Natàlia Timoneda

Institut de Ciències del Mar · Department of Marine Biology

This study aims to investigate the temporal dynamics of the epiphytic protist community on macroalgae, during the summer months, with a specific focus on fungi, and the interactions between zoosporic chytrid parasites and the proliferation of the dinoflagellates. We employed a combination of environmental sequencing techniques, incubation of natura...

The presence of phytoplankton parasites along the water column was explored at the Long‐Term Ecological Station MareChiara (LTER‐MC) in the Gulf of Naples (Mediterranean Sea) in October 2019. Microscopy analyses showed diatoms dominating the phytoplankton community in the upper layers (0–20 m). Metabarcoding data from the water column showed the pr...

Introduction: The aetiology of Kawasaki disease (KD) remains unknown. Several studies have linked the human microbiome with some diseases. However, there are limited studies on the role of the respiratory microbiome in KD. The aim of our study was to make a more thorough analysis of the causes and processes that increase the susceptibility to KD....

The interactions of parasitic fungi with their phytoplankton hosts in the marine environment is mostly unknown. In this study, we evaluated the diversity of Chytridiomycota in phytoplankton communities dominated by dinoflagellates at several coastal locations in the NW Mediterranean Sea and demonstrated the most prominent interactions of these para...

Resumen Introducción La etiología de la enfermedad de Kawasaki (EK) sigue siendo desconocida. Varios estudios han relacionado el microbioma humano con algunas enfermedades. Sin embargo, los estudios sobre el microbioma respiratorio en EK son limitados. Este estudio intenta profundizar en las causas y procesos que predisponen al desarrollo de la EK...

Fresh fruits and vegetables are susceptible to microbial contamination at every stage of the food production chain, and as a potential source of pathogens, irrigation water quality is a critical factor. Next-generation sequencing (NGS) techniques have been flourishing and expanding to a wide variety of fields. However, their application in food saf...

Parasites in aquatic systems are highly diverse and ubiquitous. In marine environments, parasite‐host interactions contribute substantially to shaping microbial communities, but their nature and complexity remain poorly understood. In this study, we examined the relationship between Perkinsea parasitoids and bloom‐forming dinoflagellate species. Ou...

Background Whole genome sequencing has emerged as a useful tool for identification and molecular characterization of pathogens. MinION (Oxford Nanopore) is a real-time third generation sequencer whose portability, affordability and speed in data production make of it an attractive device for whole genome sequencing. The objective of this study is t...

Abstract Fecal pollution of water bodies poses a serious threat for public health and ecosystems. Microbial source tracking (MST) is used to track the source of this pollution facilitating better management of pollution at the source. In this study we tested 12 MST markers to track human, ruminant, sheep, horse, pig and gull pollution to assess the...

NGS techniques are excellent tools to monitor and identify viral pathogens circulating among the population with some limitations that need to be overcome, especially in complex matrices. Sewage contains a high amount of other microorganisms that could interfere when trying to sequence viruses for which random PCR amplifications are needed before N...

Viruses (e.g., noroviruses and hepatitis A and E virus), bacteria (e.g., Salmonella spp. and pathogenic Escherichia coli) and protozoa (e.g., Cryptosporidium parvum and Giardia intestinalis) are well-known contributors to food-borne illnesses linked to contaminated fresh produce. As agricultural irrigation increases the total amount of water used a...

Fecal pollution of water bodies poses a serious threat for public health and ecosystems. Microbial source tracking (MST) using host specific bacteria are used to track the source of this potential pollution and be able to perform a better management of the pollution at the source. In this study we tested 12 molecular MST markers to track human, rum...

In Quito, the microbiological contamination of surface water represents a public health problem, mainly due to the lack of sewage treatment from urban wastewater. Contaminated water contributes to the transmission of many enteric pathogens through direct consumption, agricultural and recreational use. Among the different pathogens present in urban...

Hepatitis is a general term meaning inflammation of the liver, which can be caused by a variety of viruses. However, a substantial number of cases remain with unknown aetiology. We analysed the serum of patients with clinical signs of hepatitis using a metagenomics approach to characterize their viral species composition. Four pools of patients wit...

Individual phylogenetic trees computed from contigs over reference genome locations in HEV. (DOCX)

Individual phylogenetic trees computed from contigs over reference genome locations in Anelloviridae family. (DOCX)

The application of next-generation sequencing (NGS) techniques for the identification of viruses present in urban sewage has not been fully explored. This is partially due to a lack of reliable and sensitive protocols for studying viral diversity and to the highly complex analysis required for NGS data processing. One important step towards this go...

Microbial food-borne diseases are still frequently reported despite the implementation of microbial quality legislation to improve food safety. Among all the microbial agents, viruses are the most important causative agents of food-borne outbreaks. The development and application of a new generation of sequencing techniques to test for viral contam...

Viral sewage metagenomics is a novel field of study used for surveillance, epidemiological studies, and evaluation of waste water treatment efficiency. In raw sewage human waste is mixed with household, industrial and drainage water, and virus particles are, therefore, only found in low concentrations. This necessitates a step of sample concentrati...

Distribution of reads on kingdom level of the 16 method combinations and their associated negative controls. Samples were processed in triplicate, and the data shown is the average. _S = sample, _C = Negative extraction control. Databases used are listed in S1 Table. (PDF)

HAdV concentration measured by qPCR. (A) HAdV concentration in extracts obtained by using four different concentration methods and (B) extraction methods. The bar, box, whiskers and circles represents median, inter-quartile range, inter-quartile range times 1.5, and outliers, respectively. Asterisks represent significance level of a pairwise t-test...

Overview of reference sequence databases and associated download information. Reference sequence information can be obtained from the URL’s shown in ‘Download information’. (PDF)

Sequence information. Number of raw reads, reads after quality assessment, and reads not mapping to PhiX, and thus usable for subsequent analysis. _S = sample, _C = Negative control. (PDF)

qPCR inhibition of MNV and HAdV. Inhibition of the 16 combinations of concentration and extraction methods. Inhibition was measured using qPCR of undiluted (1:1) and tenfold diluted (1:10) DNA/RNA extracts. The values in the tables represents Δct between the undiluted and 10 fold diluted samples. A Δct = -3.3 represent a perfect 10 fold dilution. S...

MNV concentrations measured by qPCR. (A) MNV concentration in extracts obtained by using four different concentration methods and (B) extraction methods. The bar, box and whiskers represents the median, the inter-quartile range, and the inter-quartile range times 1.5, respectively. Asterisks represent significance level of a pairwise t-test with “H...

Abundance of all detected viral families. Heatmap showing the abundance of all detected viral families, measured in reads per million, in each biological replica for the different method combinations as well as the controls. _S = sample, _C = Negative control. (PDF)

Specifications of the four concentration methods applied in this study. (PDF)

Properties of the four nucleic acid extraction kits applied in this study. (PDF)

Conventional wastewater treatment does not completely remove and/or inactive viruses; consequently, viruses excreted by the population can be detected in the environment. This study was undertaken to investigate the distribution and seasonality of human viruses and faecal indicator bacteria (FIB) in a river catchment located in a typical Mediterran...

Wastewater is a valuable resource for water-scarce regions, and is becoming increasingly important due to the rising frequency of droughts as a result of climate change. The health risks derived from ingestion of lettuce that has been irrigated with effluent from a wastewater treatment plant (WWTP) in Catalonia (Spain) were estimated following a qu...