Biology subjects

Latorre, M.

Publications and source records attributed to Latorre, M..

7 recordsLinked to original sources

bioRxiv2026

Ultra-deep sequencing reveals intra-host diversity and co-infection-driven evolution of SARS-CoV-2

As COVID-19 enters an endemic phase, SARS-CoV-2 continues to diversify under ongoing immune pressure, with Omicron sublineages and episodic emergent variants sustaining reinfections worldwide. Intra-host evolution represents the earliest stage of this diversification, yet remains undercharacterized, particularly in regions with limited genomic surveillance. Here, we conducted high-throughput sequencing on 96 nasopharyngeal swab samples from Chilean individuals (2020-2022), achieving an average per-base genome coverage of [~]60,000x across the viral genome. This ultra-deep sequencing coverage enabled the identification of intra-host single-nucleotide variants (iSNVs) and co-infection events with high sensitivity and accuracy. Co-infections, especially with Omicron, significantly increased iSNV frequency and recombination, driving viral diversity. Evolutionary analysis based on the non-synonymous to synonymous ratio (dN/dS) shows that Omicron is under extensive purifying selection (global dN/dS [~] 0.55). However, Omicron co-infection cases exhibited higher dN/dS ratios ([~]0.58), suggesting a lower level of purifying selection and increased genetic diversity. Notably, the Spike gene showed dN/dS ratios indicative of positive selection (dN/dS > 1), which are more pronounced in co-infection cases than in Omicron alone. This suggests that co-infections are providing the substrate for the emergence of new variants with enhanced transmissibility and immune evasion capabilities. Together, these findings demonstrate that ultra-deep sequencing is crucial for mapping the evolutionary forces driving SARS-CoV-2 intra-host adaptation and the emergence of new variants.

genetics↗

bioRxiv2025

Effects of Willow and Pine tree growth in bacterial abundance, interactions and metabolic profile in a copper mine tailing

The Cauquenes tailings is one of the largest mine tailings in Chile and represents a significant environmental hazard due to its high copper levels and acidic pH. However, there is evidence of willow and pine tree growth in these terrains, which is unexpected given the extreme conditions of this environment. Considering the importance of plants in restoration strategies, the objective of this study was to analyze the effect that willow and pine growth have on the heavy metal contents of their surrounding soil, and the abundance, interaction, metabolic profile and assembly of the bacterial community. In the Cauquenes tailing, we collected samples from willow and pine vegetated soils as well as the surrounding non-vegetated soils. We analyzed characteristics such as heavy metal concentrations and pH levels in all sampled soils, and in tree leaves and roots. Vegetated sites exhibited lower copper levels and a neutral pH, while both tree species accumulated heavy metals in their tissues. We also determined bacterial abundance in all soil samples, and co-occurrence networks were constructed to assess bacterial interactions. Both trees promoted a higher abundance of Proteobacteria and had networks with higher modularity compared to non-vegetated soils. Finally, we estimated the metabolic profile of the bacterial community using PICRUSt 2 analysis and determined carbon source utilization with BioLog Ecoplates. PICRUSt 2 predicted higher metabolic activity in vegetated soils, and BioLog Ecoplate analysis revealed the utilization of a greater number of carbon sources. The microbial communities from vegetated soils were assembled in a deterministic manner, while the community from non-vegetated soils were stochastically assembled. In conclusion, tree growth mitigated the extreme conditions of the tailing and promoted a more active and healthier bacterial community. HighlightsO_LIWillow and pine tree can grow and mitigate toxic metal conditions in the tailings C_LIO_LIBoth trees provoked a shift in bacterial abundance and interaction network C_LIO_LIThe provoked shift was tree-dependent C_LIO_LIMicrobial activity was higher in vegetated soils C_LI

microbiology↗

bioRxiv2025

Bioprospection of culturable soil-borne bacteria with biotechnological potential for use in priming defense

BackgroundThe plant root microbiome is central to disease resistance and stress resilience. In intensive tomato production, prolonged agrochemical use disrupts microbial communities, reducing their protective functions and enabling pathogen establishment. MethodsWe integrated 16S rRNA amplicon sequencing with culture-dependent isolation to analyze microbiome shifts in tomato plants across healthy, asymptomatic, and symptomatic states in a nematode-infested field. Network analysis and machine learning were used to identify key taxa. Isolates were screened for plant growth-promoting rhizobacteria (PGPR) and nematicidal activity, and selected strains were evaluated in planta under pathogen challenge. ResultsMicrobial diversity and community complexity declined with disease severity. Gaiella occulta emerged as a potential biomarker of plant health. From 223 isolates, 45 strains exhibited PGPR and nematicidal traits. Ten were tested in tomato plants, where treatments conferred systemic resistance to Pseudomonas syringae pv tomato without fitness cost. Four strains, primarily Pseudomonas and Bacillus, triggered immune priming, enhanced root development, and three of them were co-isolated from a single asymptomatic plant. ConclusionsOur findings highlight the potential of targeted bacterial consortia to restore microbiome balance and activate immune responses in tomato. These results support the rational design of synthetic microbial communities (SynComs) for sustainable, microbiome-based crop protection.

immunology↗

bioRxiv2024

Profiling extremophile bacterial communities recovered from a mining tailing against soil ecosystems through comparative genome-resolved metagenomics and evolutionary analysis

