Biology subjects

Trotta, M.

Publications and source records attributed to Trotta, M..

3 recordsLinked to original sources

bioRxiv2025

Using low pass whole metagenome sequencing for gut microbiome profiling in an Argentine urban population

Modern urban diets are linked to gut microbiome dysbiosis and increased risk of chronic disease. While 16S rRNA sequencing is widely used, low-pass whole metagenome sequencing (WMS) offers superior insight into microbial functional capacity and community structures. In this study, we utilized low-pass WMS to characterize the gut microbiome of an Argentine urban population. We compared a health-screened Reference cohort (n=94) with an unscreened Average urban cohort (n=527), for which we analyzed taxonomic structure, microbial diversity, and predicted metabolic potential. The Average cohort displayed significantly lower alpha-diversity, primarily driven by reduced community evenness rather than richness. Functionally, this cohort showed a significantly diminished predicted capacity for synthesizing beneficial short-chain fatty acids (SCFAs) and essential vitamins B9 and B12. A longitudinal analysis of a subgroup (n=9) undertaking lifestyle modifications demonstrated that while microbial richness and SCFA production could be significantly improved, responses were highly individualized. These results reveal key functional deficits in the gut microbiome of a typical urban population, reflecting a mismatch with ancestral dietary patterns. The high inter-individual variability in response to changes in dietary patterns challenges one-size-fits-all dietary recommendations and highlights the need for personalized nutritional strategies informed by functional microbiome data.

genomics↗

bioRxiv2025

Exploring the interplay of complex carbohydrate intake, the microbiome CAZymes pool and short-chain fatty acid production in the human gut: insights from different cohorts in the Argentine population

Carbohydrate-active enzyme (CAZyme) activity in the gut microbiome has significant implications for health, including the release of nutrients otherwise inaccessible to the host and the enhancement of digestive efficiency. The primary end products of indigestible carbohydrate fermentation are short-chain fatty acids (SCFAs). We hypothesized that increased dietary fiber consumption could lead to greater SCFA production in the human gut. To investigate this, we examined the relationship between complex carbohydrate intake, CAZyme activity in the human gut microbiome, and SCFA production at the whole metagenomic level across three cohorts: a healthy reference-controlled cohort, an average cohort of individuals living in industrialized cities, and a cohort of patients with inflammatory bowel disease (IBD). Metagenomic sequencing and bioinformatic analyses were utilized to assess the diversity, abundance, and functionality of CAZymes, as well as the metabolic capacity for SCFA production. The average cohort exhibited higher alpha diversity of CAZyme families compared to the reference-controlled cohort, although subfamily composition was similar between both. A moderate negative correlation was identified between CAZyme abundance and SCFA production, indicating that a higher number of these enzymes does not directly translate to increased SCFA synthesis. In IBD patients, a decrease in the diversity and composition of CAZyme subfamilies was observed, suggesting a disruption in enzymatic functions associated with the disease. However, the overall functionality of CAZymes remained relatively stable across different health conditions, highlighting the resilience of the gut microbiome for these functions. These findings deepen our understanding of the gut microbiomes role in health and disease, emphasizing that despite variations in microbial diversity, key enzymatic functions persist. The study underscores the complexity of the non-linear relationship between complex carbohydrate metabolism and SCFA production, laying the groundwork for future research on microbiome-targeted therapeutic/dietary profile interventions in both non-disease and chronic diseases conditions.

genomics↗

bioRxiv2020

Light-driven ATP production promotes mRNA biosynthesis inside hybrid multi-compartment artificial protocells

The construction of energetically autonomous artificial protocells is one of the most urgent and challenging requirements in bottom-up synthetic biology. Here we show a hybrid multi-compartment approach to build Artificial Simplified-Autotroph Protocells (ASAPs) in an effective manner. Chromatophores obtained from Rhodobacter sphaeroides accomplish the photophosphorylation of ADP to ATP functioning as nanosized photosynthetic organellae when encapsulated inside artificial giant phospholipid vesicles. Under continuous illumination chromatophores produce ATP that in turn sustains the transcription of a DNA gene by T7 RNA polymerase inside ASAPs. Cryo-EM and time-resolved spectroscopy were used for characterizing the chromatophore morphology and the orientation of the photophosphorylation proteins, which allow high ATP production rates (up to ~100 ATP/s per ATP synthase). mRNA biosynthesis inside individual vesicles has been determined by confocal microscopy. The hybrid multi-compartment approach here proposed appears at the same time convenient and effective, and thus very promising for the construction of full-fledged artificial protocells.

synthetic biology↗