammatory bowel disease, while recent in vivo evidence suggests potential anti-inflammatory properties. Investigating "Ca. Saccharimonadia" is challenging due to their fastidious nature, making standard culturing methods impractical. Current genomic studies rely on either co-cultivation with bacterial hosts or shotgun metagenomics, both requiring advanced technical expertise and costly resources. To address this limitation, we developed an affordable and efficient protocol for enriching "Ca. Saccharimonadia" from human saliva samples, facilitating genome sequencing. Our protocol, termed the "Ca. Saccharimonadia" Enrichment (SE) protocol, consists of two mandatory phases (detachment from host bacteria and weight/size-based separation) along with an optional DNA degradation phase. We validated this method on two human saliva samples. ResultsAfter SE protocol, the two saliva showed a substantial increase in "Ca. Saccharimonadia" DNA concentration. The enriched samples enabled high-quality metagenome-assembled genomes (MAGs) to be obtained via shotgun metagenomics. ConclusionsThis study presents a cost-effective and scalable approach to studying "Ca. Saccharimonadia", overcoming prior limitations and expanding opportunities for future research on their role in human health and disease.

microbiology↗

bioRxiv2024

Robustness of time domain near infrared spectroscopy to variations in skin pigmentation

Recently, skin pigmentation has been shown to affect the performance of pulse oximeters and other light-based techniques like photoacoustic imaging, tissue oximetry, and continuous wave near infrared spectroscopy. Evaluating the robustness to changes in skin pigmentation is therefore essential for the proper use of optical technologies in the clinical scenario. We conducted systematic time domain near infrared spectroscopy measurements on calibrated tissue phantoms and in vivo on volunteers during static and dynamic (i.e., arterial occlusion) measurements. To simulate varying melanosome volume fractions in the skin, we inserted, between the target sample and the measurement probe, thin tissue phantoms made of silicone and nigrosine (skin phantoms). Additionally, we conducted an extensive measurement campaign on a large cohort of pediatric subjects, covering the full spectrum of skin pigmentation. Our findings consistently demonstrate that skin pigmentation has a negligible effect on time domain near infrared spectroscopy results, underscoring the reliability and potential of this emerging technology in diverse clinical settings.

bioengineering↗

bioRxiv2024

RecA is a reliable marker for bacterial taxonomy, even in the Candidate Phyla Radiation

Culture-independent approaches are commonly used to characterise the taxonomic composition of bacterial communities. Among these approaches, the amplicon-based metagenomics relies on specific genetic markers, such as the 16S rRNA gene, while the shotgun metagenomics annotates the whole bacterial DNA. Despite the 16S being the gold standard marker, studies highlighted its inefficiency in characterising and quantifying divergent bacterial groups such as the Candidate Phyla Radiation. On the other hand, shotgun metagenomics is highly informative and accurate but it is more expensive and requires computational resources and time. In this study, we propose RecA as a pan-bacterial genetic marker, particularly suitable for the Candidate Phyla Radiation. Indeed, we found that applying a Random Forest machine learning model on RecA amino acid sequences provides an accurate and fast taxonomic annotation across the whole bacterial tree of life. Ultimately, we produced Forestax, a tool for the characterisation and quantification of bacterial communities in metagenomics data, on the basis of RecA sequences. The analyses showed that RecA-based metagenomics has a taxonomic accuracy comparable to other multi-gene approaches, reinforcing RecA as a powerful marker for taxonomic annotation in bacteria. In perspective, RecA could be considered as a broad-spectrum marker for amplicon-based studies to overcome the limits of 16S rRNA.

microbiology↗

bioRxiv2023

On the forces shaping diversity and adaptation in the opportunistic pathogen Serratia marcescens

Bacterial species often comprise well-separated lineages, likely emerged and maintained by genetic isolation and/or ecological divergence. How these two evolutionary actors interact in the shaping of bacterial population structure is currently not fully understood. In this study, we investigated the genetic and ecological drivers underlying the evolution of Serratia marcescens, an opportunistic pathogen with high genomic flexibility and able to colonise diverse environments. Comparative genomic analyses revealed a population structure composed of five deeply-demarcated genetic clusters with open pan-genome but limited inter-cluster gene flow, partially explained by Restriction-Modification (R-M) systems incompatibility. Furthermore, a large-scale research on hundred-thousands metagenomic datasets revealed only a partial ecological separation of the clusters. Globally, two clusters only showed a peculiar gene composition and evident ecological adaptations. These results suggest that genetic isolation preceded ecological adaptations in the shaping of the species diversity, suggesting an evolutionary scenario for several bacterial species.

evolutionary biology↗