Microbial communities inhabiting mining environments harbor a diverse array of bacteria with specialized metabolic capacities adapted to extreme conditions. Here, we utilized comparative genome-resolved metagenomics of a high-quality Illumina-sequenced sample from the Cauquenes copper tailing in central Chile. We investigate the metabolic roles and evolutionary behaviors of the resident microorganisms, focusing on capacities related to copper, iron, and sulfur metabolism. We recovered 44 medium and high-quality metagenome-assembled genomes (MAGs), primarily classified belonging to phylum Actinobacteriota (21), Proteobacteria (10), and Acidobacteriota (6). These MAGs were compared to the Global Soil MAGs project (SMAG catalog), which includes bacteria from conventional or natural ecosystems, to uncover specialized properties of mining bacteria. Notably, we discovered a new phylum, Nitrospirota_A, and provided insights into the unexplored taxonomic classifications at the lowest ranks such as genus and species. Functional potential analysis revealed that the mining community has enhanced molecular capabilities associated with sulfur and copper metabolism. Evolutionary analysis revealed that mining genes involved in targeted metabolism are under strong negative selection, indicating conservative evolutionary pressure within the mining environment. In particular, it was possible to identify a MAG from the genus Acidithrix with a global dN/dS ratio greater than 1, suggesting positive selection. Additionally, core proteins essential for bacterial survival, such as flagellar motors, cell cycle regulators, and biogenesis proteins, were also under positive selection. The latter points to the need for enhanced mobility in these microorganisms to locate resources efficiently. We demonstrate that copper mining communities are diverse and possess a significant metabolic repertoire under extreme conditions in sulfur and copper proteins. Those specialized genes appear to be in a conservative state rather than undergoing adaptive evolution. This study enhances our understanding of extremophile mining microbiomes, highlighting their high variability in classification, metabolic functions, evolution, and adaptation, which can be leveraged for further biotechnological applications.

genomics↗

bioRxiv2020

Genome-wide analysis of in vivo CcpA binding with and without its key co-factor HPr in the major human pathogen group A Streptococcus.

Catabolite control protein A (CcpA) is a master regulator of carbon source utilization and contributes to the virulence of numerous medically important Gram-positive bacteria. Most functional assessments of CcpA, including interaction with its key co-factor HPr, have been performed in non-pathogenic bacteria. In this study we aimed to identify the in vivo DNA binding profile of CcpA and assess the extent to which HPr is required for CcpA-mediated regulation and DNA binding in the major human pathogen group A Streptococcus (GAS). Using a combination RNAseq/ChIPseq approach, we found that CcpA affects transcript levels of 514 of 1667 GAS genes (31%) whereas direct DNA binding was identified for 105 GAS genes. Three of the directly regulated genes encode the key GAS virulence factors Streptolysin S, PrtS (IL-8 degrading proteinase), and SpeB (cysteine protease). Mutating CcpA Val301 to Ala (strain 2221-CcpA-V301A) abolished interaction between CcpA and HPr and impacted the transcript levels of 205 genes (40%) in the total CcpA regulon. By ChIPseq analysis, CcpAV301A bound to DNA from 74% of genes bound by wild-type CcpA, but generally with lower affinity. These data delineate the direct CcpA regulon and clarify the HPr-dependent and independent activities of CcpA in a key pathogenic bacterium. Data sharing and data availabilityThe data that support the findings of this study are available from the corresponding author upon reasonable request.

microbiology↗

bioRxiv2020

Fast, Rate-Independent, Finite Element Implementation of a 3D Constrained Mixture Model of Soft Tissue Growth and Remodeling

Constrained mixture models of soft tissue growth and remodeling can simulate many evolving conditions in health as well as in disease and its treatment, but they can be computationally expensive. In this paper, we derive a new fast, robust finite element implementation based on a concept of mechanobiological equilibrium that yields fully resolved solutions and allows computation of quasi-equilibrated evolutions when imposed perturbations are slow relative to the adaptive process. We demonstrate quadratic convergence and verify the model via comparisons with semi-analytical solutions for arterial mechanics. We further examine the enlargement of aortic aneurysms for which we identify new mechanobiological insights into factors that affect the nearby non-aneurysmal segment as it responds to the changing mechanics within the diseased segment. Because this new 3D approach can be implemented within many existing finite element solvers, constrained mixture models of growth and remodeling can now be used more widely.

bioengineering↗

bioRxiv2019

Paradoxical Aortic Stiffening and Subsequent Cardiac Dysfunction in Hutchinson-Gilford Progeria Syndrome

Hutchinson-Gilford Progeria Syndrome (HGPS) is an ultra-rare disorder with devastating sequelae resulting in early death, presently believed to stem primarily from heart failure secondary to central arterial stiffening. We analyze novel longitudinal cardiovascular data from a mouse model of HGPS (LmnaG609G/G609G) using allometric scaling and advanced computational modelling and show that a late-stage increase in pulse wave velocity, with associated diastolic dysfunction but preserved systolic function, emerges with a loss of aortic function, independent of sex. Specifically, there is a dramatic late-stage loss of smooth muscle function and cells and an excessive accumulation of proteoglycans along the entire aorta, which result in a loss of biomechanical function (contractility and elastic energy storage) and marked structural stiffening despite a distinctly low intrinsic material stiffness that is consistent with the lack of functional lamin A. Importantly, vascular function appears to be normal within the low stress environment of development, only to succumb progressively to pressure-related effects of the lamin A mutation and become extreme in the peri-morbid period. Because the dramatic life-threatening aortic phenotype manifests during the last quarter of life there may be a therapeutic window in maturity that could alleviate concerns with therapies administered during early periods of arterial development.\n\nDisclosuresD.T.B is an equity holder in, and receives research and consulting support from, Inozyme Pharma, Inc. for therapeutics for ENPP1 deficiency. None of the other authors declare any conflict, financial or otherwise.

bioengineering↗